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Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Scope The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal in open access, devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. It presents structured review articles (“cards”) on genes, leukaemias, solid tumours, cancer-prone diseases, and also more traditional review articles (“deep insights”) on the above subjects and on surrounding topics. It also present case reports in hematology and educational items in the various related topics for students in Medicine and in Sciences. Editorial correspondance Jean-Loup Huret Genetics, Department of Medical Information, University Hospital F-86021 Poitiers, France tel +33 5 49 44 45 46 or +33 5 49 45 47 67 [email protected] or [email protected] The Atlas of Genetics and Cytogenetics in Oncology and Haematology is published 4 times a year by ARMGHM, a non profit organisation. Philippe Dessen is the Database Director, and Alain Bernheim the Chairman of the on-line version (Gustave Roussy Institute – Villejuif – France). http://AtlasGeneticsOncology.org © ATLAS - ISSN 1768-3262 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(2) Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Scope The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal in open access, devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. It presents structured review articles (“cards”) on genes, leukaemias, solid tumours, cancer-prone diseases, and also more traditional review articles (“deep insights”) on the above subjects and on surrounding topics. It also present case reports in hematology and educational items in the various related topics for students in Medicine and in Sciences. Editorial correspondance Jean-Loup Huret Genetics, Department of Medical Information, University Hospital F-86021 Poitiers, France tel +33 5 49 44 45 46 or +33 5 49 45 47 67 [email protected] or [email protected] The Atlas of Genetics and Cytogenetics in Oncology and Haematology is published 4 times a year by ARMGHM, a non profit organisation. Philippe Dessen is the Database Director, and Alain Bernheim the Chairman of the on-line version (Gustave Roussy Institute – Villejuif – France). http://AtlasGeneticsOncology.org © ATLAS - ISSN 1768-3262 The PDF version of the Atlas of Genetics and Cytogenetics in Oncology and Haematology is a reissue of the original articles published in collaboration with the Institute for Scientific and Technical Information (INstitut de l’Information Scientifique et Technique - INIST) of the French National Center for Scientific Research (CNRS) on its electronic publishing platform I-Revues. Online and PDF versions of the Atlas of Genetics and Cytogenetics in Oncology and Haematology are hosted by INIST-CNRS. Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Editor Jean-Loup Huret (Poitiers, France) Volume 6, Number 4, October - December 2002 Table of contents Gene Section FANCA (Fanconi anaemia complementation group A) Jean-Loup Huret 270 FANCC (Fanconi anaemia complementation group C) Jean-Loup Huret 273 FANCD2 (Fanconi anemia, complementation group D2) Jean-Loup Huret 275 FANCE (Fanconi anemia, complementation group E) Jean-Loup Huret 277 FANCF (Fanconi anemia, complementation group F) Jean-Loup Huret 279 FANCG (Fanconi anemia, complementation group G) Jean-Loup Huret 281 PLAG1 (Pleomorphic adenoma gene 1) David Gisselsson 283 Leukaemia Section Angioimmunoblastic T-cell lymphoma Antonio Cuneo, Gianluigi Castoldi 286 Lymphoepithelioid lymphoma Antonio Cuneo, Gianluigi Castoldi 288 t(2;14)(p13;q32) Jean-Loup Huret 289 t(5;14)(q35;q32) Roland Berger 290 Acute Erythroid leukaemias Sally Killick, Estella Matutes 292 t(1;13)(q32;q14) Jean-Loup Huret 294 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) t(11;14)(q13;q32) in multiple myeloma Atlas of Genetics and Cytogenetics in Oncology and Haematology Huret JL, Laï JL OPEN ACCESS JOURNAL AT INIST-CNRS t(1;7)(q21;q22) Jean-Loup Huret 296 t(3;14)(q21;q32) Jean-Loup Huret 297 t(4;11)(q21;p15) Franck Viguié 298 t(6;8)(q11;q11) Jean-Loup Huret 300 Solid Tumour Section Head and neck squamous cell carcinoma Hélène Blons 301 Cancer Prone Disease Section Congenital neutropenia Jay L Hess 304 Simpson-Golabi-Behmel syndrome Daniel Sinnett 306 Fanconi anaemia Jean-Loup Huret 308 Tuberous sclerosis (TSC) Julie Steffann, Arnold Munnich, Jean-Paul Bonnefont 311 Deep Insight Section Ataxia-Telangiectasia and variants Nancy Uhrhammer, Jacques-Olivier Bay, Susan Perlman, Richard A Gatti 313 Educational Items Section Genetic Linkage Analysis Françoise Clerget-Darpoux 323 Consanguinity Robert Kalmes, Jean-Loup Huret 334 Genealogy and Coefficient of Consanguinity, Exercices Robert Kalmes 339 Genetic Constitution of Consanguine Populations Robert Kalmes, Jean-Loup Huret 341 Prenatal Diagnosis Louis Dallaire 342 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review FANCA (Fanconi anaemia complementation group A) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Genes/FA1ID102.html DOI: 10.4267/2042/37891 This article is an update of: Joenje H. FANCA (Fanconi anaemia A). Atlas Genet Cytogenet Oncol Haematol.2002;6(2):82-84. Huret JL. FA1 (Fanconi anaemia 1). Atlas Genet Cytogenet Oncol Haematol.1998;2(3):81-82. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Function Identity Part of the FA complex with FANCC, FANCE, FANCF, and FANCG; this complex is only found in the nucleus. FANCA and FANCG form a complex in the cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated) FANCD2, downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the non-ubiquinated form. Other names: FACA; FAA; FA1 HGNC (Hugo): FANCA Location: 16q24.3 DNA/RNA Description 43 exons spanning 80 kb; 4365 bp open reading frame. Transcription 5.5 kb mRNA Protein Description 1455 amino acids; 163 kDa; 2 nuclear localisation signals (NLS) consensus sequences in N-terminus and a leucine zipper in 1069-1090, none proven to functional as such; FANCA is normally phosphorylated. Homology No known homology or functional motifs. Mutations Expression Germinal Wide: brain, placenta, testis, tonsils (mRNA); in mice: protein expression predominant in lymphoid organs, testis, ovary. Various nucleotide substitutions, deletions, or insertions have been described. Over 90% of the mutations are private, with about 30% being relatively large deletions. Founder mutations have been described in South Africa. Localisation Both cytoplasmic and nuclear. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 270 FANCA (Fanconi anaemia complementation group A) Huret JL Implicated in an arginine-rich domain. 26;274(48):34212-8 Fanconi anaemia (FA) Kupfer G, Naf D, Garcia-Higuera I, Wasik J, Cheng A, Yamashita T, Tipping A, Morgan N, Mathew CG, D'Andrea AD. A patient-derived mutant form of the Fanconi anemia protein, FANCA, is defective in nuclear accumulation. Exp Hematol. 1999 Apr;27(4):587-93 FANCA is implicated in the FA complementation group A; it represents about 70% of FA cases. Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia and squamous cell carcinoma). Prognosis Fanconi anaemia's prognosis is poor; mean survival is 20 years: patients die of bone marrow failure (infections, haemorrhages), leukaemia, or solid cancer. It has recently been shown that significant phenotypic differences were found between the various complementation groups. In FA group A, patients homozygous for null mutations had an earlier onset of anemia and a higher incidence of leukemia than those with mutations producing an altered protein. Patients homozygous for null mutations in FANCA are highrisk groups with a poor hematologic outcome and should be considered as candidates both for frequent monitoring and early therapeutic intervention. Cytogenetics Spontaneously enhanced chromatid-type aberrations (breaks, gaps, interchanges; increased rate of breaks compared to control, when induced by specific clastogens known as DNA cross-linking agents (e.g. mitomycin C, diepoxybutane). Biol Chem. 1999 Nov Lightfoot J, Alon N, Bosnoyan-Collins L, Buchwald M. Characterization of regions functional in the nuclear localization of the Fanconi anemia group A protein. Hum Mol Genet. 1999 Jun;8(6):1007-15 McMahon LW, Walsh CE, Lambert MW. Human alpha spectrin II and the Fanconi anemia proteins FANCA and FANCC interact to form a nuclear complex. J Biol Chem. 1999 Nov 12;274(46):32904-8 Morgan NV, Tipping AJ, Joenje H, Mathew CG. High frequency of large intragenic deletions in the Fanconi anemia group A gene. Am J Hum Genet. 1999 Nov;65(5):1330-41 Waisfisz Q, de Winter JP, Kruyt FA, de Groot J, van der Weel L, Dijkmans LM, Zhi Y, Arwert F, Scheper RJ, Youssoufian H, Hoatlin ME, Joenje H. A physical complex of the Fanconi anemia proteins FANCG/XRCC9 and FANCA. Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10320-5 Waisfisz Q, Morgan NV, Savino M, de Winter JP, van Berkel CG, Hoatlin ME, Ianzano L, Gibson RA, Arwert F, Savoia A, Mathew CG, Pronk JC, Joenje H. Spontaneous functional correction of homozygous fanconi anaemia alleles reveals novel mechanistic basis for reverse mosaicism. Nat Genet. 1999 Aug;22(4):379-83 Walsh CE, Yountz MR, Simpson DA. Intracellular localization of the Fanconi anemia complementation group A protein. Biochem Biophys Res Commun. 1999 Jun 16;259(3):594-9 Balta G, de Winter JP, Kayserili H, Pronk JC, Joenje H. Fanconi anemia A due to a novel frameshift mutation in hotspot motifs: lack of FANCA protein. Hum Mutat. 2000 Jun;15(6):578 References The Fanconi anaemia/breast cancer consortium.. Positional cloning of the Fanconi anaemia group A gene. Nat Genet. 1996 Nov;14(3):324-8 de Winter JP, van der Weel L, de Groot J, Stone S, Waisfisz Q, Arwert F, Scheper RJ, Kruyt FA, Hoatlin ME, Joenje H. The Fanconi anemia protein FANCF forms a nuclear complex with FANCA, FANCC and FANCG. Hum Mol Genet. 2000 Nov 1;9(18):2665-74 Lo Ten Foe JR, Rooimans MA, Bosnoyan-Collins L, Alon N, Wijker M, Parker L, Lightfoot J, Carreau M, Callen DF, Savoia A, Cheng NC, van Berkel CG, Strunk MH, Gille JJ, Pals G, Kruyt FA, Pronk JC, Arwert F, Buchwald M, Joenje H. Expression cloning of a cDNA for the major Fanconi anaemia gene, FAA. Nat Genet. 1996 Nov;14(3):320-3 Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group. Blood. 2000 Dec 15;96(13):4064-70 Kupfer GM, Näf D, Suliman A, Pulsipher M, D'Andrea AD. The Fanconi anaemia proteins, FAA and FAC, interact to form a nuclear complex. Nat Genet. 1997 Dec;17(4):487-90 Levran O, Erlich T, Magdalena N, Gregory JJ, Batish SD, Verlander PC, Auerbach AD. Sequence variation in the Fanconi anemia gene FAA. Proc Natl Acad Sci U S A. 1997 Nov 25;94(24):13051-6 Garcia-Higuera I, Kuang Y, Denham J, D'Andrea AD. The fanconi anemia proteins FANCA and FANCG stabilize each other and promote the nuclear accumulation of the Fanconi anemia complex. Blood. 2000 Nov 1;96(9):3224-30 Yamashita T, Kupfer GM, Naf D, Suliman A, Joenje H, Asano S, D'Andrea AD. The fanconi anemia pathway requires FAA phosphorylation and FAA/FAC nuclear accumulation. Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):13085-90 Huber PA, Medhurst AL, Youssoufian H, Mathew CG. Investigation of Fanconi anemia protein interactions by yeast two-hybrid analysis. Biochem Biophys Res Commun. 2000 Feb 5;268(1):73-7 Garcia-Higuera I, Kuang Y, Näf D, Wasik J, D'Andrea AD. Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Mol Cell Biol. 1999 Jul;19(7):4866-73 Kuang Y, Garcia-Higuera I, Moran A, Mondoux M, Digweed M, D'Andrea AD. Carboxy terminal region of the Fanconi anemia protein, FANCG/XRCC9, is required for functional activity. Blood. 2000 Sep 1;96(5):1625-32 Kruyt FA, Abou-Zahr F, Mok H, Youssoufian H. Resistance to mitomycin C requires direct interaction between the Fanconi anemia proteins FANCA and FANCG in the nucleus through Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) J van de Vrugt HJ, Cheng NC, de Vries Y, Rooimans MA, de Groot J, Scheper RJ, Zhi Y, Hoatlin ME, Joenje H, Arwert F. 271 FANCA (Fanconi anaemia complementation group A) Huret JL Cloning and characterization of murine fanconi anemia group A gene: Fanca protein is expressed in lymphoid tissues, testis, and ovary. Mamm Genome. 2000 Apr;11(4):326-31 Otsuki T, Furukawa Y, Ikeda K, Endo H, Yamashita T, Shinohara A, Iwamatsu A, Ozawa K, Liu JM. Fanconi anemia protein, FANCA, associates with BRG1, a component of the human SWI/SNF complex. Hum Mol Genet. 2001 Nov 1;10(23):2651-60 Wong JC, Alon N, Norga K, Kruyt FA, Youssoufian H, Buchwald M. Cloning and analysis of the mouse Fanconi anemia group A cDNA and an overlapping penta zinc finger cDNA. Genomics. 2000 Aug 1;67(3):273-83 Qiao F, Moss A, Kupfer GM. Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner. J Biol Chem. 2001 Jun 29;276(26):23391-6 Futaki M, Watanabe S, Kajigaya S, Liu JM. Fanconi anemia protein, FANCG, is a phosphoprotein and is upregulated with FANCA after TNF-alpha treatment. Biochem Biophys Res Commun. 2001 Feb 23;281(2):347-51 Ren J, Youssoufian H. Functional analysis of the putative peroxidase domain of FANCA, the Fanconi anemia complementation group A protein. Mol Genet Metab. 2001 Jan;72(1):54-60 Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol Cell. 2001 Feb;7(2):249-62 Yagasaki H, Adachi D, Oda T, Garcia-Higuera I, Tetteh N, D'Andrea AD, Futaki M, Asano S, Yamashita T. A cytoplasmic serine protein kinase binds and may regulate the Fanconi anemia protein FANCA. Blood. 2001 Dec 15;98(13):3650-7 Gregory JJ Jr, Wagner JE, Verlander PC, Levran O, Batish SD, Eide CR, Steffenhagen A, Hirsch B, Auerbach AD. Somatic mosaicism in Fanconi anemia: evidence of genotypic reversion in lymphohematopoietic stem cells. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2532-7 Yamashita T, Nakahata T. Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes. Int J Hematol. 2001 Jul;74(1):33-41 Grompe M, D'Andrea A. Fanconi anemia and DNA repair. Hum Mol Genet. 2001 Oct 1;10(20):2253-9 Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J. Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia. Hum Mol Genet. 2002 Feb 15;11(4):439-44 McMahon LW, Sangerman J, Goodman SR, Kumaresan K, Lambert MW. Human alpha spectrin II and the FANCA, FANCC, and FANCG proteins bind to DNA containing psoralen interstrand cross-links. Biochemistry. 2001 Jun 19;40(24):7025-34 This article should be referenced as such: Huret JL. FANCA (Fanconi anaemia complementation group A). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):270272. Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG. Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway. Hum Mol Genet. 2001 Feb 15;10(4):423-9 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 272 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review FANCC (Fanconi anaemia complementation group C) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Genes/FACC101.html DOI: 10.4267/2042/37892 This article is an update of: Huret JL. FACC (Fanconi anaemia complementation group C). Atlas Genet Cytogenet Oncol Haematol.1998;2(1):10-11. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Expression Identity Wide, in particular in the bones; high expression in proliferating cells, low in differentiated cells. Other names: FAC HGNC (Hugo): FANCC Location: 9q22.3 Local order: next to PTCH and XPAC Localisation Cytoplasmic (mostly) and nuclear. Function Part of the FA complex with FANCA, FANCE, FANCF, and FANCG; this complex is only found in the nucleus. FANCA and FANCG form a complex in the cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated) FANCD2, downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the non-ubiquinated form. FANCC may have mutlifunctional roles, in addition to its involvement in the FA pathway. FANCC binds to cdc2 (mitotic cyclin-dependent kinase), STAT1, GRP94 (a chaperon protein), NADPH, and a number of other proteins; involved in DNA repair and in suppressing interferon gamma induced cellular apoptosis. Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. DNA/RNA Description 14 exons; spans 80 kb. Transcription mRNA of 2.3, 3.2, and 4.6 kb (alternative splicing in 5', variable 3' untranslated region, exon 13 skipping). Protein Description 558 amino acids; 63 kDa. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 273 FANCC (Fanconi anaemia complementation group C) Huret JL D'Andrea AD, Grompe M. Molecular biology of Fanconi anemia: implications for diagnosis and therapy. Blood. 1997 Sep 1;90(5):1725-36 Homology No known homology. Garcia-Higuera I, Kuang Y, Näf D, Wasik J, D'Andrea AD. Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Mol Cell Biol. 1999 Jul;19(7):4866-73 Mutations Germinal Most mutations are found in exon1, intron 4, and exon 14. Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group. Blood. 2000 Dec 15;96(13):4064-70 Implicated in Fanconi anaemia (FA) FACC is implicated in the FA complementation group C; it represents about 15% of FA cases. Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia). Prognosis Fanconi anaemia's prognosis is poor; mean survival is 16 years: patients die of bone marrow failure (infections, haemorrhages), leukaemia, or androgen therapy related liver tumours. It has recently been shown that significant phenotypic differences were found between the various complementation groups. FA group C patients had less somatic abnormalities. However, there is a certain clinical heterogeneity. Cytogenetics Spontaneous, chromatid/chromosome breaks; increased rate of breaks compared to control, when induced by breaking agent. Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol Cell. 2001 Feb;7(2):249-62 Grompe M, D'Andrea A. Fanconi anemia and DNA repair. Hum Mol Genet. 2001 Oct 1;10(20):2253-9 Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG. Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway. Hum Mol Genet. 2001 Feb 15;10(4):423-9 Pang Q, Christianson TA, Keeble W, Diaz J, Faulkner GR, Reifsteck C, Olson S, Bagby GC. The Fanconi anemia complementation group C gene product: structural evidence of multifunctionality. Blood. 2001 Sep 1;98(5):1392-401 Qiao F, Moss A, Kupfer GM. Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner. J Biol Chem. 2001 Jun 29;276(26):23391-6 Yamashita T, Nakahata T. Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes. Int J Hematol. 2001 Jul;74(1):33-41 References Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J. Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia. Hum Mol Genet. 2002 Feb 15;11(4):439-44 Strathdee CA, Gavish H, Shannon WR, Buchwald M. Cloning of cDNAs for Fanconi's anaemia by functional complementation. Nature. 1992 Apr 30;356(6372):763-7 This article should be referenced as such: Gibson RA, Buchwald M, Roberts RG, Mathew CG. Characterisation of the exon structure of the Fanconi anaemia group C gene by vectorette PCR. Hum Mol Genet. 1993 Jan;2(1):35-8 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Huret JL. FANCC (Fanconi anaemia complementation group C). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):273274. 274 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review FANCD2 (Fanconi anemia, complementation group D2) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Genes/FAD.html DOI: 10.4267/2042/37893 This article is an update of: Huret JL. FAD (Fanconi anaemia group D). Atlas Genet Cytogenet Oncol Haematol.1998;2(3):83. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Function Identity The FA complex is comprised of: FANCA, FANCC, FANCE, FANCF, and FANCG; this complex is only found in the nucleus. FANCA and FANCG form a complex in the cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated ) FANCD2 (i.e. FANCD2-L), downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the nonubiquinated form (FANCD2-S). FANCD2co-localizes with BRCA1 in DNA damagedinduced loci and in the synaptonemal complex of meotic chromosomes as well. Other names: FAD; FAD2; FACD; FANCD HGNC (Hugo): FANCD2 Location: 3p25-26 Local order: not far from XPC, in 3p25. Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. DNA/RNA Description 44 exons; 4356 bp open reading frame; the first exon is non-coding. Protein Homology Description Significant homologies can be found with proteins from various species. 1452 amino acids; 155 kDa (FANCD2-S isoform, for short), and 162 kDa (FANCD2-L isoform, for long) by ubiquitin addition. Implicated in Expression Fanconi anaemia (FA) Weak. FANCD2 is implicated in the FA complementation group D, a heterogeneous group, with at least 2 genes: FANCD2, and a yet undiscovered FANCD1. FA complementation group D represents about 1% of FA Localisation Nucleus. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 275 FANCD2 (Fanconi anemia, complementation group D2) Huret JL Hejna JA, Timmers CD, Reifsteck C, Bruun DA, Lucas LW, Jakobs PM, Toth-Fejel S, Unsworth N, Clemens SL, Garcia DK, Naylor SL, Thayer MJ, Olson SB, Grompe M, Moses RE. Localization of the Fanconi anemia complementation group D gene to a 200-kb region on chromosome 3p25.3. Am J Hum Genet. 2000 May;66(5):1540-51 cases. In FA complementation group D patients, the FA complex is normal, in contrast with results found in group A, B (with a yet unknown gene), C, E, F, and G patients. Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia and squamous cell carcinoma). Prognosis Fanconi anaemia's prognosis is poor; mean survival is 20 years: patients die of bone marrow failure (infections, haemorrhages), leukaemia, or solid cancer. It has recently been shown that significant phenotypic differences were found between the various complementation groups. Patients from the rare groups FA-D, FA-E, and FA-F had somatic abnormalities more frequently. Cytogenetics Spontaneously enhanced chromatid-type aberrations (breaks, gaps, interchanges; increased rate of breaks compared to control, when induced by specific clastogens known as DNA cross-linking agents (e.g. mitomycin C, diepoxybutane). Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol Cell. 2001 Feb;7(2):249-62 Grompe M, D'Andrea A. Fanconi anemia and DNA repair. Hum Mol Genet. 2001 Oct 1;10(20):2253-9 Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG. Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway. Hum Mol Genet. 2001 Feb 15;10(4):423-9 Qiao F, Moss A, Kupfer GM. Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner. J Biol Chem. 2001 Jun 29;276(26):23391-6 Timmers C, Taniguchi T, Hejna J, Reifsteck C, Lucas L, Bruun D, Thayer M, Cox B, Olson S, D'Andrea AD, Moses R, Grompe M. Positional cloning of a novel Fanconi anemia gene, FANCD2. Mol Cell. 2001 Feb;7(2):241-8 Wilson JB, Johnson MA, Stuckert AP, Trueman KL, May S, Bryant PE, Meyn RE, D'Andrea AD, Jones NJ. The Chinese hamster FANCG/XRCC9 mutant NM3 fails to express the monoubiquitinated form of the FANCD2 protein, is hypersensitive to a range of DNA damaging agents and exhibits a normal level of spontaneous sister chromatid exchange. Carcinogenesis. 2001 Dec;22(12):1939-46 References Whitney M, Thayer M, Reifsteck C, Olson S, Smith L, Jakobs PM, Leach R, Naylor S, Joenje H, Grompe M. Microcell mediated chromosome transfer maps the Fanconi anaemia group D gene to chromosome 3p. Nat Genet. 1995 Nov;11(3):341-3 Yamashita T, Nakahata T. Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes. Int J Hematol. 2001 Jul;74(1):33-41 D'Andrea AD, Grompe M. Molecular biology of Fanconi anemia: implications for diagnosis and therapy. Blood. 1997 Sep 1;90(5):1725-36 Yang Y, Kuang Y, Montes De Oca R, Hays T, Moreau L, Lu N, Seed B, D'Andrea AD. Targeted disruption of the murine Fanconi anemia gene, Fancg/Xrcc9. Blood. 2001 Dec 1;98(12):3435-40 Garcia-Higuera I, Kuang Y, Näf D, Wasik J, D'Andrea AD. Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Mol Cell Biol. 1999 Jul;19(7):4866-73 Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J. Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia. Hum Mol Genet. 2002 Feb 15;11(4):439-44 Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group. Blood. 2000 Dec 15;96(13):4064-70 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) This article should be referenced as such: Huret JL. FANCD2 (Fanconi anemia, complementation group D2). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):275276. 276 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review FANCE (Fanconi anemia, complementation group E) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Genes/FANCEID293.html DOI: 10.4267/2042/37894 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated) FANCD2, downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the non-ubiquinated form. Identity Other names: FACE; FAE HGNC (Hugo): FANCE Location: 6p21 Local order: located between the 60S ribosomal protein RPL10Aand a ZNF127 like protein. Homology No known homology. Implicated in Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Fanconi anaemia (FA) DNA/RNA FANCE is implicated in the FA complementation group E; it represents about 2% of FA cases. Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia). Prognosis Fanconi anaemia's prognosis is poor; mean survival is 20 years (depending on mutation, treatment): patients die of bone marrow failure (infections, haemorrhages), leukaemia, or androgen therapy related liver tumours. It has recently been shown that significant phenotypic differences were found between the various complementation groups. Patients from the rare groups FA-D, FA-E, and FA-F had somatic abnormalities more frequently. Description The gene spans 15 kb and contains 10 exons; 1611 bp open reading frame. Protein Description 536 amino acids, 60 kDa; contains two potential nuclear localization signals. Function Part of the FA complex with FANCA, FANCC, FANCF, and FANCG. ; this complex is only found in the nucleus. FANCA and FANCG form a complex in the Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 277 FANCE (Fanconi anemia, complementation group E) Huret JL Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol Cell. 2001 Feb;7(2):249-62 Cytogenetics Spontaneous, chromatid/chromosome breaks; increased rate of breaks compared to control, when induced by breaking agent. Grompe M, D'Andrea A. Fanconi anemia and DNA repair. Hum Mol Genet. 2001 Oct 1;10(20):2253-9 References Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG. Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway. Hum Mol Genet. 2001 Feb 15;10(4):423-9 Garcia-Higuera I, Kuang Y, Näf D, Wasik J, D'Andrea AD. Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Mol Cell Biol. 1999 Jul;19(7):4866-73 Qiao F, Moss A, Kupfer GM. Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner. J Biol Chem. 2001 Jun 29;276(26):23391-6 de Winter JP, Léveillé F, van Berkel CG, Rooimans MA, van Der Weel L, Steltenpool J, Demuth I, Morgan NV, Alon N, Bosnoyan-Collins L, Lightfoot J, Leegwater PA, Waisfisz Q, Komatsu K, Arwert F, Pronk JC, Mathew CG, Digweed M, Buchwald M, Joenje H. Isolation of a cDNA representing the Fanconi anemia complementation group E gene. Am J Hum Genet. 2000 Nov;67(5):1306-8 Yamashita T, Nakahata T. Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes. Int J Hematol. 2001 Jul;74(1):33-41 Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J. Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia. Hum Mol Genet. 2002 Feb 15;11(4):439-44 Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group. Blood. 2000 Dec 15;96(13):4064-70 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) This article should be referenced as such: Huret JL. FANCE (Fanconi anemia, complementation group E). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):277278. 278 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review FANCF (Fanconi anemia, complementation group F) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Genes/FANCFID294.html DOI: 10.4267/2042/37895 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology FANCA and FANCG form a complex in the cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated) FANCD2, downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the non-ubiquinated form. Identity Other names: FAF HGNC (Hugo): FANCF Location: 11p15 Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Homology DNA/RNA ROM (prokaryote). Description Implicated in 1 exon; 1124 bp open reading frame. Fanconi anaemia (FA) Protein FANCF is implicated in the FA complementation group F; it represents about 2-3% of FA cases. Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia and squamous cell carcinoma). Prognosis Fanconi anaemia's prognosis is poor; mean survival is 20 years: patients die of bone marrow failure (infections, haemorrhages), leukaemia, or solid cancer. It has recently been shown that significant phenotypic differences were found between the various complementation groups. Patients from the rare groups Description 374 amino acids ; 42 kDa. Expression Weak. Localisation Predominantly nuclear. Function Part of the FA complex with FANCA, FANCC, FANCE, and FANCG; this complex is only found in the nucleus. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 279 FANCF (Fanconi anemia, complementation group F) Huret JL Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol Cell. 2001 Feb;7(2):249-62 FA-D, FA-E, and FA-F had somatic abnormalities more frequently. Cytogenetics Spontaneously enhanced chromatid-type aberrations (breaks, gaps, interchanges; increased rate of breaks compared to control, when induced by specific clastogens known as DNA cross-linking agents (e.g. mitomycin C, diepoxybutane). Grompe M, D'Andrea A. Fanconi anemia and DNA repair. Hum Mol Genet. 2001 Oct 1;10(20):2253-9 Holmes RK, Harutyunyan K, Shah M, Joenje H, Youssoufian H. Correction of cross-linker sensitivity of Fanconi anemia group F cells by CD33-mediated protein transfer. Blood. 2001 Dec 15;98(13):3817-22 References Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG. Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway. Hum Mol Genet. 2001 Feb 15;10(4):423-9 Garcia-Higuera I, Kuang Y, Näf D, Wasik J, D'Andrea AD. Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Mol Cell Biol. 1999 Jul;19(7):4866-73 Qiao F, Moss A, Kupfer GM. Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner. J Biol Chem. 2001 Jun 29;276(26):23391-6 de Winter JP, Rooimans MA, van Der Weel L, van Berkel CG, Alon N, Bosnoyan-Collins L, de Groot J, Zhi Y, Waisfisz Q, Pronk JC, Arwert F, Mathew CG, Scheper RJ, Hoatlin ME, Buchwald M, Joenje H. The Fanconi anaemia gene FANCF encodes a novel protein with homology to ROM. Nat Genet. 2000 Jan;24(1):15-6 Siddique MA, Nakanishi K, Taniguchi T, Grompe M, D'Andrea AD. Function of the Fanconi anemia pathway in Fanconi anemia complementation group F and D1 cells. Exp Hematol. 2001 Dec;29(12):1448-55 de Winter JP, van der Weel L, de Groot J, Stone S, Waisfisz Q, Arwert F, Scheper RJ, Kruyt FA, Hoatlin ME, Joenje H. The Fanconi anemia protein FANCF forms a nuclear complex with FANCA, FANCC and FANCG. Hum Mol Genet. 2000 Nov 1;9(18):2665-74 Yamashita T, Nakahata T. Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes. Int J Hematol. 2001 Jul;74(1):33-41 Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J. Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia. Hum Mol Genet. 2002 Feb 15;11(4):439-44 Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group. Blood. 2000 Dec 15;96(13):4064-70 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) This article should be referenced as such: Huret JL. FANCF (Fanconi anemia, complementation group F). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):279-280. 280 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review FANCG (Fanconi anemia, complementation group G) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Genes/FANCGID295.html DOI: 10.4267/2042/37896 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Function Identity Description Part of the FA complex with FANCA, FANCC, FANCE, and FANCF; this complex is only found in the nucleus. FANCA and FANCG form a complex in the cytoplasm, through a N-term FANCA (involving the nuclear localization signal) - FANCG interaction; FANCC join the complex; phosphorylation of FANCA would induce its translocation into the nucleus.This FA complex translocates into the nucleus, where FANCE and FANCF are present; FANCE and FANCF join the complex. The FA complex subsequently interacts with FANCD2 by monoubiquitination of FANCD2 during S phase or following DNA damage. Activated (ubiquinated) FANCD2, downstream in the FA pathway, will then interact with other proteins involved in DNA repair, possibly BRCA1; after DNA repair, FANCD2 return to the non-ubiquinated form. 14 exons; 1869 bp open reading frame. Homology Transcription No known homology. 2.2 and 2.5 kb. Mutations Protein Germinal Description Wide range of mutations (splice, nonsense, missense). 622 amino acids, 69 kDa; contains a leucine zipper; can be phosphorylated. Implicated in Expression Fanconi anaemia (FA) Weak; testis, thymus, lymphoblasts. FANCG is implicated in the FA complementation group G; it represents about 10% of FA cases. Disease Fanconi anaemia is a chromosome instability syndrome/cancer prone disease (at risk of leukaemia and squamous cell carcinoma). Other names: FAG; XRCC9 complementing defective repair 9) HGNC (Hugo): FANCG Location: 9p13 (X-ray repair Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. DNA/RNA Localisation Predominantly nuclear. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 281 FANCG (Fanconi anemia, complementation group G) Huret JL Prognosis Fanconi anaemia's prognosis is poor; mean survival is 20 years: patients die of bone marrow failure (infections, haemorrhages), leukaemia, or solid cancer. It has recently been shown that significant phenotypic differences were found between the various complementation groups. FA group G patients had more severe cytopenia and a higher incidence of leukemia. FA group G patients are high-risk groups with a poor hematologic outcome and should be considered as candidates both for frequent monitoring and early therapeutic intervention. Cytogenetics Spontaneously enhanced chromatid-type aberrations (breaks, gaps, interchanges; increased rate of breaks compared to control, when induced by specific clastogens known as DNA cross-linking agents (e.g. mitomycin C, diepoxybutane). protein, FANCG/XRCC9, is required for functional activity. Blood. 2000 Sep 1;96(5):1625-32 References Qiao F, Moss A, Kupfer GM. Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner. J Biol Chem. 2001 Jun 29;276(26):23391-6 Futaki M, Watanabe S, Kajigaya S, Liu JM. Fanconi anemia protein, FANCG, is a phosphoprotein and is upregulated with FANCA after TNF-alpha treatment. Biochem Biophys Res Commun. 2001 Feb 23;281(2):347-51 Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol Cell. 2001 Feb;7(2):249-62 Grompe M, D'Andrea A. Fanconi anemia and DNA repair. Hum Mol Genet. 2001 Oct 1;10(20):2253-9 Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG. Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway. Hum Mol Genet. 2001 Feb 15;10(4):423-9 Nakanishi K, Moran A, Hays T, Kuang Y, Fox E, Garneau D, Montes de Oca R, Grompe M, D'Andrea AD. Functional analysis of patient-derived mutations in the Fanconi anemia gene, FANCG/XRCC9. Exp Hematol. 2001 Jul;29(7):842-9 Liu N, Lamerdin JE, Tucker JD, Zhou ZQ, Walter CA, Albala JS, Busch DB, Thompson LH. The human XRCC9 gene corrects chromosomal instability and mutagen sensitivities in CHO UV40 cells. Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9232-7 Wilson JB, Johnson MA, Stuckert AP, Trueman KL, May S, Bryant PE, Meyn RE, D'Andrea AD, Jones NJ. The Chinese hamster FANCG/XRCC9 mutant NM3 fails to express the monoubiquitinated form of the FANCD2 protein, is hypersensitive to a range of DNA damaging agents and exhibits a normal level of spontaneous sister chromatid exchange. Carcinogenesis. 2001 Dec;22(12):1939-46 de Winter JP, Waisfisz Q, Rooimans MA, van Berkel CG, Bosnoyan-Collins L, Alon N, Carreau M, Bender O, Demuth I, Schindler D, Pronk JC, Arwert F, Hoehn H, Digweed M, Buchwald M, Joenje H. The Fanconi anaemia group G gene FANCG is identical with XRCC9. Nat Genet. 1998 Nov;20(3):281-3 Yamashita T, Nakahata T. Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes. Int J Hematol. 2001 Jul;74(1):33-41 Garcia-Higuera I, Kuang Y, Näf D, Wasik J, D'Andrea AD. Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Mol Cell Biol. 1999 Jul;19(7):4866-73 Yang Y, Kuang Y, Montes De Oca R, Hays T, Moreau L, Lu N, Seed B, D'Andrea AD. Targeted disruption of the murine Fanconi anemia gene, Fancg/Xrcc9. Blood. 2001 Dec 1;98(12):3435-40 Waisfisz Q, de Winter JP, Kruyt FA, de Groot J, van der Weel L, Dijkmans LM, Zhi Y, Arwert F, Scheper RJ, Youssoufian H, Hoatlin ME, Joenje H. A physical complex of the Fanconi anemia proteins FANCG/XRCC9 and FANCA. Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10320-5 Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J. Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia. Hum Mol Genet. 2002 Feb 15;11(4):439-44 Demuth I, Wlodarski M, Tipping AJ, Morgan NV, de Winter JP, Thiel M, Gräsl S, Schindler D, D'Andrea AD, Altay C, Kayserili H, Zatterale A, Kunze J, Ebell W, Mathew CG, Joenje H, Sperling K, Digweed M. Spectrum of mutations in the Fanconi anaemia group G gene, FANCG/XRCC9. Eur J Hum Genet. 2000 Nov;8(11):861-8 Futaki M, Igarashi T, Watanabe S, Kajigaya S, Tatsuguchi A, Wang J, Liu JM. The FANCG Fanconi anemia protein interacts with CYP2E1: possible role in protection against oxidative DNA damage. Carcinogenesis. 2002 Jan;23(1):67-72 Koomen M, Cheng NC, van de Vrugt HJ, Godthelp BC, van der Valk MA, Oostra AB, Zdzienicka MZ, Joenje H, Arwert F. Reduced fertility and hypersensitivity to mitomycin C characterize Fancg/Xrcc9 null mice. Hum Mol Genet. 2002 Feb 1;11(3):273-81 Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group. Blood. 2000 Dec 15;96(13):4064-70 This article should be referenced as such: Huret JL. FANCG (Fanconi anemia, complementation group G). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):281282. Kuang Y, Garcia-Higuera I, Moran A, Mondoux M, Digweed M, D'Andrea AD. Carboxy terminal region of the Fanconi anemia Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 282 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Gene Section Mini Review PLAG1 (Pleomorphic adenoma gene 1) David Gisselsson Department of Clinical Genetics, Lund University Hospital, 221 85 Lund, Sweden (DG) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Genes/PLAG1ID74.html DOI: 10.4267/2042/37897 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Localisation Identity Nuclear. HGNC (Hugo): PLAG1 Location: 8q12 Local order: (316 cR / 86 Mb from 8pter) Function One of the N-terminal nuclear localisation signals (NLS1) interacts with karyopherin a2, which escorts proteins into the nucleus. Three of the seven Zn-finger domains are responsible for interaction with DNA and PLAG1 specifically activates transcription from its consensus binding site. Potential PLAG1 binding sites have been found in the promoter of IGF2. DNA/RNA Description 7313 bp, 5 exons, 4 introns. Transcription Homology At least two splicing variants, including and excluding the second exon. Mouse and rat Plag1. Mutations Protein Somatic Description Involved in chromosome rearrangements in epithelial and mesenchymal tumours. These are typically complex structural abnormalities, resulting in an exchange of regulatory elements and abnormal expression of PLAG1. 500 amino acids with at least three functional regions: 1. Two N-terminal nuclear localisation signals, 2. Seven canonical zinc-finger domains, 3. A serine rich C-terminus. Expression Heart, placenta, spleen, prostate, testis, ovary, small intestine, several tumours. Schematic view of the gene with approximate sizes of introns (kb) and exons (bp); the coding region (violet) translates into a 500 amino acid product with three functional subunits. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 283 PLAG1 (Pleomorphic adenoma gene 1) Gisselsson D Implicated in References Pleomorphic adenoma of the salivary gland Kas K, Röijer E, Voz M, Meyen E, Stenman G, Van de Ven WJ. A 2-Mb YAC contig and physical map covering the chromosome 8q12 breakpoint cluster region in pleomorphic adenomas of the salivary glands. Genomics. 1997 Aug 1;43(3):349-58 Disease Benign epithelial tumour. Prognosis Recovery after surgical removal. Cytogenetics The most common breakpoints are 3p21, 8q12, and 12q15. Hybrid/Mutated gene The following translocations have been reported to result in hybrid genes involving PLAG1: - t(3;8)(p21;q12): CTNNB1 CTNNB1/PLAG1 - t(5;8)(p13;q12): LIFR/PLAG1 Also, rearrangements between PLAG1 and TCEA1 have been detected in cases with normal karyotypes. Abnormal protein Fusions occur in the 5' regulatory regions, leading to promoter swapping and activation of PLAG1 expression while preserving coding sequences. Kas K, Voz ML, Röijer E, Aström AK, Meyen E, Stenman G, Van de Ven WJ. Promoter swapping between the genes for a novel zinc finger protein and beta-catenin in pleiomorphic adenomas with t(3;8)(p21;q12) translocations. Nat Genet. 1997 Feb;15(2):170-4 Kas K, Voz ML, Hensen K, Meyen E, Van de Ven WJ. Transcriptional activation capacity of the novel PLAG family of zinc finger proteins. J Biol Chem. 1998 Sep 4;273(36):2302632 Voz ML, Aström AK, Kas K, Mark J, Stenman G, Van de Ven WJ. The recurrent translocation t(5;8)(p13;q12) in pleomorphic adenomas results in upregulation of PLAG1 gene expression under control of the LIFR promoter. Oncogene. 1998 Mar;16(11):1409-16 Aström AK, Voz ML, Kas K, Röijer E, Wedell B, Mandahl N, Van de Ven W, Mark J, Stenman G. Conserved mechanism of PLAG1 activation in salivary gland tumors with and without chromosome 8q12 abnormalities: identification of SII as a new fusion partner gene. Cancer Res. 1999 Feb 15;59(4):918-23 Queimado L, Lopes C, Du F, Martins C, Bowcock AM, Soares J, Lovett M. Pleomorphic adenoma gene 1 is expressed in cultured benign and malignant salivary gland tumor cells. Lab Invest. 1999 May;79(5):583-9 Carcinoma ex pleomorphic adenoma Disease Malignant epithelial tumour arising from pleomorphic adenoma. Prognosis 30% five-year survival. Cytogenetics Complex karyotype including t(3;8)(p23;q12). Hybrid/Mutated gene Intragenic PLAG1 rearrangements demonstrated by fluorescence in situ hybridisation. Röijer E, Kas K, Behrendt M, Van de Ven W, Stenman G. Fluorescence in situ hybridization mapping of breakpoints in pleomorphic adenomas with 8q12-13 abnormalities identifies a subgroup of tumors without PLAG1 involvement. Genes Chromosomes Cancer. 1999 Jan;24(1):78-82 Astrom A, D'Amore ES, Sainati L, Panarello C, Morerio C, Mark J, Stenman G. Evidence of involvement of the PLAG1 gene in lipoblastomas. Int J Oncol. 2000 Jun;16(6):1107-10 Hibbard MK, Kozakewich HP, Dal Cin P, Sciot R, Tan X, Xiao S, Fletcher JA. PLAG1 fusion oncogenes in lipoblastoma. Cancer Res. 2000 Sep 1;60(17):4869-72 Lipoblastoma Voz ML, Agten NS, Van de Ven WJ, Kas K. PLAG1, the main translocation target in pleomorphic adenoma of the salivary glands, is a positive regulator of IGF-II. Cancer Res. 2000 Jan 1;60(1):106-13 Disease Benign fat-forming tumour of childhood. Prognosis Recovery after surgical removal. Cytogenetics Structural abnormalities involving 8q11-13. Hybrid/Mutated gene The following rearrangements have been reported to result in hybrid genes involving PLAG1: - del(8)(q12q24), r(8): HAS2/PLAG1 - t(7;8)(p22;q13): COL1A2/HAS2 Abnormal protein Fusions occur in the 5' regulatory regions, leading promoter swapping and activation of PLAG1 expression while preserving coding sequences. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Voz ML, Van de Ven WJ, Kas K. First insights into the molecular basis of pleomorphic adenomas of the salivary glands. Adv Dent Res. 2000 Dec;14:81-3 Debiec-Rychter M, Van Valckenborgh I, Van den Broeck C, Hagemeijer A, Van de Ven WJ, Kas K, Van Damme B, Voz ML. Histologic localization of PLAG1 (pleomorphic adenoma gene 1) in pleomorphic adenoma of the salivary gland: cytogenetic evidence of common origin of phenotypically diverse cells. Lab Invest. 2001 Sep;81(9):1289-97 Gisselsson D, Hibbard MK, Dal Cin P, Sciot R, Hsi BL, Kozakewich HP, Fletcher JA. PLAG1 alterations in lipoblastoma: involvement in varied mesenchymal cell types and evidence for alternative oncogenic mechanisms. Am J Pathol. 2001 Sep;159(3):955-62 284 PLAG1 (Pleomorphic adenoma gene 1) Gisselsson D Jin C, Martins C, Jin Y, Wiegant J, Wennerberg J, Dictor M, Gisselsson D, Strömbeck B, Fonseca I, Mitelman F, Tanke HJ, Höglund M, Mertens F. Characterization of chromosome aberrations in salivary gland tumors by FISH, including multicolor COBRA-FISH. Genes Chromosomes Cancer. 2001 Feb;30(2):161-7 Enlund F, Nordkvist A, Sahlin P, Mark J, Stenman G. Expression of PLAG1 and HMGIC proteins and fusion transcripts in radiation-associated pleomorphic adenomas. Int J Oncol. 2002 Apr;20(4):713-6 Hensen K, Van Valckenborgh IC, Kas K, Van de Ven WJ, Voz ML. The tumorigenic diversity of the three PLAG family members is associated with different DNA binding capacities. Cancer Res. 2002 Mar 1;62(5):1510-7 Szpirer C, Kas K, Laes JF, Rivière M, Van Vooren P, Szpirer J. Assignment of the rat pleiomorphic adenoma genes (Plag1, Plagl1, Plagl2) by in situ hybridization and radiation hybrid mapping. Cytogenet Cell Genet. 2001;94(1-2):94-5 This article should be referenced as such: Braem CV, Kas K, Meyen E, Debiec-Rychter M, Van De Ven WJ, Voz ML. Identification of a karyopherin alpha 2 recognition site in PLAG1, which functions as a nuclear localization signal. J Biol Chem. 2002 May 31;277(22):19673-8 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Gisselsson D. PLAG1 (Pleomorphic adenoma gene 1). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):283-285. 285 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Mini Review Angioimmunoblastic T-cell lymphoma Antonio Cuneo, Gianluigi Castoldi Hematology Section, Department of Biomedical Sciences, University of Ferrara, Corso Giovecca 203, Ferrara, Italy (AC, GLC) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/AngioimmunoblID2124.html DOI: 10.4267/2042/37898 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology small-to-large cells resembling immunoblasts and atypical clear cells with round nucleus and abundant pale cytoplasm. The latter cells may occur in small aggregates or sheets. Identity Alias Angioimmunoblastic disprotidemia. lymphadenopathy with Treatment Some patients respond to steroids; in steroidunresponsive patients multiagent chemotherapy usually produces short lasting responses. Clinics and pathology Phenotype/cell stem origin Evolution The lymphoma cell is a peripheral T lymphocyte in various stages of differentiation. The neoplastic clone expresses T-cell antigens and is usually CD4+. The malignant T-cells are believed to secrete cytokines responsible for the polyclonal B-cell hyperplasia observed in involved nodes. Clonality studies demonstrated a monoclonal rearrangement of the bchain of the T-cell receptor (TCR) in the majority of cases. In some cases clonality could not be demonstrated. This led some authors to postulate the existence of at least two types of AILD, namely a reactive and benign type and a lymphomatous form. Few patients present spontaneous or steroid-induced remission; the majority of cases feature an aggressive disease with short survival despite chemotherapy. Most patients die with infection and active disease. Prognosis Median survival is about 1-3 years. Cytogenetics Note A mixture of normal and abnormal cells is usually seen in the vast majority of cases. The cytogenetic picture at disease presentation may be normal in some cases which may develop clonal abnormalites during the course of the disease. The following karyotype pattern can be found. Etiology The disease is rare. Clinics The disease preferentially affects elderly males (maleto-female ratio 3:1, median age around 60 years). Most patients present with generalized lymphadenopathy, hepatosplenomegaly, skin rash and general symptoms (fever, weight loss). Polyclonal hypergammaglobulinemia is a common finding. Cytogenetics morphological Clonal abnormalities defining a stemline, with one or more sidelines (approximately 30-50% of the cases). Normal karyotype (10-30% of the cases). Single cells with unrelated chromosome anomalies (1020%). Unrelated clones with aberrant karyotypes, each carrying single unrelated additional anomalies (1020%). Recurrent chromosome changes in those cases with an abnormal clone include trisomy 3, trisomy 5 and Pathology The lymph node architecture is effaced and no reactive germinal centres are usually observed. The infiltrate may involve the perinodal fat. There is a proliferation of high endothelial venules with clusters of follicular dendritic cells. The lymphoid infiltrate consists of Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 286 Angioimmunoblastic T-cell lymphoma Cuneo A, Castoldi GL Schlegelberger B, Feller A, Gödde E, Grote W, Lennert K. Stepwise development of chromosomal abnormalities in angioimmunoblastic lymphadenopathy. Cancer Genet Cytogenet. 1990 Nov 1;50(1):15-29 trisomy X A 14q+ chromosome is a recurrent structural defect. Recurrent breakpoints include 1p31-32; 3p2425; 4p13; 9q21-22; 12q13; 14q11; 14q32 The presence of abnormal metapahses in unstimulated cultures was associated with failure to respond to therapy and with shorter survival, as was the case with +X, structural aberrations of chromosome 1, and complex karyotype. The latter cytogenetic parameter maintained prognostic predictivity at multivariate analysis. Schlegelberger B, Himmler A, Gödde E, Grote W, Feller AC, Lennert K. Cytogenetic findings in peripheral T-cell lymphomas as a basis for distinguishing low-grade and high-grade lymphomas. Blood. 1994 Jan 15;83(2):505-11 Schlegelberger B, Zwingers T, Hohenadel K, Henne-Bruns D, Schmitz N, Haferlach T, Tirier C, Bartels H, Sonnen R, Kuse R. Significance of cytogenetic findings for the clinical outcome in patients with T-cell lymphoma of angioimmunoblastic lymphadenopathy type. J Clin Oncol. 1996 Feb;14(2):593-9 Cytogenetics molecular Using probes for the detection of +3, +5 and +X, the vast majority of cases can be shown to carry aneuploidy. Kumaravel TS, Tanaka K, Arif M, Ohshima K, Ohgami A, Takeshita M, Kikuchi M, Kamada N. Clonal identification of trisomies 3, 5 and X in angioimmunoblastic lymphadenopathy with dysproteinemia by fluorescence in situ hybridization. Leuk Lymphoma. 1997 Feb;24(5-6):523-32 References Whang Peng J, Knutsen T. Cytogenetics of non Hodgkin's lymphomas Magrath I (Ed) The non Hodgkin's lymphomas 2nd edition. Arnold, London 1997. Delmer A, Zittoun R. Other peripheral T-cell lymphomas. Magrath I (Ed) The non Hodgkin's lymphomas 2nd edition.. Frizzera G, Kaneko Y, Sakurai M. Angioimmunoblastic lymphadenopathy and related disorders: a retrospective look in search of definitions. Leukemia. 1989 Jan;3(1):1-5 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) This article should be referenced as such: Cuneo A, Castoldi GL. Angioimmunoblastic T-cell lymphoma. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):286-287. 287 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication Lymphoepithelioid lymphoma Antonio Cuneo, Gianluigi Castoldi Hematology Section, Department of Biomedical Sciences, University of Ferrara, Corso Giovecca 203, Ferrara, Italy (AC) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/LymphoepithLymphoID2005.html DOI: 10.4267/2042/37899 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Evolution Identity The disease usually runs a relatively aggressive clinical course. Alias Lennert's lymphoma Prognosis Clinics and pathology Median survival of 16 to 32 months was reported in some studies. Phenotype/cell stem origin Cytogenetics Peripheral CD4+ T-cell lymphoma Epidemiology Note Clonal aberrations are reported in the vast majority of cases. Chromosome 3 is frequently involved: trisomy 3; 3q rearrangements (duplication of bands 3q22-24 or 3q22 breaks) are recurrent abnormalities; A 6qchromosome was also reported. The disease is rare. Clinics The patients present superficial lymph node involvement. The cervical areas are predominantly affected, whereas thoracic adenopathies and deep abdominal involvement occur unfrequently at presentation. References Delmer A, Zittoun R. Other peripheral T-cell lymphomas. Magrath I (Ed) The non Hodgkin's lymphomas 2nd edition. Pathology The disease cannot be separated from the broad category of peripheral T-cell lymphoma (PTL). PTL is characterized by a heterogeneous cellular composition with small and large cells with an inflammarory background. Lennert's lymphoma can be recognized by the presence of numerous epithelioid histiocytes usually grouped in small clusters. Lennert's lymphoma is not considered as a distinct clinicopathological entity. Gödde-Salz E, Feller AC, Lennert K. Cytogenetic and immunohistochemical analysis of lymphoepithelioid cell lymphoma (Lennert's lymphoma): further substantiation of its T-cell nature. Leuk Res. 1986;10(3):313-23 Kristoffersson U, Heim S, Olsson H, Akerman M, Mitelman F. Cytogenetic studies in non-Hodgkin lymphomas--results from surgical biopsies. Hereditas. 1986;104(1):1-13 This article should be referenced as such: Cuneo A, Castoldi GL. Lymphoepithelioid lymphoma. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):288. Treatment The disease must be treated with multiagent chemotherapy and/or radiation therapy as for other PTL. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 288 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(2;14)(p13;q32) Jean Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0214p13q32ID1231.html DOI: 10.4267/2042/37900 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Clinics and pathology References Disease Ueshima Y, Bird ML, Vardiman JW, Rowley JD. A 14;19 translocation in B-cell chronic lymphocytic leukemia: a new recurring chromosome aberration. Int J Cancer. 1985 Sep 15;36(3):287-90 Found so far in 6 cases of chronic lymphocytic leukemia (CLL), 1 diffuse, mixed small/large cell non Hogkin lymphoma (NHL), and 3 cases of acute lymphocytic leukemia (ALL): one T-ALL and two (CD10+) B-ALL. Nishida K, Taniwaki M, Misawa S, Abe T. Nonrandom rearrangement of chromosome 14 at band q32.33 in human lymphoid malignancies with mature B-cell phenotype. Cancer Res. 1989 Mar 1;49(5):1275-81 Epidemiology Uckun FM, Gajl-Peczalska KJ, Provisor AJ, Heerema NA. Immunophenotype-karyotype associations in human acute lymphoblastic leukemia. Blood. 1989 Jan;73(1):271-80 Sex ratio: 5 male and 5 female patients; CLL cases were aged 10, 15, 58, 59, and 62 years; ALL cases were 2, 4, and 5 year old children. Yoffe G, Howard-Peebles PN, Smith RG, Tucker PW, Buchanan GR. Childhood chronic lymphocytic leukemia with (2;14) translocation. J Pediatr. 1990 Jan;116(1):114-7 Prognosis 5 CLL cases were dead after 27-49 months survival; the 3 ALL cases were alive at 29+-34+ months of follow up. Watson MS, Land VJ, Carroll AJ, Pullen J, Borowitz MJ, Link MP, Amylon M, Behm FG. t(2;14)(p13;q32): a recurring abnormality in lymphocytic leukemia. A Pediatric Oncology Group study. Cancer Genet Cytogenet. 1992 Feb;58(2):121-4 Cytogenetics Geisler CH, Philip P, Christensen BE, Hou-Jensen K, Pedersen NT, Jensen OM, Thorling K, Andersen E, Birgens HS, Drivsholm A, Ellegaard J, Larsen JK, Plesner T, Brown P, Andersen PK, Hansen MM. In B-cell chronic lymphocytic leukaemia chromosome 17 abnormalities and not trisomy 12 are the single most important cytogenetic abnormalities for the prognosis: a cytogenetic and immunophenotypic study of 480 unselected newly diagnosed patients. Leuk Res. 1997 NovDec;21(11-12):1011-23 Cytogenetics morphological Sole anomaly in 2 of 8 documented cases; often found in complex karyotypes; no recurrent accompanying anomaly so far. Genes involved and proteins Sonoki T, Matsuzaki H, Satterwhite E, Nakazawa N, Hata H, Tucker PW, Taniwaki M, Kuribayashi N, Harada N, Matsuno F, Mitsuya H. A plasma cell leukemia patient showing bialleic 14q translocations: t(2;14) and t(11;14). Acta Haematol. 1999;101(4):197-201 BCL11A Location 2p13-15 Protein 6 Kruppel C2H2 zinc fingers, a prolin rich domain, and an acidic domain. Satterwhite E, Sonoki T, Willis TG, Harder L, Nowak R, Arriola EL, Liu H, Price HP, Gesk S, Steinemann D, Schlegelberger B, Oscier DG, Siebert R, Tucker PW, Dyer MJ. The BCL11 gene family: involvement of BCL11A in lymphoid malignancies. Blood. 2001 Dec 1;98(12):3413-20 IgH This article should be referenced as such: Location 14q32 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Huret JL. t(2;14)(p13;q32). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):289. 289 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(5;14)(q35;q32) Roland Berger Inserm U 434 and SD 401 No. 434 CNRS, Institut de Génétique Moléculaire, 27, rue Juliette Dodu, 75010 Paris, France (RB) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0514q35q32ID1227.html DOI: 10.4267/2042/37901 This article is an update of: Huret JL. t(5;14)(q35;q32). Atlas Genet Cytogenet Oncol Haematol.2002;6(2):130-131. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Identity t(5;14)(q35;q32) FISH - Courtesy Melanie Zenger and Claudia Haferlach. Clinics and pathology Prognosis Disease Present data suggest that t(5;14)(q35;q32) is associated with poor outcome, but confirmatory data is necessary prior to conclude. T cell acute lymphoblastic leukemia (ALL). Phenotype/cell stem origin Cytogenetics Cortical T cell leukemia (CD1a+, CD10+). Cytogenetics morphological Epidemiology Cryptic translocation (banded karyotype). Often apparently normal karyotype with banding techniques. Frequent in T-cell ALL in children (in about 20% of childhood T-cell ALLs); less frequent in adult T-ALL. Not seen in B-cell ALL. Cytogenetics molecular t(5;14)(q35;q32) can be detected with FISH techniques. Several probes may be used: chromosome painting, combination of painting probes and YAC, multicolor- Cytology FAB nomenclature: L1 or L2 ALL. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 290 t(5;14)(q35;q32) Berger R FISH with adequate probes. The localization of the chromosomal breakpoint with BACs/PACs will be performed in a second step. Result of the chromosomal anomaly Additional anomalies Fusion protein Variable. Description No fusion protein, but abnormal expression of HOX11L2. Oncogenesis HOX11L2 is transcriptionally activated, due to control by CITP2 regulatory sequences. Genes involved and proteins Note The consequence of the translocation is the ectopic expression of the HOX11L2, gene normally located to 5q35, and normally not expressed in ALL without 5q rearrangement. The "deregulation" of HOX11L2 expression is thought to result from abnormal control of the gene by CTPI2, located to 14q32, as a consequence of the chromosomal rearrangement. The chromosome 5 breakpoint is usually located within the locus of another gene, RanBP17, often disrupted by the chromosomal rearrangement. The breakpoint on chromosome 5 is consequently distant from the gene abnormally expressed (HOX11L2). References Bernard OA, Busson-LeConiat M, Ballerini P, Mauchauffé M, Della Valle V, Monni R, Nguyen Khac F, Mercher T, PenardLacronique V, Pasturaud P, Gressin L, Heilig R, Daniel MT, Lessard M, Berger R. A new recurrent and specific cryptic translocation, t(5;14)(q35;q32), is associated with expression of the Hox11L2 gene in T acute lymphoblastic leukemia. Leukemia. 2001 Oct;15(10):1495-504 Ballerini P, Blaise A, Busson-Le Coniat M, Su XY, ZucmanRossi J, Adam M, van den Akker J, Perot C, Pellegrino B, Landman-Parker J, Douay L, Berger R, Bernard OA. HOX11L2 expression defines a clinical subtype of pediatric T-ALL associated with poor prognosis. Blood. 2002 Aug 1;100(3):9917 HOX11L2 Location 5q35 Protein Homeobox domain; belongs to HOX 11 family. Ferrando AA, Neuberg DS, Staunton J, Loh ML, Huard C, Raimondi SC, Behm FG, Pui CH, Downing JR, Gilliland DG, Lander ES, Golub TR, Look AT. Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell. 2002 Feb;1(1):75-87 Hélias C, Leymarie V, Entz-Werle N, Falkenrodt A, Eyer D, Costa JA, Cherif D, Lutz P, Lessard M. Translocation t(5;14)(q35;q32) in three cases of childhood T cell acute lymphoblastic leukemia: a new recurring and cryptic abnormality. Leukemia. 2002 Jan;16(1):7-12 This article should be referenced as such: Berger R. t(5;14)(q35;q32). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):290-291. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 291 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Mini Review Acute Erythroid leukaemias Sally Killick, Estella Matutes Department of Haematology, St George's Hospital Medical School, London, UK (EM) Published in Atlas Database: July 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/M6ANLLID1215.html DOI: 10.4267/2042/37902 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology chromatin, distinct nucleoli and deeply basophilic cytoplasm that often have vacuoles. Occasionally the blasts can resemble acute lymphoblastic leukaemia, distinction can be made by immunophenotyping. The erythroid nature of the blasts can be shown by electron microscopy demonstrating free ferritin particles. The blasts are negative for Sudan black B and myeloperoxidase (MPO), but positive for PAS in a block pattern. Identity Alias M6-ANLL erythroleukaemia and pure erythoid leukaemia. Note Criteria for diagnosis of acute erythroid leukaemia. Erythroleukaemia Historically, AML with erythroid features has been designated M6 by the French-American-British (FAB) group. The FAB criteria for M6 diagnosis are: bone marrow erythroblasts equal to or greater than 50% and blasts equal to or greater than 30% of the non-erythroid cells. The World Health Organization (WHO) have recently recommended that the requisite blast percentage for a diagnosis of AML be 20% or greater, and this includes erythroid leukaemia. AML M6 would equate to the new WHO definition of erythroleukaemia (erythroid/ myeloid). If there are less than 20% blasts, the diagnosis is refractory anaemia with an excess of blasts (RAEB). Trilineage dysplasia is common but is not a prerequisite for diagnosis. Erythroid dysplasia may manifest as binuclearity, nucleo-cytoplasmic asynchrony and vacuolation. The morphological appearance of the myeloblasts is not characteristic and they may contain Auer rods. Myeloperoxidase and Sudan black B stains may be positive in the myeloblasts. The iron stain may show ringed sideroblasts and PAS may be positive in the erythroid precursors in a block or diffuse pattern. Pure erythoid leukaemia In addition to the typical AML M6 (erythroleukaemia), there is a second subtype of acute erythoid leukaemia where there is a neoplastic proliferation of immature cells entirely committed to the erythroid series (>80% of marrow cells) without evidence of a myeloid component. This is termed pure erythroid leukaemia by the WHO. Morphology is characterised by medium sized erythroblasts with fine nuclear Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Clinics and pathology Epidemiology Acute erythroid leukaemia is an uncommon form of acute myeloid leukaemia (AML), accounting for approximately 3-4% of cases. Perhaps more than other subtypes of AML, it may represent the evolution or transformation of a myelodysplastic syndrome (MDS), and may be secondary to previous chemotherapy, immunosuppressive treatment or radiotherapy given for a wide range of malignant or non-malignant diseases. It is more commonly associated with exposure to alkylating agents or benzene than other subtypes of AML. Clinics Acute erythroid leukaemia presents with symptoms and signs of cytopenias. It is more common in adults than in children. Cytology Immunophenotype - Erythroleukaemia: The myeloid blasts express a variety of myeloid markers, similar to othe subtypes of AML - CD13, CD33, CD117 (ckit) and MPO. The erythroblasts lack myeloid antigens but are positive to glycophorin A. - Pure erythroid leukaemia: Erythroid blasts which have differentiated will be positive with glycophorin A but negative with MPO and myeloid markers. The 292 Acute Erythroid leukaemias Killick S, Matutes E more immature blasts are difficult to identify as erythroid because they are usually negative for glycophorin A. Immature erythroid progenitors may be detected using carbonic anhydrase 1 or CD36. Although CD36 is not specific for erythroid progenitors, negative markers for megakaryocytes and monocytes will aid the diagnosis. References Bennett JM, Catovsky D, Daniel MT, Flandrin G, Galton DA, Gralnick HR, Sultan C. Proposed revised criteria for the classification of acute myeloid leukemia. A report of the French-American-British Cooperative Group. Ann Intern Med. 1985 Oct;103(4):620-5 Breton-Gorius J, Villeval JL, Mitjavila MT, Vinci G, Guichard J, Rochant H, Flandrin G, Vainchenker W. Ultrastructural and cytochemical characterization of blasts from early erythroblastic leukemias. Leukemia. 1987 Mar;1(3):173-81 Treatment The prognosis of acute erythroid leukaemia is reported as poor. It is, however, important to differentiate de novo from secondary or therapy related erythroid leukaemia, where the later have a worse prognosis. Remission induction for de novo disease is similar to other subtypes of AML; however the poor outcome has been linked to short remission duration. Patients with complex karyotypes or abnormalities of chromosomes 5 and/or 7 have a higher relapse rate than those with normal or simple karyotypes. Data from the Medical Research Council AML10 trial show reduced relapse rates in patients with both standard and poor risk AML after autologous bone marrow transplantation. It may, therefore, be reasonable to consider early stem cell transplantation in first complete remission in patients with acute erythroid leukaemia, particularly those with a poor risk karyotype. Cuneo A, Van Orshoven A, Michaux JL, Boogaerts M, Louwagie A, Doyen C, Dal Cin P, Fagioli F, Castoldi G, Van den Berghe H. Morphologic, immunologic and cytogenetic studies in erythroleukaemia: evidence for multilineage involvement and identification of two distinct cytogeneticclinicopathological types. Br J Haematol. 1990 Jul;75(3):34654 Olopade OI, Thangavelu M, Larson RA, Mick R, Kowal-Vern A, Schumacher HR, Le Beau MM, Vardiman JW, Rowley JD. Clinical, morphologic, and cytogenetic characteristics of 26 patients with acute erythroblastic leukemia. Blood. 1992 Dec 1;80(11):2873-82 Burnett AK, Goldstone AH, Stevens RM, Hann IM, Rees JK, Gray RG, Wheatley K. Randomised comparison of addition of autologous bone-marrow transplantation to intensive chemotherapy for acute myeloid leukaemia in first remission: results of MRC AML 10 trial. UK Medical Research Council Adult and Children's Leukaemia Working Parties. Lancet. 1998 Mar 7;351(9104):700-8 Cytogenetics Killick S, Matutes E, Powles RL, Min T, Treleaven JG, Rege KP, Atra A, Catovsky D. Acute erythroid leukemia (M6): outcome of bone marrow transplantation. Leuk Lymphoma. 1999 Sep;35(1-2):99-107 Cytogenetics morphological There is no unique chromosome abnormality described in acute erythroid leukaemia, however complex karyotypes with multiple structural abnormalities are common. Chromosomes 5 and 7 are the most frequently affected. These findings are also characteristically found in therapy-related AML and MDS, however loss or deletion of 5q is higher in de novo erythroid leukaemia whilst loss or deletion of 7q is higher in therapy related AML. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Jaffe EE, Harris NL, Stein H, Vardiman J. WHO Tumours of haemopoietic and lymphoid tissues. IRAC Press, 2001. This article should be referenced as such: Killick S, Matutes E. Acute Erythroid leukaemias. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):292-293. 293 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(1;13)(q32;q14) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: July 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0113q32q14ID1251.html DOI: 10.4267/2042/37904 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Identity t(1;13)(q32;q13) G- banding - Courtesy Melanie Zenger and Claudia Haferlach. Clinics and pathology Prognosis Disease One patient died at 10 mths, the other is alive at 24 months+. Diffuse large B-cell lymphoma (DLBCL). Cytogenetics Epidemiology Cytogenetics morphological Only 2 cases so far, aged 39 and 57 years; 2 male patients. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Unbalanced form der(1)t(1;13) in one case. 294 t(1;13)(q32;q14) Huret JL Cytogenetics molecular References The anomaly had been uncovered by SKY. Nanjangud G, Rao PH, Hegde A, Teruya-Feldstein J, Donnelly G, Qin J, Jhanwar SC, Zelenetz AD, Chaganti RS. Spectral karyotyping identifies new rearrangements, translocations, and clinical associations in diffuse large B-cell lymphoma. Blood. 2002 Apr 1;99(7):2554-61 Genes involved and proteins Note Genes involved are yet unknown. This article should be referenced as such: Huret JL. t(1;13)(q32;q14). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):294-295. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 295 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(1;7)(q21;q22) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: July 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0107q21q22ID1252.html DOI: 10.4267/2042/37903 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Cytogenetics molecular Clinics and pathology The anomaly had been uncovered by SKY. Disease Genes involved and proteins Diffuse large B-cell lymphoma (DLBCL). Epidemiology Note Genes involved are yet unknown. Only 2 cases so far, aged 43 and 66 years; 1 male and 1 female patient. References Pathology Nanjangud G, Rao PH, Hegde A, Teruya-Feldstein J, Donnelly G, Qin J, Jhanwar SC, Zelenetz AD, Chaganti RS. Spectral karyotyping identifies new rearrangements, translocations, and clinical associations in diffuse large B-cell lymphoma. Blood. 2002 Apr 1;99(7):2554-61 The 2 cases were centroblastic. Prognosis Patients died at 10 months and 33 mths. Cytogenetics This article should be referenced as such: Cytogenetics morphological Huret JL. t(1;7)(q21;q22). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):296. Unbalanced form der(1)t(1;7) in one case. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 296 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(3;14)(q21;q32) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: July 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0314q21q32ID1250.html DOI: 10.4267/2042/37905 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Cytogenetics molecular Clinics and pathology The anomaly had been uncovered by SKY. Disease References Diffuse large B-cell lymphoma (DLBCL). Epidemiology Nanjangud G, Rao PH, Hegde A, Teruya-Feldstein J, Donnelly G, Qin J, Jhanwar SC, Zelenetz AD, Chaganti RS. Spectral karyotyping identifies new rearrangements, translocations, and clinical associations in diffuse large B-cell lymphoma. Blood. 2002 Apr 1;99(7):2554-61 Only 2 cases so far, aged 73 and 83 years, 1 male and 1 female patients. Prognosis 5 mths+ and lost to follow up. This article should be referenced as such: Cytogenetics Huret JL. t(3;14)(q21;q32). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):297. Cytogenetics morphological Unbalanced form der(14) t(3;14) in 1 case, three way translocation t(1;3.14) in the other case. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 297 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Mini Review t(4;11)(q21;p15) Franck Viguié Laboratoire de Cytogénétique - Service d'Hématologie Biologique, Hôpital Hôtel-Dieu, 75181 Paris Cedex 04, France (FV) Published in Atlas Database: July 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0411q21p15ID1191.html DOI: 10.4267/2042/37906 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Clinics Identity No notable particular aspect. Note Not to be confused with a variant of the classical t(4 ;11)(q21;q23) translocation. Prognosis Probably unfavorable, median survival below 18 months; improved by allogeneic bone marrow transplantation. Cytogenetics Cytogenetics morphological In approximately 2/3 of cases; 2 cases with 12p-. Cytogenetics molecular Two BAC clones 290A12 and 118H17 (California Institute of Technology BAC library) encompasses all NUP98 gene and are split by translocation. Variants Not described. Genes involved and proteins t(4;11)(q21;p15) G- banding - Courtesy Diane H. Norback, Eric B. Johnson, Sara Morrison-Delap Cytogenetics at theWaisman Center RAP1GDS1 Clinics and pathology Location 4q22.3 Protein SmgGDS, 558 amino acids; stimulates GDP --> GTP transition in a series of small GTP-binding proteins (g proteins) including rap1a, rap1b, K-ras, rac1, rac2, rhoA and ralB. Somatic mutations Not involved in other known clonal rearrangement associated with tumoral proliferation. Disease T-cell acute lymphoblastic leukemia. Phenotype/cell stem origin Lymphoblasts, either L1 or L2 in the FAB classification; mature T and myeloid markers variably co-expressed. Epidemiology Rare, approximately 10 cases described; evaluated to 25% of adult T-ALL; not evaluated in childhood ALL; both sexes equally involved; found in children or young adults. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) NUP98 Location 11p15.4 298 t(4;11)(q21;p15) Viguié F t(4;11) generates only one chimeric protein 5' - NUP98 - RAP1GDS1 - 3' which contains a variable part of NUP98 and the totality of smgGDS except for the initial methionine. Protein Nucleoporin 98, a 98 kDa component of the nuclear pore complex implicated in nucleo-cytoplasmic transport. Somatic mutations involved in different types of acute myeloid leukemia, as fusion gene with HOX A9, DDX10, HOX D13, TOP1, PMX1 and LEDGF, resulting respectively from t(7;11)(p15;p15), inv(11)(p15q22), t(2;11)(q31;p15), t(11;20)(p15;q11), t(1;11)(q23;p15) and t(9;11)(p22;p15). References Kalatzis V, Peters GB, Dobrovic A. Mapping of the chromosome 11 breakpoint of the t(4;11)(q21;p14-15) translocation. Cancer Genet Cytogenet. 1993 Sep;69(2):122-5 Hussey DJ, Nicola M, Moore S, Peters GB, Dobrovic A. The (4;11)(q21;p15) translocation fuses the NUP98 and RAP1GDS1 genes and is recurrent in T-cell acute lymphocytic leukemia. Blood. 1999 Sep 15;94(6):2072-9 Result of the chromosomal anomaly Mecucci C, La Starza R, Negrini M, Sabbioni S, Crescenzi B, Leoni P, Di Raimondo F, Krampera M, Cimino G, Tafuri A, Cuneo A, Vitale A, Foà R. t(4;11)(q21;p15) translocation involving NUP98 and RAP1GDS1 genes: characterization of a new subset of T acute lymphoblastic leukaemia. Br J Haematol. 2000 Jun;109(4):788-93 Hybrid gene Description NUP98 breakpoint in the intron between exons B and C; 5'-part of NUP98 is fused in frame with the whole coding sequence of RAP1GDS1; fusion gene called NRG: 5'-NUP-RAP1GDS1-3'. Variant described with breakpoint in NUP98 before exon A. Cimino G, Sprovieri T, Rapanotti MC, Foà R, Mecucci C, Mandelli F. Molecular evaluation of the NUP98/RAP1GDS1 gene frequency in adults with T-acute lymphoblastic leukemia. Haematologica. 2001 Apr;86(4):436-7 This article should be referenced as such: Fusion protein Viguié F. t(4;11)(q21;p15). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):298-299. Description Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 299 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Leukaemia Section Short Communication t(6;8)(q11;q11) Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: July 2002 Online updated version: http://AtlasGeneticsOncology.org/Anomalies/t0608q11q11ID1253.html DOI: 10.4267/2042/37907 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Clinics and pathology Genes involved and proteins Disease Diffuse large B-cell lymphoma (DLBCL). Note Genes involved are yet unknown. Epidemiology References Only 2 cases so far, aaged 42 and 57 years; 2 female patients. Nanjangud G, Rao PH, Hegde A, Teruya-Feldstein J, Donnelly G, Qin J, Jhanwar SC, Zelenetz AD, Chaganti RS. Spectral karyotyping identifies new rearrangements, translocations, and clinical associations in diffuse large B-cell lymphoma. Blood. 2002 Apr 1;99(7):2554-61 Prognosis One patient is alive at 12 months+, the other one died at 31 mths. This article should be referenced as such: Cytogenetics Huret JL. t(6;8)(q11;q11). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):300. Cytogenetics morphological The anomaly had been uncovered by SKY. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 300 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Solid Tumour Section Mini Review Head and neck squamous cell carcinoma Hélène Blons U490 INSERM Toxicologie Moléculaire, 45 rue des saints pères, 75006 Paris, France (HB) Published in Atlas Database: May 2002 Online updated version: http://AtlasGeneticsOncology.org/Tumors/HeadNeckSquamID6368.html DOI: 10.4267/2042/37908 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology in DNA repair enzymes or in carcinogens metabolizing enzymes supports the role of heredity in HNSCC. Among the polymorphism tested, GSTM1 and GSTT1 null phenotypes are associated with an increased risk of HNSCC. Concerning XRCC1, the Arg allele (Arg194Trp) and the Gln allele (Arg399Gln) are also linked to an increased risk of oral and pharyngeal cancers. Clinics and pathology Disease Head and neck cancer as defined here includes the squamous cell carcinomas of the oral cavity, pharynx and larynx. This malignancy is an important public health problem worldwide with more than 500000 new cases diagnosed each year. Patients often present with advanced stage disease and despite combined therapy outcome remains poor. For early stage, patients can be at high risk for second primary when cured of their initial cancer which poses the main threat to survival. Pathology Head and neck cancer are usually diagnosed in men after 50, patients can present with one or more distinct localization (10-15% at diagnosis) and 25% will develop a second cancer within 5 years from diagnosis. Cancer can develop from leucoplakia, erythroplakia or apparently normal epithelium. Premalignant lesions showing abnormal DNA content are at high risk of transformation. Clinical prognosis factors counts, tumor size, node involvement and smoking habits. Tumor markers related to prognosis counts EGFR expression, cyclin D1 or cyclin E expression, serum soluble IL-2 receptor concentrations and loss of chromosome arm 18q. Etiology The major risk factor for head and neck cancer is chronic exposure of epithelia to tobacco smoke and alcohol. Environmental factors such as wood and cement dusts as well as human papilloma virus type 16 and 18 (HPV) infection have been related to an increased risk of developing head and neck squamous cell carcinoma (HNSCC). Recent studies confirm that oropharyngeal tumors are often HPV-positive and compose a distinct clinical and pathological entity with less TP53 mutations and better prognosis as compared to HPV negative tumors. Epstein Barr Virus infection is related to nasopharyngeal SCC in south china and oral cavity tumors are frequent in betel chewers. Treatment First goal is locoregional control achieved by surgery or radiotherapy. For high staged tumors combined surgery+/-radiotherapy+/-chemotherapy can be used. New treatment strategies are in development. Adenovirus have been developed that restore TP53 or P16 activity or that selectively replicates in TP53 deficient cells. Agents that inhibit signal transduction as tyrosine kinase inhibitors are also under evaluation in HNSCC specially those targeting the EGF receptor. Epidemiology Both hereditary and environmental factors are implicated in head and neck carcinogenesis and their roles are difficult to separate. Several cancer prone syndromes are associated with a increased risk of head and neck cancer, including Lynch-II, Bloom syndrome, Fanconi anemia, ataxia telagiectasia and Li-fraumeni syndrome. But genetic susceptibility to head and neck cancer is more likely to be due to various degrees of DNA maintenance after exposure to tobacco carcinogens. Mutagen sensitivity tests, polymorphism Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Cytogenetics Note Chromosomal abnormalities are very frequent in head and neck tumors leading to very complex caryotypes 301 Head and neck squamous cell carcinoma Blons H - Chromosome arm 13q: No mutation in RB were identified in HNSCC. - Chromosome arm 10q: No mutation in PTEN were identified in HNSCC. Oncogenes - Chromosome band 11q13: EMS1, FGF3, FGF4 et CCND1 are amplified in HNSCC. - Chromosome arm 3q: The PIK3CA gene but not p63 is likely to be the target of 3q26-qter gain. - The Wnt, APC, bcatenin pathway: No mutation in the bcatenin gene in HNSCC. - MAP kinase pathway: The only head and neck tumors with constitutive RAS activation are from Indian and Taiwanese patients that can harbor HRAS or KRAS mutation. - Epigenetic alteration in HNSCC: Genes can be inactivated by promoter hypermethylation, in head and neck cancer the phenomenon has been demonstrated for several genes including P16, MGMT and DAPkinase. DAP-kinase is implicated in INFg mediated apoptosis and DAP-kinase promoter hypermethylation is related to advance stage tumors. with more than 70% of tumors being aneuploïd. Although most chromosome arms can be targeted by loss or gain of fragments, cytogenetic studies, Comparative Genome Hybridization (CGH) studies and molecular genetics studies demonstrated the existence of recurrent alterations some of which are found early in carcinogenesis. Loss of chromosome arm 3p and/or 9p is found in over 80% of tumors, loss of 17p involves more than 50% of the cases these alterations are associated with early tumor development. Losses of 5q, 8p, 4q 10q or 13q are found in nearly 30% of tumors and loss of 11p in less than 20% these alterations are preferentially associated with tumor progression. Concerning fragments gain, amplification at 11q and 3q clearly participate in head and neck carcinogenesis and concern nearly 70% of the cases. 3q amplification is seen in early tumor development. Studies showed that patterns of chromosomal alterations can be associated with clinical parameters such as deletions at 10q25-q26 and 11p13-p14 that are significant for metastasizing carcinoma and amplification of 11q could be a bad prognosis factor. Tumor proliferation is known to result from activation of growth promoting pathways and inhibition of growth downregulation pathways. Several chromosomal segments involved in head and neck carcinogenesis harbor genes implicated in growth regulation. Tumor suppressor genes - Chromosome arm 3p: At least three regions have been identified at 3p 3p13-3p21, 3p21.3-3p23, 3p25. Four genes have been studied for the presence of inactivating mutations VHL, TGFbRII, FHIT and OGG1. Very few mutations have been found in TGFbRII and only abnormal transcripts were detected for FHIT leading to the conclusion that it is still unclear whether or not these genes are the targets of 3p deletions. - Chromosome arm 9p: CDNK2A (P16) is a cell cycle regulatory gene located at 9p that is down regulated in HNSCC through homozygous deletion or promoter hypermethylation. - Chromosome arm 17p: TP53 is mutated in over 60% of HNSCC there is a good correlation between mutation and LOH at 17p. In HNSCC 50% of TP53 mutations are nonsense, deletions, insertions or splice site junctions mutations and 50% are missenses. It has been clearly demonstrated that smoke carcinogens have a causal role in the formation of TP53 mutations and that the prevalence is greater in heavy smoker patients. TP53 mutations could be an indicator of a bad response to neoadjuvant chemotherapy in HNSCC - Chromosome arm 18q: Loss of 18q is linked to bad prognosis in HNSCC. Genes SMAD2, SMAD4 and DCC do not seem to be the right targets. The delineation of a common region of loss at 18q22 did not allow the identification of a new tumor suppressor gene. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) References Decker J, Goldstein JC. Risk factors in head and neck cancer. N Engl J Med. 1982 May 13;306(19):1151-5 Chang SE, Bhatia P, Johnson NW, Morgan PR, McCormick F, Young B, Hiorns L. Ras mutations in United Kingdom examples of oral malignancies are infrequent. Int J Cancer. 1991 May 30;48(3):409-12 Maestro R, Gasparotto D, Vukosavljevic T, Barzan L, Sulfaro S, Boiocchi M. Three discrete regions of deletion at 3p in head and neck cancers. Cancer Res. 1993 Dec 1;53(23):5775-9 Adamson R, Jones AS, Field JK. Loss of heterozygosity studies on chromosome 17 in head and neck cancer using microsatellite markers. Oncogene. 1994 Jul;9(7):2077-82 Ah-See KW, Cooke TG, Pickford IR, Soutar D, Balmain A. An allelotype of squamous carcinoma of the head and neck using microsatellite markers. Cancer Res. 1994 Apr 1;54(7):1617-21 Kuo MY, Jeng JH, Chiang CP, Hahn LJ. Mutations of Ki-ras oncogene codon 12 in betel quid chewing-related human oral squamous cell carcinoma in Taiwan. J Oral Pathol Med. 1994 Feb;23(2):70-4 Bockmühl U, Schwendel A, Dietel M, Petersen I. Distinct patterns of chromosomal alterations in high- and low-grade head and neck squamous cell carcinomas. Cancer Res. 1996 Dec 1;56(23):5325-9 Califano J, van der Riet P, Westra W, Nawroz H, Clayman G, Piantadosi S, Corio R, Lee D, Greenberg B, Koch W, Sidransky D. Genetic progression model for head and neck cancer: implications for field cancerization. Cancer Res. 1996 Jun 1;56(11):2488-92 Catimel G. Head and neck cancer: chemotherapy. Drugs. 1996 Jan;51(1):73-88 guidelines for Cloos J, Spitz MR, Schantz SP, Hsu TC, Zhang ZF, Tobi H, Braakhuis BJ, Snow GB. Genetic susceptibility to head and neck squamous cell carcinoma. J Natl Cancer Inst. 1996 Apr 17;88(8):530-5 302 Head and neck squamous cell carcinoma Blons H Mao L, Fan YH, Lotan R, Hong WK. Frequent abnormalities of FHIT, a candidate tumor suppressor gene, in head and neck cancer cell lines. Cancer Res. 1996 Nov 15;56(22):5128-31 Blons H, Cabelguenne A, Carnot F, Laccourreye O, de Waziers I, Hamelin R, Brasnu D, Beaune P, Laurent-Puig P. Microsatellite analysis and response to chemotherapy in headand-neck squamous-cell carcinoma. Int J Cancer. 1999 Aug 20;84(4):410-5 Mao L, Lee JS, Fan YH, Ro JY, Batsakis JG, Lippman S, Hittelman W, Hong WK. Frequent microsatellite alterations at chromosomes 9p21 and 3p14 in oral premalignant lesions and their value in cancer risk assessment. Nat Med. 1996 Jun;2(6):682-5 Cheng L, Sturgis EM, Eicher SA, Char D, Spitz MR, Wei Q. Glutathione-S-transferase polymorphisms and risk of squamous-cell carcinoma of the head and neck. Int J Cancer. 1999 Jun 21;84(3):220-4 Patel AM, Incognito LS, Schechter GL, Wasilenko WJ, Somers KD. Amplification and expression of EMS-1 (cortactin) in head and neck squamous cell carcinoma cell lines. Oncogene. 1996 Jan 4;12(1):31-5 Gupta VK, Schmidt AP, Pashia ME, Sunwoo JB, Scholnick SB. Multiple regions of deletion on chromosome arm 13q in headand-neck squamous-cell carcinoma. Int J Cancer. 1999 Oct 22;84(5):453-7 El-Naggar AK, Lai S, Clayman G, Lee JK, Luna MA, Goepfert H, Batsakis JG. Methylation, a major mechanism of p16/CDKN2 gene inactivation in head and neck squamous carcinoma. Am J Pathol. 1997 Dec;151(6):1767-74 Sturgis EM, Castillo EJ, Li L, Zheng R, Eicher SA, Clayman GL, Strom SS, Spitz MR, Wei Q. Polymorphisms of DNA repair gene XRCC1 in squamous cell carcinoma of the head and neck. Carcinogenesis. 1999 Nov;20(11):2125-9 Frank CJ, McClatchey KD, Devaney KO, Carey TE. Evidence that loss of chromosome 18q is associated with tumor progression. Cancer Res. 1997 Mar 1;57(5):824-7 Bartsch H, Nair U, Risch A, Rojas M, Wikman H, Alexandrov K. Genetic polymorphism of CYP genes, alone or in combination, as a risk modifier of tobacco-related cancers. Cancer Epidemiol Biomarkers Prev. 2000 Jan;9(1):3-28 Bockmühl U, Wolf G, Schmidt S, Schwendel A, Jahnke V, Dietel M, Petersen I. Genomic alterations associated with malignancy in head and neck cancer. Head Neck. 1998 Mar;20(2):145-51 Cabelguenne A, Blons H, de Waziers I, Carnot F, Houllier AM, Soussi T, Brasnu D, Beaune P, Laccourreye O, Laurent-Puig P. p53 alterations predict tumor response to neoadjuvant chemotherapy in head and neck squamous cell carcinoma: a prospective series. J Clin Oncol. 2000 Apr;18(7):1465-73 Izzo JG, Papadimitrakopoulou VA, Li XQ, Ibarguen H, Lee JS, Ro JY, El-Naggar A, Hong WK, Hittelman WN. Dysregulated cyclin D1 expression early in head and neck tumorigenesis: in vivo evidence for an association with subsequent gene amplification. Oncogene. 1998 Nov 5;17(18):2313-22 Götte K, Hadaczek P, Coy JF, Wirtz HW, Riedel F, Neubauer J, Hörmann K. Fhit expression is absent or reduced in a subset of primary head and neck cancer. Anticancer Res. 2000 MarApr;20(2A):1057-60 Okami K, Wu L, Riggins G, Cairns P, Goggins M, Evron E, Halachmi N, Ahrendt SA, Reed AL, Hilgers W, Kern SE, Koch WM, Sidransky D, Jen J. Analysis of PTEN/MMAC1 alterations in aerodigestive tract tumors. Cancer Res. 1998 Feb 1;58(3):509-11 Kleist B, Poetsch M, Bankau A, Werner E, Herrmann FH, Lorenz G. First hints for a correlation between amplification of the Int-2 gene and infection with human papillomavirus in head and neck squamous cell carcinomas. J Oral Pathol Med. 2000 Oct;29(9):432-7 Pearlstein RP, Benninger MS, Carey TE, Zarbo RJ, Torres FX, Rybicki BA, Dyke DL. Loss of 18q predicts poor survival of patients with squamous cell carcinoma of the head and neck. Genes Chromosomes Cancer. 1998 Apr;21(4):333-9 Forastiere A, Koch W, Trotti A, Sidransky D. Head and neck cancer. N Engl J Med. 2001 Dec 27;345(26):1890-900 Wang LE, Sturgis EM, Eicher SA, Spitz MR, Hong WK, Wei Q. Mutagen sensitivity to benzo(a)pyrene diol epoxide and the risk of squamous cell carcinoma of the head and neck. Clin Cancer Res. 1998 Jul;4(7):1773-8 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) This article should be referenced as such: Blons H. Head and neck squamous cell carcinoma. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):301-303. 303 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Cancer Prone Disease Section Mini Review Congenital neutropenia Jay L Hess Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, 413b Stellar Chance Laboratories, Philadelphia, PA 19104, USA (JLH) Published in Atlas Database: May 2002 Online updated version: http://AtlasGeneticsOncology.org/Kprones/CongenitNeutropID10073.html DOI: 10.4267/2042/37909 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology common in males. Cyclic forms are slightly more common in females.SCN patients develop frequent fevers, skin infections and stomatitis with organisms such as E. coli, S. aureus, and Pseudomonas species. 90% of patients are diagnosed by 6 months of age. Patients tend to develop hematological malignancies (see below). Pathology: The absolute neutrophil count is usually less than 0.2x109 /L. The bone marrow of affected patients shows an arrest in maturation at the promyelocyte stage, often with a monocytosis and sometimes with eosinophilia. The peripheral blood shows a paucity of neutrophils and often monocytosis and eosinophilia. Identity Alias Severe chronic neutropenia (SCN) Kostmann syndrome Note Severe chronic neutropenia is a general term that applies to both congenital and acquired cases. Kostmann syndrome is a subtype of chronic neutropenia with onset in early childhood with an autosomal recessive pattern of development. The term congenital neutropenia is used interchangeably although some authors argue that the term is more appropriate for sporadic cases. Neoplastic risk Clinics Roughly 50% of patients present with myelodysplastic syndromes (MDS), another 10% with therapy associated MDS, 25% with de novo acute myeloid leukemia (AML), and the remainder with a range of other myeloproliferative disorders. The majority of MDS patients transform into AML with a short preleukemic phase. Note Severe chronic neutropenia (SCN) is a heterogeneous group of disorders characterized by chronic neutropenia and serious recurrent infections. The defining characteristic of all of these diseases is the presence of severe neutropenia with absolute neutrophil counts of less than 0.5x109 /L on three separate occasions over a six week period. Some clinically distinctive cases, known as cyclic neutropenia show oscillation in neutrophil levels with a periodicity of approximately 21 days. SCN is distinguished from ShwatchmanDiamond Syndrome by the absence of exocrine pancreas deficiency and growth retardation. Treatment More than 90% of patients respond to G-CSF therapy, which may result in cyclic oscillations in neutrophil count. G-CSF therapy may be complicated by significant bone loss and the development of AML. Hematopoietic stem cell transplantation has shown promise in the treatment of non-responders. Phenotype and clinics Prognosis Phenotype stem cell origin: Constitutional disorder affecting myeloid lineage cells. Epidemiology: The disease is most common in causcasians and presents in childhood. Clinical features: Congenital neutropenia usually presents in early childhood and is slightly more With the advent of G-CSF therapy infectious deaths are rare. Approximately 10% of patients develop AML. This is associated in almost all cases with G-CSF-R mutations. This is not thought to be the direct result of G-CSF therapy but rather an underlying predisposition for the development of myeloid leukemia. Cyclic Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 304 Congenital neutropenia Hess JL Belaaouaj A, McCarthy R, Baumann M, Gao Z, Ley TJ, Abraham SN, Shapiro SD. Mice lacking neutrophil elastase reveal impaired host defense against gram negative bacterial sepsis. Nat Med. 1998 May;4(5):615-8 neutropenia patients do not have an increased risk for development of acute leukemia. Cytogenetics Horwitz M, Benson KF, Person RE, Aprikyan AG, Dale DC. Mutations in ELA2, encoding neutrophil elastase, define a 21day biological clock in cyclic haematopoiesis. Nat Genet. 1999 Dec;23(4):433-6 Inborn conditions The majority of patients have point mutations involving neutrophil elastase located at chromosome 19p13.3. Dale DC, Person RE, Bolyard AA, Aprikyan AG, Bos C, Bonilla MA, Boxer LA, Kannourakis G, Zeidler C, Welte K, Benson KF, Horwitz M. Mutations in the gene encoding neutrophil elastase in congenital and cyclic neutropenia. Blood. 2000 Oct 1;96(7):2317-22 Cytogenetics of cancer Cases complicated by the development of AML most commonly show monosomy 7or trisomy 21. Activating RAS mutations are seen in roughly 50% of secondary AML cases. Dale DC, Person RE, Bolyard AA, Aprikyan AG, Bos C, Bonilla MA, Boxer LA, Kannourakis G, Zeidler C, Welte K, Benson KF, Horwitz M. Mutations in the gene encoding neutrophil elastase in congenital and cyclic neutropenia. Blood. 2000 Oct 1;96(7):2317-22 Genes involved and proteins Freedman MH, Bonilla MA, Fier C, Bolyard AA, Scarlata D, Boxer LA, Brown S, Cham B, Kannourakis G, Kinsey SE, Mori PG, Cottle T, Welte K, Dale DC. Myelodysplasia syndrome and acute myeloid leukemia in patients with congenital neutropenia receiving G-CSF therapy. Blood. 2000 Jul 15;96(2):429-36 Note Most patients show point mutations in ELA2, a protein that is present in azurophilic granules. In one series of 22 patients 17 different mutations were identified. Most of these were missense mutations. The association between defects in the serine protease ELA2 and neutropenia is thought to involve shortened myeloid progenitor survival. The mechanism of this is obscure. This does not appear to be either loss of function or gain of function (i.e. through cytotoxicity). The evidence to date best supports a dominant negative mechanism whereby the activity of the wild type protein is inhibited. One report suggested that mutation of ELA2 alone was not sufficient for the neutropenia phenotype. It is noteworthy in this regard that mice with knockout of ELA2 show disorders in neutrophil function but not neutropenia. Zeidler C, Welte K, Barak Y, Barriga F, Bolyard AA, Boxer L, Cornu G, Cowan MJ, Dale DC, Flood T, Freedman M, Gadner H, Mandel H, O'Reilly RJ, Ramenghi U, Reiter A, Skinner R, Vermylen C, Levine JE. Stem cell transplantation in patients with severe congenital neutropenia without evidence of leukemic transformation. Blood. 2000 Feb 15;95(4):1195-8 Carlsson G, Fasth A. Infantile genetic agranulocytosis, morbus Kostmann: presentation of six cases from the original "Kostmann family" and a review. Acta Paediatr. 2001 Jul;90(7):757-64 Germeshausen M, Schulze H, Ballmaier M, Zeidler C, Welte K. Mutations in the gene encoding neutrophil elastase (ELA2) are not sufficient to cause the phenotype of congenital neutropenia. Br J Haematol. 2001 Oct;115(1):222-4 Li FQ, Horwitz M. Characterization of mutant neutrophil elastase in severe congenital neutropenia. J Biol Chem. 2001 Apr 27;276(17):14230-41 References Dong F, Brynes RK, Tidow N, Welte K, Löwenberg B, Touw IP. Mutations in the gene for the granulocyte colony-stimulatingfactor receptor in patients with acute myeloid leukemia preceded by severe congenital neutropenia. N Engl J Med. 1995 Aug 24;333(8):487-93 This article should be referenced as such: Hess JL. Congenital neutropenia. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):304-305. Welte K, Dale D. Pathophysiology and treatment of severe chronic neutropenia. Ann Hematol. 1996 Apr;72(4):158-65 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 305 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Cancer Prone Disease Section Mini Review Simpson-Golabi-Behmel syndrome Daniel Sinnett Division of Hematology-oncology, Research Centre, Sainte-Justine Hospital, 3175 Côte Sainte-Catherine, Montreal, H3T 1C5, Québec, Canada (DS) Published in Atlas Database: May 2002 Online updated version: http://AtlasGeneticsOncology.org/Kprones/SimpsonGolabiID10038.html DOI: 10.4267/2042/37910 This article is an update of: Punnett HH. Simpson-Golabi-Behmel. Atlas Genet Cytogenet Oncol Haematol 2000;4(4):221 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology mesoderm-derived tissues, and its expression is downregulated in most adult tissue, implying a potential role in development. GPC3 is a heparan sulfate proteoglycan (HSPG) that is attached to the cell surface via a glycosyl-phosphatidylinositol (GPI) anchor. Function: HSPGs of the cell surface are highly interactive macromolecules playing various roles in cell migration, proliferation, differentiation and adhesion, and participating in many developmental and pathological processes. Mutations Germinal: Most cases are caused by deletions of different exons in the GPC3 genes. The exact role of GPC3 in the etiology of SGBS is still unknown. The renal dysplasia observed in both SGBS patients and GPC3-deficient mice could be explained by the participation of GPC3 in the control of renal branching morphogenesis by modulating the actions of several different growth factors, including BMP2, BMP7 and fibroblast growth factor 7. Identity Inheritance X-linked with heterogeneity; most families map Xq26; one large pedigree maps to Xp22. Clinics Phenotype and clinics Characterized by a wide variety of clinical manifestations including pre-natal and post-natal overgrowth syndrome SGBS is phenotypically similar to BeckwithWiedemann syndrome (BWS) suggesting that at least part of the SGBS phenotype could be due to increased IGF-II signalling. Xq26: coarse facieses with mandibular overgrowth, cleft palate, heart defects, hernias, supernumerary nipples, renal and skeletal abnormalities. Xp22: lethal form, multiple anomalies, hydrops fetalis, death within first 8 weeks of life. Neoplastic risk References Increased risk of embryonal tumors, including Wilms tumor, neuroblastoma; one case of hepatocellular carcinoma reported. Filmus J, Church JG, Buick RN. Isolation of a cDNA corresponding to a developmentally regulated transcript in rat intestine. Mol Cell Biol. 1988 Oct;8(10):4243-9 Genes involved and proteins Hughes-Benzie RM, Hunter AG, Allanson JE, Mackenzie AE. Simpson-Golabi-Behmel syndrome associated with renal dysplasia and embryonal tumor: localization of the gene to Xqcen-q21. Am J Med Genet. 1992 Apr 15-May 1;43(1-2):42835 glypican-3 (GPC3) Location Xq26 David G. Integral membrane heparan sulfate proteoglycans. FASEB J. 1993 Aug;7(11):1023-30 Protein Description: GPC3 is highly expressed in embryonal tissues such as the developing intestine and the Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Hughes-Benzie RM, Pilia G, Xuan JY, Hunter AG, Chen E, Golabi M, Hurst JA, Kobori J, Marymee K, Pagon RA, Punnett HH, Schelley S, Tolmie JL, Wohlferd MM, Grossman T, 306 Simpson-Golabi-Behmel syndrome Sinnett D Schlessinger D, MacKenzie AE. Simpson-Golabi-Behmel syndrome: genotype/phenotype analysis of 18 affected males from 7 unrelated families. Am J Med Genet. 1996 Dec 11;66(2):227-34 Brzustowicz LM, Farrell S, Khan MB, Weksberg R. Mapping of a new SGBS locus to chromosome Xp22 in a family with a severe form of Simpson-Golabi-Behmel syndrome. Am J Hum Genet. 1999 Sep;65(3):779-83 Pilia G, Hughes-Benzie RM, MacKenzie A, Baybayan P, Chen EY, Huber R, Neri G, Cao A, Forabosco A, Schlessinger D. Mutations in GPC3, a glypican gene, cause the SimpsonGolabi-Behmel overgrowth syndrome. Nat Genet. 1996 Mar;12(3):241-7 Murthy SS, Shen T, De Rienzo A, Lee WC, Ferriola PC, Jhanwar SC, Mossman BT, Filmus J, Testa JR. Expression of GPC3, an X-linked recessive overgrowth gene, is silenced in malignant mesothelioma. Oncogene. 2000 Jan 20;19(3):410-6 Paine-Saunders S, Viviano BL, Zupicich J, Skarnes WC, Saunders S. glypican-3 controls cellular responses to Bmp4 in limb patterning and skeletal development. Dev Biol. 2000 Sep 1;225(1):179-87 Eggenschwiler J, Ludwig T, Fisher P, Leighton PA, Tilghman SM, Efstratiadis A. Mouse mutant embryos overexpressing IGF-II exhibit phenotypic features of the Beckwith-Wiedemann and Simpson-Golabi-Behmel syndromes. Genes Dev. 1997 Dec 1;11(23):3128-42 Tumova S, Woods A, Couchman JR. Heparan sulfate proteoglycans on the cell surface: versatile coordinators of cellular functions. Int J Biochem Cell Biol. 2000 Mar;32(3):26988 Lapunzina P, Badia I, Galoppo C, De Matteo E, Silberman P, Tello A, Grichener J, Hughes-Benzie R. A patient with Simpson-Golabi-Behmel syndrome and hepatocellular carcinoma. J Med Genet. 1998 Feb;35(2):153-6 DeBaun MR, Ess J, Saunders S. Simpson Golabi Behmel syndrome: progress toward understanding the molecular basis for overgrowth, malformation, and cancer predisposition. Mol Genet Metab. 2001 Apr;72(4):279-86 Li M, Squire JA, Weksberg R. Molecular genetics of Wiedemann-Beckwith syndrome. Am J Med Genet. 1998 Oct 2;79(4):253-9 Grisaru S, Cano-Gauci D, Tee J, Filmus J, Rosenblum ND. Glypican-3 modulates BMP- and FGF-mediated effects during renal branching morphogenesis. Dev Biol. 2001 Mar 1;231(1):31-46 Neri G, Gurrieri F, Zanni G, Lin A. Clinical and molecular aspects of the Simpson-Golabi-Behmel syndrome. Am J Med Genet. 1998 Oct 2;79(4):279-83 Pellegrini M, Pilia G, Pantano S, Lucchini F, Uda M, Fumi M, Cao A, Schlessinger D, Forabosco A. Gpc3 expression correlates with the phenotype of the Simpson-Golabi-Behmel syndrome. Dev Dyn. 1998 Dec;213(4):431-9 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) This article should be referenced as such: Sinnett D. Simpson-Golabi-Behmel syndrome. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):306-307. 307 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Cancer Prone Disease Section Mini Review Fanconi anaemia Jean-Loup Huret Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Kprones/FA10001.html DOI: 10.4267/2042/37911 This article is an update of: Huret JL. Fanconi anaemia. Atlas Genet Cytogenet Oncol Haematol 1998;2(2):68-69 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology in FA, and it has been assumed that 'it is reasonable to regard the Fanconi anemia genotype as "preleukemia"'; mean age at diagnosis: 13-15 yrs Hepatocarcinoma (androgen-therapy induced) in 10%; mean age at diagnosis: 16 yrs. Other cancers in 2-5%: in particular squamous cell carcinoma. Identity Alias Fanconi pancytopenia Note Fanconi anaemia is a chromosome instability syndrome with progressive bone marrow failure and an increased risk of cancers. Inheritance Autosomal recessive; frequency is about 2.5/105 newborns. Treatment Androgens and steroids to improve haematopoietic functions; bone marrow transplantation prevents from terminal pancytopenia, and from ANLL as well. Prognosis Clinics Mean age at death: 16 years; most patients die from marrow aplasia (haemorrhage, sepsis), and others from malignancies; MDS and ANLL in FA bear a very poor prognosis (median survival of about 6 mths); survival is also poor in the case of a squamous cell carcinoma. It has recently been shown that significant phenotypic differences were found between the various complementation groups (see below). In FA group A, patients homozygous for null mutations had an earlier onset of anemia and a higher incidence of leukemia than those with mutations producing an altered protein. FA group G patients had more severe cytopenia and a higher incidence of leukemia. FA group C patients had less somatic abnormalities, which, in reverse, were more frequent in the rare groups FA-D, FA-E, and FAF. FA group G patients patients and patients homozygous for null mutations in FANCA are highrisk groups with a poor hematologic outcome and should be considered as candidates both for Phenotype and clinics Growth retardation (70% of cases). Skin abnormalities: hyperpigmentation and/or café au lait spots in 80%. Squeletal malformations (60%), particularly radius axis defects (absent or hypoplastic thumb or radius...). No immune deficiency (in contrast with most other chromosome instability syndromes). Progressive bone marrow failure; mean age of onset of anemia: 8 yrs; diagnosis made before onset of haematologic manifestations in only 30%. Other: renal anomalies, hypogonadism, mental impairment, heart defects, and perhaps diabetes mellitus, also occur in 10 to 30% of cases. Neoplastic risk Myelodysplasia (MDS) and acute non lyphocytic leukaemia (ANLL): 15% of cases; i.e. a 15000 fold increased risk of MDS and ANLL has been evaluated Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 308 Fanconi anaemia Huret JL A: gaps; B: breaks; C: deletion; D: triradials; E: quadriradials; F: complex figures; G: dicentric. Giemsa staining - Editor. Cytogenetics The most prevalent complementation groups are: group A (65-70% of cases), groups C and G (10-15% each) Rare complementation groups are groups B, D, E, and F (Six genes have been discovered, corresponding to the frequent phenotypes: FANCA in 16q24, FANCC in 9q22, and FANCG in 9p13, and to the rarer phenotypes FANCD2 in 3p25. FANCE in 6p21, and FANCF in 11p15.The genes FANCB and FANCD1 have yet to be uncovered. Inborn conditions To be noted frequent monitoring and early therapeutic intervention. There may also be a certain degree of clinical heterogeneity.according to the degree of mosaicism. Therefore, clinical manifestations may be variable within a given family, according to the stage of embryonic development at which the somatic reverse mutation occurred. Spontaneous chromatid/chromosome breaks, triradials, quadriradials. Hypersensitivity to the clastogenic effect of DNA cross-linking agents (increased rate of breaks and radial figures); diepoxybutane, mitomycin C, or mechlorethamine hydrochlorid are used for diagnosis. Note Clinical diagnosis may, in certain cases, be very difficult; cytogenetic ascertainment is then particularly useful; however, cytogenetic diagnosis may also, at times, be very uncertain; this is a great problem when bone marrow engraftment has been decided in a pancytopenic patient: if this patient has FA, bone marrow conditioning must be very mild, as FA cells are very clastogen sensitive. The recent discover of genes involved in the disease should improve diagnostic ascertainment. FA patients (i.e. patients with defective alleles) may have, in a percentage of cells, a somatic reversion (by revert mutation towards wild-type gene); such a phenomenon is also known in Bloom syndrome, another chromosome instability syndrome. Cytogenetics of cancer various clonal anomalies are found in MDS or ANLL in Fanconi anaemia patients, such as the classical 5/del(5q), and -7/del(7q), found in 10 % of cases; telomeres appear to be non randomly involved in FA's clonal anomalies. Other findings Note Slowing of the cell cycle (G2/M transition, with accumulating of cells in G2). Impaired oxygen metabolism. Defective P53 induction. References Glanz A, Fraser FC. Spectrum of anomalies in Fanconi anaemia. J Med Genet. 1982 Dec;19(6):412-6 Genes involved and proteins Huret JL, Tanzer J, Guilhot F, Frocrain-Herchkovitch C, Savage JR. Karyotype evolution in the bone marrow of a patient with Fanconi anemia: breakpoints in clonal anomalies of this disease. Cytogenet Cell Genet. 1988;48(4):224-7 Note There are 7 complementation groups (A to G). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 309 Fanconi anaemia Huret JL Auerbach AD, Allen RG. Leukemia and preleukemia in Fanconi anemia patients. A review of the literature and report of the International Fanconi Anemia Registry. Cancer Genet Cytogenet. 1991 Jan;51(1):1-12 Faivre L, Guardiola P, Lewis C, Dokal I, Ebell W, Zatterale A, Altay C, Poole J, Stones D, Kwee ML, van Weel-Sipman M, Havenga C, Morgan N, de Winter J, Digweed M, Savoia A, Pronk J, de Ravel T, Jansen S, Joenje H, Gluckman E, Mathew CG. Association of complementation group and mutation type with clinical outcome in fanconi anemia. European Fanconi Anemia Research Group. Blood. 2000 Dec 15;96(13):4064-70 Strathdee CA, Duncan AM, Buchwald M. Evidence for at least four Fanconi anaemia genes including FACC on chromosome 9. Nat Genet. 1992 Jun;1(3):196-8 Strathdee CA, Gavish H, Shannon WR, Buchwald M. Cloning of cDNAs for Fanconi's anaemia by functional complementation. Nature. 1992 Apr 30;356(6372):763-7 Garcia-Higuera I, Taniguchi T, Ganesan S, Meyn MS, Timmers C, Hejna J, Grompe M, D'Andrea AD. Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. Mol Cell. 2001 Feb;7(2):249-62 Butturini A, Gale RP, Verlander PC, Adler-Brecher B, Gillio AP, Auerbach AD. Hematologic abnormalities in Fanconi anemia: an International Fanconi Anemia Registry study. Blood. 1994 Sep 1;84(5):1650-5 Grompe M, D'Andrea A. Fanconi anemia and DNA repair. Hum Mol Genet. 2001 Oct 1;10(20):2253-9 Medhurst AL, Huber PA, Waisfisz Q, de Winter JP, Mathew CG. Direct interactions of the five known Fanconi anaemia proteins suggest a common functional pathway. Hum Mol Genet. 2001 Feb 15;10(4):423-9 Diatloff-Zito C, Duchaud E, Viegas-Pequignot E, Fraser D, Moustacchi E. Identification and chromosomal localization of a DNA fragment implicated in the partial correction of the Fanconi anemia group D cellular defect. Mutat Res. 1994 May 1;307(1):33-42 Qiao F, Moss A, Kupfer GM. Fanconi anemia proteins localize to chromatin and the nuclear matrix in a DNA damage- and cell cycle-regulated manner. J Biol Chem. 2001 Jun 29;276(26):23391-6 . Positional cloning of the Fanconi anaemia group A gene. Nat Genet. 1996 Nov;14(3):324-8 Lo Ten Foe JR, Rooimans MA, Bosnoyan-Collins L, Alon N, Wijker M, Parker L, Lightfoot J, Carreau M, Callen DF, Savoia A, Cheng NC, van Berkel CG, Strunk MH, Gille JJ, Pals G, Kruyt FA, Pronk JC, Arwert F, Buchwald M, Joenje H. Expression cloning of a cDNA for the major Fanconi anaemia gene, FAA. Nat Genet. 1996 Nov;14(3):320-3 Yamashita T, Nakahata T. Current knowledge on the pathophysiology of Fanconi anemia: from genes to phenotypes. Int J Hematol. 2001 Jul;74(1):33-41 Callén E, Samper E, Ramírez MJ, Creus A, Marcos R, Ortega JJ, Olivé T, Badell I, Blasco MA, Surrallés J. Breaks at telomeres and TRF2-independent end fusions in Fanconi anemia. Hum Mol Genet. 2002 Feb 15;11(4):439-44 D'Andrea AD, Grompe M. Molecular biology of Fanconi anemia: implications for diagnosis and therapy. Blood. 1997 Sep 1;90(5):1725-36 This article should be referenced as such: Garcia-Higuera I, Kuang Y, Näf D, Wasik J, D'Andrea AD. Fanconi anemia proteins FANCA, FANCC, and FANCG/XRCC9 interact in a functional nuclear complex. Mol Cell Biol. 1999 Jul;19(7):4866-73 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Huret JL. Fanconi anaemia. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):308-310. 310 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Cancer Prone Disease Section Mini Review Tuberous sclerosis (TSC) Julie Steffann, Arnold Munnich, Jean-Paul Bonnefont INSERM U393, Groupe Hospitalier Necker-Enfants Malades, Tour Lavoisier 2, 149 rue de Sèvres, 75743 Paris Cedex15, France (JS, AM, JPB) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Kprones/TuberSclerosID10014.html DOI: 10.4267/2042/37912 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology - Multiple retinal nodular hamartomas - Cortical tuber - Subependymal nodule - Subependymal giant cell astrocytoma - Cardiac rhabdomyoma, single or multiple - Lymphangiomyomatosis - Renal angiomyolipoma Minor features: - Multiple, randomly distributed pits in dental enamel - Hamartomatous rectal polyps - Bone cysts - Cerebral white matter radial migration lines - Gingival fibromas - Nonrenal hamartoma - Retinal achromic patch - "confetti " skin lesions - Multiple renal cysts Identity Alias Bourneville disease; Epiloia Inheritance Frequency: 1/6000-1/10000 birth. First genetic cause of epilepsy associated with mental retardation = epiloia. 2/3 of cases are sporadic, 1/3 are inherited. Genetic heterogeneity: two genes, TSC1 and TSC2, account for the majority of cases. Somatic mosaicism has been reported in association with a milder form of the disease. Germinal mosaicism has been described and must be taken into account for genetic counselling. Autosomal dominant with almost complete penetrance but variable expressivity. Clinics Neoplastic risk Note Disability in TSC patients most often results from the involvement of brain. Two types of lesions are static (hamartias); cortical tubers, and subcortical heterotopic nodules, whereas subependymal nodules are often progressive (hamartoma), hence the term subependymal giant cell astrocytoma. Renal angiomyolipomas, often multiple and bilateral, (75% of children withTSC). occasionnally (< 2-3%), turn into renal carcinomaonly later in life. Cardiac rhabdomyomas, often congenital, tend to regress in infancy, remain identical in same size through out childhood and can then either again regress or progress (girls) in adolescence. Brain tumors, (incidence 5-14%), are mostly (>90%) subependymal giant cell astrocytomas, or ependymomas. Hamartomas also occur in liver, spleen, and various tissues. Pulmonary lymphangiomyomatosis is a destructive lung disease characterized by a diffuse hamartomatous proliferation of smooth muscle cells in lungs. Phenotype and clinics The definition of the tuberous sclerosis complex requires either two major features or one major feature plus two minor features. Major features: - Facial angiofibromasor forehead plaque - Non traumatic ungual or periungual fibroma - Hypomelanotic macules (three or more) - Shagreen patch ( connective tissue nevus) Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 311 Tuberous sclerosis (TSC) Steffann J et al. No special feature. Mutations Germinal: Most TSC1 and TSC2 mutations are truncating mutations. Both large deletions and missense mutations are not uncommon at TSC2 locus, whereas most TSC1 mutations are small truncating lesions. Somatic: Loss of heterozygosity has been described in some tumor types, such as angiomyolipomas, giant cell astrocytomas, or rhabdomyomas, but is rare in cortical tubers. Genes involved and proteins References Note Two genes are involved, TSC1 and TSC2. The patients with TSC1 mutations would have a milder form of the disease, compared to those with TSC2 mutations. Kobayashi T, Hirayama Y, Kobayashi E, Kubo Y, Hino O. A germline insertion in the tuberous sclerosis (Tsc2) gene gives rise to the Eker rat model of dominantly inherited cancer. Nat Genet. 1995 Jan;9(1):70-4 Cytogenetics Inborn conditions Increased frequency of premature centromere disjonction (PCD) in cultured fibroblasts, especially for chromosome 3. Cytogenetics of cancer Bosi G, Lintermans JP, Pellegrino PA, Svaluto-Moreolo G, Vliers A. The natural history of cardiac rhabdomyoma with and without tuberous sclerosis. Acta Paediatr. 1996 Aug;85(8):92831 TSC1 Location 9q34 Note Accounts for about 50% of TSC patients. DNA/RNA Description : 23 exons. Protein Note: Tumor suppressor. Description: Hamartin and tuberin cohybridize in vivo. Hamartin is a growth inhibitory protein, affecting cell proliferation via deregulation of G1 phase, possibly by regulating cellular adhesion through ezrin-radixinmoiesin family proteins and the small GTP-binding protein RHO. Carbonara C, Longa L, Grosso E, Mazzucco G, Borrone C, Garrè ML, Brisigotti M, Filippi G, Scabar A, Giannotti A, Falzoni P, Monga G, Garini G, Gabrielli M, Riegler P, Danesino C, Ruggieri M, Magro G, Migone N. Apparent preferential loss of heterozygosity at TSC2 over TSC1 chromosomal region in tuberous sclerosis hamartomas. Genes Chromosomes Cancer. 1996 Jan;15(1):18-25 Au KS, Hebert AA, Roach ES, Northrup H. Complete inactivation of the TSC2 gene leads to formation of hamartomas. Am J Hum Genet. 1999 Dec;65(6):1790-5 Jones AC, Shyamsundar MM, Thomas MW, Maynard J, Idziaszczyk S, Tomkins S, Sampson JR, Cheadle JP. Comprehensive mutation analysis of TSC1 and TSC2-and phenotypic correlations in 150 families with tuberous sclerosis. Am J Hum Genet. 1999 May;64(5):1305-15 Roach ES, DiMario FJ, Kandt RS, Northrup H. Tuberous Sclerosis Consensus Conference: recommendations for diagnostic evaluation. National Tuberous Sclerosis Association. J Child Neurol. 1999 Jun;14(6):401-7 TSC2 Location 16p13 Note Accounts for about 50% of TSC patients. DNA/RNA Description: 41 exons. Protein Note: Tumor suppressor. Fonctions: as a GTPase activating protein which activates the Ras-related family of small GTP-binding proteins such as Rap1 and Rab5. Inhibits the G1/S transition and promotes entry to the G0 phase. The Eker rat, a naturally occuring animal model of TSC, has an autosomal dominant trait of renal cell carcinoma caused by a germline mutation in the rat TSC2 gene. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Verhoef S, Bakker L, Tempelaars AM, Hesseling-Janssen AL, Mazurczak T, Jozwiak S, Fois A, Bartalini G, Zonnenberg BA, van Essen AJ, Lindhout D, Halley DJ, van den Ouweland AM. High rate of mosaicism in tuberous sclerosis complex. Am J Hum Genet. 1999 Jun;64(6):1632-7 Cheadle JP, Reeve MP, Sampson JR, Kwiatkowski DJ. Molecular genetic advances in tuberous sclerosis. Hum Genet. 2000 Aug;107(2):97-114 Mizuguchi M, Takashima S. Neuropathology of tuberous sclerosis. Brain Dev. 2001 Nov;23(7):508-15 This article should be referenced as such: Steffann J, Munnich A, Bonnefont JP. Tuberous sclerosis (TSC). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):311-312. 312 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Deep Insight Section Ataxia-Telangiectasia and variants Nancy Uhrhammer, Jacques-Olivier Bay, Susan Perlman, Richard A Gatti Centre Jean-Perrin, BP 392, 63000 Clermont-Ferrand, France (NU, JOB, RAG) Published in Atlas Database: April 2002 Online updated version: http://AtlasGeneticsOncology.org/Deep/ATMID20006.html DOI: 10.4267/2042/37913 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Ataxia-telangiectasia (A-T) is an autosomal recessive multisystem disorder with early-onset cerebellar ataxia as its defining neurologic feature. It is the most common, recessively inherited, cerebellar ataxia in children under 5 years of age, with a prevalence of 1/40,000 to 1/100,000 live births (Swift, 1985). The accompanying extra-neural features aid in its clinical diagnosis and include conjunctival and cutaneous telangiectases, elevated levels of serum alpha-fetoprotein, chromosome aberrations, immunodeficiency with recurrent sinopulmonary infection, cancer susceptibility, and radiation hypersensitivity. Since identification of the causative gene, ATM (for Ataxia-Telangiectasia mutated), on chromosome 11q22-q23 (Gatti et al., 1988; Savitsky et al., 1995), the molecular basis of certain aspects of the disease have become clearer, though others remain to be elucidated (Gatti et al., 1998; Meyn, 1997; Shiloh and Rotman, 1996). Note: see also cards on genes ATM, and NBS1 , and on cancer prone diseases Ataxia telangectasia and Nijmegen breakage syndrome. or more diffusely. They do not occur on internal organs nor are they generally associated with bleeding problems. Cancer Risk Over the course of their lives, nearly 40% of A-T patients will develop a malignancy (Morrell et al., 1986). Roughly 85% of these malignancies will be either leukemia or lymphoma, which in younger patients may occasionally precede the onset of ataxia. Children will most often develop acute lymphocytic leukemia (ALL) of T-cell origin, rather than the pre-B cell form seen in common childhood ALL. Leukemia in older A-T patients is usually an aggressive T-cell process with morphology similar to a chronic lymphoblastic leukemia (T-CLL, or T-cell prolymphocytic leukemia, T-PLL) (Taylor et al., 1996). Lymphomas are more often non-Hodgkin's, extranodal, infiltrative, B-cell types, and harder to diagnose in their early stages (Murphy et al., 1999). Solid tumors of other tissues occur more commonly as the A-T patient matures, and are being seen in greater numbers as these patients are living longer (Morrell, 1968). CLINICAL FEATURES Neurologic Features Progressive cerebellar ataxia is almost always the presenting symptom and becomes apparent as early as the first year of life. Truncal and gait ataxia are slowly and steadily progressive, although between the ages of 2 and 5 years normal development of motor skills may temporarily mask this decline. This cerebellar degeneration typically leads to wheelchair dependence by the second decade. Migration abnormalities of prenatal Purkinje cell (PC) as well as post-natal PC degeneration have been seen (Vinters et al., 1985), with thinning of the molecular and granule cell layers and minor changes in dentate and olivary nuclei and medullary tracts. Oculomotor abnormalities may also be seen. The typical patient with A-T is of normal intelligence, although the motor abnormalities make formal psychometric testing and standard learning programs difficult. Telangiectasia Telangiectases appear an average of two to four years after onset of the neurologic syndrome and are progressive. They are composed of dilated capillaries in the conjunctiva, and, later, on the ears, over the bridge of the nose, in the antecubital fossae, behind the knees, Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Radiosensitivity 313 Ataxia-Telangiectasia and variants Uhrhammer N et al. Treatment of A-T patients with cancer with conventional doses of ionizing radiation results in lifethreatening sequelae characteristic of much higher doses. In vitro, fibroblasts and lymphoblasts from A-T homozygotes show sensitivity to a number of radiomimetic and free-radical-producing agents (Taylor et al., 1985; Shiloh et al., 1985). This finding led to the development of the highly sensitive and reasonably specific diagnostic test, the colony survival assay (CSA) (Huo et al., 1994). Recurrent infectious disease Moderate cellular and humoral immunodeficiency, with low levels of certain immunoglobulin classes, in conjunction with difficulties in swallowing, lead to frequent pulmonary infections in A-T patients. The incidence and severity of infections varies widely between patients, with some being severely affected, while others have no particular difficulty. Other clinical features A-T, as in other syndromes manifesting chromosomal instability (e.g., Fanconi anemia, xeroderma pigmentosum xeroderma pigmentosum, Bloom syndrome), shows progeroid features (Gatti and Walford, 1981). Young A-T patients may have strands of gray hair or keratoses and basal cell carcinomas. These signs may be related to the accelerated telomeric shortening mentioned above, to increased tissue turnover, and/or to the exaggerated effects of oxidative damage. Endocrine defects typically result in gonadal abnormalities. Most female patients ultimately begin regular menstrual cycles, but may enter menopause prematurely. Most male patients develop normal secondary sexual characteristics. Retardation in somatic growth is seen in about 75%. Pituitary function studies show no consistent abnormalities. Some patients develop insulin-resistant diabetes in their late teens, with hyperglycemia without glycosuria or ketosis, possibly due to a particular IgM antibody directed against insulin receptors (Gatti and Walford, 1981). BIOLOGICAL FEATURES AFP levels are usually elevated, and are a reliable clinical marker after the age of 2. The high levels of AFP are felt to be of hepatic origin and may be accompanied by elevations of other liver enzymes, with no evidence of liver disease at postmortem (Ishiguro et al., 1986; Gatti and Walford, 1981; McFarlin et al., 1972). Virtually all A-T homozygotes that have come to postmortem examination have a small, embryonic thymus, but the resulting immunodeficiencies can be quite variable, even within the same family, suggesting a problem with maturation of B and T cell precursors. IgA, IgE, and IgG2 deficiencies are most common, with the accompanying risk of recurrent sinopulmonary infection (Roifman and Gelfand, 1985). Elevated serum IgM levels may occasionally progress to a high blood viscosity syndrome, with splenomegaly, lymphoadenopathy, neutropenia, thrombocytopenia, and congestive heart failure. T-cell deficiencies occur in half the patients, with abnormal skin test antigen and PHA responses (Paganelli et al., 1992). In a British study of 70 patients (Woods and Taylor, 1992), 10% had severe immunodeficiencies, while nearly 40% had normal immunologic function. CLINICOPATHOLOGY OF THE A-T HETEROZYGOTE The carrier frequency for ATM is estimated at 1%. Carriers are normal neurologically, although they have in vitro radiosensitivity values that are intermediate between homozygotes and normals (Taylor et al., 1985; Paterson et al., 1985; Weeks et al., 1991). It remains unclear whether this translates to any greater risk during exposure to ionizing radiation clinically (diagnostic X-rays, radiation therapy), although results from Broeks suggest that A-T heterozygotes are more frequent among breast cancer patients who develop a second breast tumor after radiotherapy (Broeks et al., 2000). Studies of mice heterozygous for Atm show an increased frequency of dysplastic breast cells in irradiated animals, supporting an increased cancer risk for heterozygotes that is related to their mutagen exposure (Weil et al., 2001). These data suggest that perhaps Swift's recommendation that female relatives of A-T patients avoid mammography is good advice, although the benefit drawn from early detection is largely thought to outweigh the very small chance that the screening could actually provoke a breast tumor, especially when up-to-date mammography equipment with the lowest possible dose is used. Excessive numbers of ATM heterozygotes have not been identified among patients over-reacting to radiotherapy, nor have ATM heterozygotes diagnosed with cancer been noted to have unusual reactions to irradiation, CYTOGENETIC FEATURES Karyotyping of peripheral lymphocytes from A-T homozygotes shows nonrandom chromosomal rearrangements which preferentially involve chromosomal breakpoints at 14q11, 14q32, 7q35, 7p14, 2pll, and 22q11, and correlate with the regions of the Tcell and B-cell receptor gene complexes (Aurias, 1986). Telomere shortening and fusions, with normal telomerase activity (Pandita et al., 1995), have been observed in peripheral blood lymphocytes of A-T patients, especially in pre-leukemic T-cell clones (Metcalfe et al., 1996). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 314 Ataxia-Telangiectasia and variants Uhrhammer N et al. cancer cases than in the healthy population (Gatti et al., 1999). These changes include missense and silent mutations as well as nucleotide changes in the introns. Although some of these will certainly turn out to be innocuous polymorphisms, others may indeed be associated with reduced or altered function of the ATM protein. Loss of heterozygosity (LOH) at the ATM locus has been found in 30 to 60% of cancers, (Hampton et al., 1994; Rio et al., 1998; Uhrhammer et al., 1999), suggesting that ATM may have a role in tumorigenesis, although it is difficult to interpret this type of study due to the large region of chromosome 11q that may be involved in the LOH, and the fact that genes near to ATM may also be involved. In addition, in breast and colon cancer the incidence of LOH at the ATM locus is not very much higher than background. The demonstration of the inactivation of the ATM protein in tumors would more precisely define its importance. A few cases have been described, where the wild-type allele of ATM is inactivated in the tumor tissue of a heterozygote, but the loss of ATM has not been described generally in breast oncogenesis (Chen et al., 1998; Vorechovsky et al., 1996b; Bay et al., 1999). More definitive studies using antibodies against ATM on tumor tissue sections are underway in several laboratories. Somatic mutations of both alleles of ATM have been found in T-prolymphocytic leukemia, in mantle cell lymphoma and in chronic B-lymphoid leukemias, suggesting that in these types of malignancy ATM does play a tumor-suppressor role (Vorechovsky et al., 1998; Stankovic et al., 1999; Bullrich et al., 1999; Shaffner et al., 2000). This is an interesting finding, because although A-T homozygotes are prone to these types of cancer, they have not been described in A-T heterozygotes. suggesting that their radiosensitivity in vivo is not great (Clarke et al., 1998; Hall et al., 1998). CANCER RISK OF AT CARRIERS Several authors have reported that the incidence of cancer in A-T heterozygotes was higher than that in the general population, most notably breast cancer in female heterozygotes less than 60 years of age (Swift et al., 1991; Pippard et al., 1988; Borreson et al., 1990). Other cancers were also mentioned, such as stomach and liver cancer (Swift et al., 1991; Chessa et al., 1994). Several authors now agree that the relative risk of breast cancer in heterozygotes is between 3.3 and 3.9 (Easton, 1994; Inskip et al., 1999; Athma et al., 1996; Janin et al., 1999), with a greater RR at younger ages and no significantly increased risk above age 60, while the relative risk for other types of cancer is not elevated. This modest risk, however, may correspond to a significant percentage of breast cancer in the population at large being attributable to heterozygosity at ATM: if 1% of the population is heterozygous at ATM, and the RR of breast cancer is about 3, then 2 to 4% of new breast cancer cases may be due to defects in ATM. A few groups have searched for constitutional ATM mutations in circulating lymphocytes from sporadic breast cancer cases, and have not found an increased carrier frequency (Fitzgerald et al., 1996; Bebb et al., 1999). Thus, it seems that heterozygosity for ATM is not associated with a tendency toward breast cancer, even though family studies indicate increased risk. There may be several reasons for this discrepancy, first, PTT only identifies 60 to 70% of mutations in A-T homozygotes, and these are not necessarily representative of those associated with breast cancer (Telatar et al., 1996). Secondly, the frequency of A-T heterozygotes in the population is not well defined, although 1% is often cited (Swift et al., 1986; Easton, 1994). Therefore, the low numbers of constitutional mutations found in the above studies do not exclude a role for ATM in breast cancer. Larger study populations and more sensitive techniques to detect ATM mutations are needed before any significant difference between the study and control groups can be reliably defined. Other groups have looked for ATM mutations in familial breast cancer familial breast cancer, again without finding excessive numbers of constitutional heterozygotes (Vorechovsky et al., 1996a; Bay et al., 1998; Chen et al., 1998). It is in fact unlikely that heterozygosity for ATM would lead to identifiable cancer families, due to the low relative risk involved. Although the truncating mutations found in A-T patients have not been found frequently in breast cancer patients, it is curious that small changes in the ATM sequence are found much more frequently in breast Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) STRUCTURE AND FUNCTION OF THE ATM PROTEIN The gene: The ATM gene occupies ~150 kb of 11q22.3-q23.1 (Platzer et al., 1997) (Fig1). ATM is transcribed from a bi-directional promoter that also drives expression of the NPAT/Cand3/E14 gene (Platzer et al., 1997; Imai et al., 1997), although the significance of this coexpression is unknown. There are also two alternative exons 1, although differential expression of the mRNA isoforms in different tissues or in response to different stimuli has not been described, nor is there any change in the amino acid sequence of the resulting protein, since translation is initiated in exon 3. The 13 kb ATM mRNA, with its 9168 bp of coding sequence, appears to be expressed in most tissues and stages of development (Savitsky et al., 1995). 315 Ataxia-Telangiectasia and variants Uhrhammer N et al. Figure 1: The ATM gene at 11q22.3-q23.1 is transcribed from a bodirectional promoter. Microsatellite loci are found in introns 25 (NS22) and 63 (D11S2179). S phase arrest: the phosphorylation of cAbl also serves to halt progression within S phase by inhibiting Rad51Rad51, a single-stranded DNA binding protein essential for replication. Replication Protein A (RPA), another protein essential for the progression of DNA replication, is inhibited by ATM through phosphorrylation of its 34 kDa subunit. ATM has been shown to phosphorylate Ser222 of the FANCD2 protien, which is essential for S phase arrest in response to treatment with DNA cross-linking agents (Grompe and D'Andrea, 2001). Two authors have shown that ATM is not, however, required for the decatenation checkpoints in S phase or late G2 phase, underlining the existence of multiple checkpoints throughout the cell cycle (Montecucco et al., 2001; Deming et al., 2001). Abnormalities in S phase lead to the quantifiable phenotype known as ‘radiation resistant DNA synthesis’, or RDS in cells from A-T homozygotes. G2 cell cycle arrest: ATM inhibits cells from entering mitosis after irradiation through the phosphorylation of at least two targets, Chk1 and Chk2. The literature is occasionally indistinct on the subject of G2 arrest in AT cells, most likely because there are two arrest points, and only one is defective in A-T. Immediately after DNA damage, the defective cell cycle checkpoint can be measured as a failure to diminish the numbers of cells that enter mitosis in the hours that follow irradiation. In contrast, at later times there is clearly an increase in G2 cells which is readily detectable by FACS analysis. This late G2 accumulation is due to cells that were in G1 or S at the time of irradiation, which replicated their DNA in spite of the presence of DSBs, and which have now triggered a distinct G2 checkpoint. ATM and radiation-induced apoptosis: Radiosensitivity is a constant feature of A-T and is thought to be due to excessive apoptosis. How ATM inhibits apoptosis is not completely understood, and may be different according to the type of tissue studied. One route is through the phosphorylation of IkB. IkB is an inhibitor of NFkB, and its phosphorylation leads to the release of NFkB sequestered in the cytoplasm. NFkB now translocates to the nucleus, where it acts as a transcriptional regulator of anti-apoptotic genes. A second level of apoptosis control acts through p53, Notably, expression does not vary with the cell cycle or increase in response to irradiation (Brown et al., 1997). Homologs of ATM have been identified in other mammals and in fish and amphibians, though no true yeast homolog has been identified. Several proteins with homology to ATM have been found, including the catalytic subunit of DNA-PK and ATR. The greatest similarity between these proteins is in the kinase domain, and together they form a sub-family of PI3kinase-related proteins. The protein: The 350 kDa ATM protein contains a leucine zipper, a domain with homology to the S. pombe Rad3 protein, and a protein kinase domain homologous to the PI3K family (Chen and Lee, 1996). ATM is localized mostly to the nucleus, but is also found in cytoplasmic vesicles (Chen and Lee, 1996; Gately et al., 1998; Watters et al., 1997). ATM has been shown to associate with DNA, with particular affinity for DNA ends (Smith et al., 1999). This DNA end-binding activity suggests that ATM might be the/a primary sensor of DNA doublestrand breaks (DSBs). In the presence of DNA DSB damage, ATM phosphorylates a variety of protein targets and activates several different signaling cascades (Figure 2). In contrast to the mRNA, ATM protein does become more abundant in response to IR, although only in cells such as lymphocytes that express low basal levels: no change is seen in cells expressing high levels of ATM (Fang et al., 2001). In addition, ATM becomes more tightly attached to the nuclear matrix and/or chromatin in the presence of DNA damage (Andegeko et al., 2001). G1 cell cycle arrest: ATM induces G1 phase arrest through the action of several intermediates. One of the most important targets is the phosphorylation of p53 on ser15 (Canman et al., 1998; Khanna et al., 1998; Watterman et al., 1998). Among the genes whose transcription is induced by p53 is the cdk-inhibitor p21Waf1/Cip1 p21Waf1/Cip1, which plays a key role in inhibiting the transition from G1 to S phase. ATM also induces G1 arrest through the phosphorylation of cAbl (Shafman et al., 1997; Baskaran et al., 1997), which in turn activates both the p53 homolog p73 and the SAPK pathway to block progression to S phase. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 316 Ataxia-Telangiectasia and variants Uhrhammer N et al. Figure 2. In response to DNA double-strand breaks, ATM interacts with many different proteins to induce cell cycle arrest, increase DNA repair, and inhibits apoptosis. though the mechanism is likely to be indirect. Cultured A-T fibroblasts undergo apoptosis in response to irradiation, and this process may be inhibited by the inactivation of p53. As we have seen, ATM activates the cell cycle arrest functions of p53, but it is as yet unknown how the inhibition of p53’s pro-apoptotic functions works. It is possible that ATM-/- cells allow replication of damaged DNA templates, which in turn trigger p53 through independent mechanisms. A third pathway through which ATM inhibits apoptosis might be through the ceramide synthesis cascade. This signaling cascade is initiated at the cell membrane in response to irradiation, and is dysregulated in A-T cells. It is not yet known how ATM is involved, and whether the detection of DNA damage is necessary or if ATM might detect some other damage signal. Most of the functions described above take place in the nucleus, where ATM surveys the DNA for DSBs, and phosphorylates its substrates when necessary. The phosphorylation of IkB (and possibly of cAbl) occurs in the cytoplasm, however, and the proteins of the ceramide signaling pathway are located on membranes accessible from the cytoplasm. Some authors have proposed that the pool of ATM associated with cytoplasmic vesicles performs functions distinct from Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) genomic surveillance. ATM has been shown to associate with beta-adaptin in the cytoplasm and may be involved in vesicle trafficking and intercellular communication, and it is this aspect which may eventually explain the specific degeneration of cerebellar Purkinje cells. ATM and DSB repair A-T cells exhibit subtle defects in DSB repair: they take longer to repair DSBs and the repair of plasmid substrates is often inexact. While ATM itself does not seem to play a direct role in the rejoining of DSBs, it is involved in the control of this process. As we have seen, ATM activates GADD45 indirectly though p53. In addition, BRCA1 has been shown to be phosphorylated by ATM in response to DSBs and this phosphorylation is essential to relieve the radiation sensitivity of BRCA1-mutant cells (Cortez et al., 1999). BRCA1 has been described as being necessary for the aggregation of Rad51 complexes or Rad50/Mre11/nibrin at DSB sites, in addition to being a transcriptional activator. Rad50 and Rad51 are both required for the repair of DSBs, and BRCA1 may provide a link in the signaling cascade that activates repair. Finally, ATM probably activates DSB repair through Rad50/Mre11/nibrin independently from 317 Ataxia-Telangiectasia and variants Uhrhammer N et al. intermediate between that of A-T patients and normal subjects. Intriguingly, these cellular phenotypes of ATLD are identical to those of NBS patients, even though the neural phenotypes are different (there being no micro-cephaly or mental retardation in ATLD, nor cerebellar ataxia in NBS). Recall that NBS patients have mutations in the gene encoding nibrin, a subunit of Rad50/Mre11/nibrin. The four patients described with hMre11 mutations are two homozygotes for a nonsense mutation at codon 633, and two compound heterozygotes for a null mutation and a substitution of serine for asparagine at amino acid 117. Both the nonsense and missense mutated proteins produce stable products that are able to associate with Rad50 and nibrin, although the aggregation of this complex at DSB sites is abnormal. Data from mMre11 knockout mice indicate that these human mutations are most likely to be partially functional, because a null allele of mMre11 is lethal during embryogenesis, as are null alleles for mRad50 (mice with Nbs1 mutations have are similar to Atm-/mice, with growth retardation, lymphoid developmental defects, lymphoid thymomas, radiosensitivity and female - though not male - sterility) (Xiao and Weaver, 1997; Kang et al., 2002). The interaction between ATM and Mre11 is becoming more clear. The Rad50/Mre11/nibrin complex has described as containing (an) additional protein(s) of high molecular weight, and probably associates loosely or transiently with several other proteins, including BRCA1 and ATM. Clearly, ATM, Mre11, nibrin, and BRCA1 are all required for the aggregation of Rad50 at DSB sites. ATM phosphorylates both nibrin and Mre11, and in the absence of nibrin, ATM fails to phosphorylate Mre11 (Wu et al., 2000; Kim et al., 1999). Rad50, Mre11, and the yeast analog of nibrin, xrs5, all perform essential repair functions and their loss is lethal. The loss of regulatory proteins such as ATM or BRCA1, or the reduced function of nibrin or Mre11 is tolerated but decreases the efficiency of repair. How do the known molecular functions of ATM explain the disease? 1. Radiosensitivity: without ATM, DNA damage triggers apoptosis in sensitive cell types. Radiosensitivity is not due to acquired mutations and karyotypic inviability, but to programmed cell elimination. 2. Cancer risk: A-T cells either create or tolerate chromosomal rearrangements more than other cells. These rearrangements may hit genes critical for normal cell growth and thus initiate cancer. The lack of ATM is not directly tumorigenic, but rather allows other mutation events. The stereotypical chromosomal rearrangements seen in A-T lymphocytes are evidence of this problem with genomic stability. A new study in Atm-/- mice, however, showed that spontaneous BRCA1. Two groups have now shown that ATM phosphorylates H2AX within seconds of DSB damage (Burma et al., 2001; Andegeko et al., 2001). H2AX-P promotes chromatin decondensation and is a major signal for DNA repair. The speed of this phosphorylation also provides more circumstantial evidence for ATM as an actual sensor of DSBs, although there is as yet no direct evidence for this. Cells experiencing DSB damage in G1 or G0 repair this damage through non-homologous end joining, a process controlled by DNA-PK. The relationship between ATM and DNA-PK is as yet unclear, since the abundant Ku subunits of DNA-PK can bind to DNA ends on their own and recruit DNA-PKcs to the sites for repair. This temporal difference in the choice of DSB repair mechanism may be the main reason why two apparently redundant mechanisms are both essential, another being that some are unrepairable by NHEJ due to the poor quality of the DNA ends. In any case, Atm-/-/SCID double-knockout mice are inviable after 12 days gestation (Gurley 2001), demonstrating the additive effect of these two DSB signaling/repair proteins. Ku70 has been shown now to be essential for the binding of the Rad50 / Mre11 / nibrin complex at DSB sites, however, and the similarities of the cellular phenotypes of A-T and NBS (nibrin-deficient) cells suggests that this may provide the link between ATM and DNA-PK. Cells experiencing DSB damage in G2 favor homologous recombination between sister chromatids for repair. ATM and Mre11: Since the cloning of ATM, the vast majority of A-T patients have been found to carry mutations in the ATM gene. There are a few cases, however, where no mutation was detectable in the gene, and the ATM protein was present in cellular extracts. Stewart has now described mutations in the hMre11a gene in four such patients from two families (1999). Interestingly, cell fusion experiments in the 1980’s indicated that there were four complementation groups for A-T (Jaspers et al., 1988). After the cloning of ATM, it was shown that mutations in this one gene were present in all four ‘complementation groups’, sometimes identical mutations, and the multigenic theory of A-T was essentially discarded as an experimental artifact (Savitsky et al., 1995). The hMre11a gene is located about 30 cM proximal to ATM on the long arm of chromosome 11, at band q22.1. The phenotypes of human patients with ATM and hypomorphic hMre11 mutations are very nearly identical. ATLD patients (for ataxia-telangiectasia-like disorder) may have a slightly milder phenotype than AT patients, but still within the range of phenotypes found for classic A-T patients. The phenotypic differences are apparent at the cellular level: the induction of p53 is nearly normal, and clonogenic survival and radioresistant DNA synthesis curves are Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 318 Ataxia-Telangiectasia and variants Uhrhammer N et al. mutation rates were not increased in samples of ear and spleen tissue, suggesting that not all tissues are equally sensitive to the effects of ATM loss (Turker et al., 1999). 3. Immunodeficiency: without ATM, the process of V(D)J recombination is not properly supervised, and aberrant chromosomes are created. Most cells recognize the anomaly and commit suicide (leading to the hypoplastic thymus), but others escape this control and are detected as circulating lymphocytes carrying the 7;7, 7;14, and 14;14 rearrangements characteristic of A-T. That the immunodeficiency in A-T is not as severe as other syndromes reflects the ability of A-T cells to create functional V(D)J recombination events at reduced frequency. 4. Cerebellar degeneration: this aspect of A-T is as yet unexplained by the known molecular functions of the protein, though several theories have been advanced. 1) aberrant migration of Purkinje cells 2) oxidative damage leads to cell death; 3) an autoimmune process destroys the Purkinje cells. An excess of oxidative stress in the cerebellum (and elsewhere) is currently the favored hypothesis for this degeneration (Stern et al., 2002). TREATMENT OF A-T At present there is no definitive gene-based therapy, neuroprotective therapy, or neural-restorative therapy to halt or reverse progression of the neurologic symptoms of A-T. The extraneural symptoms have many conventional treatment options, especially in the important areas of pulmonary infection and malignancy. Infection is usually with common microbes, not opportunistic organisms (despite the combined immuno-deficiency), so prompt treatment with appropriate antibiotics and attention to aggressive pulmonary hygiene can prevent future complications (resistant infections, bronchiectasis, chronic respiratory failure, and aspiration). Regular physical examinations with blood counts and blood chemistries can serve as an early screen for leukemia/lymphoma and other cancers. Routine pelvic exams and breast exams in young women, prostate screening in young men, and skin exams in both should be instituted. Non-radiologic imaging studies should be used when any area of concern is raised (MRI, ultrasound). Should a malignancy occur, treatment protocols utilizing lower doses of radiation therapy and alternatives to radiomimetic and neurotoxic agents should be sought, and chemotherapy protocols with a high risk of developing a second malignancy (topoisomerase inhibitors) should be modified. Young children presenting with leukemia or lymphoma, or any other malignancy, should be screened for the presence of A-T before a treatment regimen is begun. Because of the extreme cancer susceptibility of these patients, they should be encouraged to avoid excess sun exposure by keeping skin covered and wearing a hat and sunscreen when outdoors. Neurorehabilitation strategies and symptomatic medication can improve neurologic performance and reduce the risk of long-term complications from increasing immobility (deconditioning, contractures, decubiti, pneumonia, bladder infections, and constipation). Physical therapy can help the patient maintain independence, continue in school, and enjoy leisure pursuits with family and friends. Pool exercise, speech therapy, remedial learning programs, and appropriate adaptive equipment also reduce the ultimate handicaps of these patients. Most A-T patients in the United States and Western Europe live well beyond 20 years, thanks to improved health maintenance and rehabilitation options. This is a major change from just a few years ago, when it was unusual for patients to live past their teens, but much work still needs to be done. GENOTYPE/PHENOTYPE CORRELATIONS Over 300 disease-causing ATM mutations have been identified, extending over each of the 66 exons, and patients from non-consanguineous families are typically compound heterozygotes. Although founder effect mutations account for significant proportions of A-T patients in various ethnic populations, they do not account for significant numbers of A-T patients in heterogeneous populations such as the United States. A-T variants, who do not meet all the clinical criteria for A-T (i.e., relatively late-onset of ataxia or chorea, unusually long survival, absence of telangiectases, normal AFP levels, normal immune status, intermediate levels of radiosensitivity) have been shown for the most part to have ATM mutations. These have been homo- or at least heterozygous for milder missense, splice-site, or small, non-critical insertion/deletion abnormalities that could allow production of up to 17% of normal ATM protein. Nonsense, frame-shift, or in-frame changes, causing two truncating mutations, with production of little or no ATM protein in over 85% of patients, result in the more typical A-T phenotype with lower mean survivals. Many other patients with phenotypes typical of A-T (DiRocco, 1999; Hernandez et al., 1993) have not been shown to have mutations in the ATM gene, and may represent mutations in other genes that interact with the ATM protein. One of these proteins has been identified as Mre11, as discussed above. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) References McFarlin DE, Strober W, Waldmann TA. Ataxia-telangiectasia. Medicine (Baltimore). 1972 Jul;51(4):281-314 319 Ataxia-Telangiectasia and variants Uhrhammer N et al. Gatti RA, Walford RL. Immune function and features of afing in chromosomal instability syndromes In: Immunological Aspects of Aging, Segre and Smith, Eds. Marcel Dekker, New York 1981, pp449-465. Weeks DE, Paterson MC, Lange K, Andrais B, Davis RC, Yoder F, Gatti RA. Assessment of chronic gamma radiosensitivity as an in vitro assay for heterozygote identification of ataxia-telangiectasia. Radiat Res. 1991 Oct;128(1):90-9 Paterson MC et al. 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Science. 1999 Nov 5;286(5442):1162-6 breast cancer-susceptibility. Feb;66(2):494-500 J Hum Genet. 2000 Schaffner C, Idler I, Stilgenbauer S, Döhner H, Lichter P. Mantle cell lymphoma is characterized by inactivation of the ATM gene. Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2773-8 Gatti RA, Tward A, Concannon P. Cancer risk in ATM heterozygotes: a model of phenotypic and mechanistic differences between missense and truncating mutations. Mol Genet Metab. 1999 Dec;68(4):419-23 Wu X, Ranganathan V, Weisman DS, Heine WF, Ciccone DN, O'Neill TB, Crick KE, Pierce KA, Lane WS, Rathbun G, Livingston DM, Weaver DT. ATM phosphorylation of Nijmegen breakage syndrome protein is required in a DNA damage response. Nature. 2000 May 25;405(6785):477-82 Inskip HM, Kinlen LJ, Taylor AM, Woods CG, Arlett CF. Risk of breast cancer and other cancers in heterozygotes for ataxiatelangiectasia. Br J Cancer. 1999 Mar;79(7-8):1304-7 Janin N, Andrieu N, Ossian K, Laugé A, Croquette MF, Griscelli C, Debré M, Bressac-de-Paillerets B, Aurias A, Stoppa-Lyonnet D. Breast cancer risk in ataxia telangiectasia (AT) heterozygotes: haplotype study in French AT families. Br J Cancer. 1999 Jun;80(7):1042-5 Andegeko Y, Moyal L, Mittelman L, Tsarfaty I, Shiloh Y, Rotman G. Nuclear retention of ATM at sites of DNA double strand breaks. J Biol Chem. 2001 Oct 12;276(41):38224-30 Burma S, Chen BP, Murphy M, Kurimasa A, Chen DJ. ATM phosphorylates histone H2AX in response to DNA doublestrand breaks. J Biol Chem. 2001 Nov 9;276(45):42462-7 Kim ST, Lim DS, Canman CE, Kastan MB. Substrate specificities and identification of putative substrates of ATM kinase family members. J Biol Chem. 1999 Dec 31;274(53):37538-43 Deming PB, Cistulli CA, Zhao H, Graves PR, Piwnica-Worms H, Paules RS, Downes CS, Kaufmann WK. The human decatenation checkpoint. 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Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11134-9 Montecucco A, Rossi R, Ferrari G, Scovassi AI, Prosperi E, Biamonti G. Etoposide induces the dispersal of DNA ligase I from replication factories. Mol Biol Cell. 2001 Jul;12(7):2109-18 Stankovic T, Weber P, Stewart G, Bedenham T, Murray J, Byrd PJ, Moss PA, Taylor AM. Inactivation of ataxia telangiectasia mutated gene in B-cell chronic lymphocytic leukaemia. Lancet. 1999 Jan 2;353(9146):26-9 Weil MM, Kittrell FS, Yu Y, McCarthy M, Zabriskie RC, Ullrich RL. Radiation induces genomic instability and mammary ductal dysplasia in Atm heterozygous mice. Oncogene. 2001 Jul 19;20(32):4409-11 Stewart GS, Maser RS, Stankovic T, Bressan DA, Kaplan MI, Jaspers NG, Raams A, Byrd PJ, Petrini JH, Taylor AM. The DNA double-strand break repair gene hMRE11 is mutated in individuals with an ataxia-telangiectasia-like disorder. Cell. 1999 Dec 10;99(6):577-87 Kang J, Bronson RT, Xu Y. Targeted disruption of NBS1 reveals its roles in mouse development and DNA repair. EMBO J. 2002 Mar 15;21(6):1447-55 Turker MS, Gage BM, Rose JA, Ponomareva ON, Tischfield JA, Stambrook PJ, Barlow C, Wynshaw-Boris A. Solid tissues removed from ATM homozygous deficient mice do not exhibit a mutator phenotype for second-step autosomal mutations. Cancer Res. 1999 Oct 1;59(19):4781-3 Stern N, Hochman A, Zemach N, Weizman N, Hammel I, Shiloh Y, Rotman G, Barzilai A. Accumulation of DNA damage and reduced levels of nicotine adenine dinucleotide in the brains of Atm-deficient mice. J Biol Chem. 2002 Jan 4;277(1):602-8 Uhrhammer N, Bay J, Pernin D, Rio P, Grancho M, Kwiatkowski F, Gosse-Brun S, Daver A, Bignon Y. Loss of heterozygosity at the ATM locus in colorectal carcinoma. Oncol Rep. 1999 May-Jun;6(3):655-8 This article should be referenced as such: Uhrhammer N, Bay JO, Perlman S, Gatti RA. AtaxiaTelangiectasia and variants. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):313-322. Broeks A, Urbanus JH, Floore AN, Dahler EC, Klijn JG, Rutgers EJ, Devilee P, Russell NS, van Leeuwen FE, van 't Veer LJ. ATM-heterozygous germline mutations contribute to Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Am 322 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Educational Items Section Genetic Linkage Analysis Françoise Clerget-Darpoux Unité de Recherche d'Epidémiologie Génétique, INSERM U535, Kremlin-Bicêtre, France (FCD) Published in Atlas Database: May 2002 Online updated version: http://AtlasGeneticsOncology.org/Educ/LinkageLongID30031EL.html DOI: 10.4267/2042/37914 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology I- Genetic linkage analysis I-1. Recombination fraction I- 2. Definition of the "lod score" of a family I- 3. Test for linkage I- 4. Estimation of the recombination fraction I- 5. Recombination fraction for a disease locus and a marker locus I- 6. Linkage analysis for three loci : the phenomenon of interference I- 7. References II- Genetic heterogeneity of localization II- 1. The "Predivided sample test" II- 2. The "Admixture Test" II- 3. Generalization of the "admixture test" II- 4. References III- Statistical properties of the method of lod scores III- 1. The test procedure III- 1.1. Impact of non-sequentiality III- 1.2. Maximization of the lod score over the [0, 1/2] interval III- 1.3 References III-2. Genotype information III-2.1. Ambiguity in phenotype-genotype relationships at the disease locus III-2.2. Ambiguity in the marker genotype III-2.3. Gamete disequilibrium between alleles at the disease locus and at the marker locus III-3. The problem of multiple tests III-4. References reflected in the recombination fraction, θ which is the percentage of the gametes transmitted by the parents to be recombined. If they are transmitted independently, there will be the same number of recombined gametes as there are parental gametes, and so θ = 1/2. If they are I- Genetic linkage analysis Investigating the linked segregation of genes situated at different loci is a way of testing the independence of their transmission. This concept of independence is also Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 323 Genetic Linkage Analysis Clerget-Darpoux F not transmitted independently, then the parenteral gametes are transmitted preferentially to the recombined gametes, and 0≤ θ<1/2. In this case, there is said to be "linkage" between the two loci. I-1. Recombination fraction Let us consider the caseof two loci, A and B, with two codominant alleles at each of these loci, A1, A2 and B1, B2 respectively. Such an individual can produce four types of gamete: A1B1 A2B1 A1B2 A2B2 Two situations are possible: Figure 3 Gametes A1B1 and A2B2 are said to be "parental". In the offspring, as in the parents, A1 is "coupled" with B1 (and A2 is "coupled" with B2). The gametes A1B2 and A2 B1 are therefore described as being "recombined". An uneven number of recombination or "crossing-over" phenomena have occurred between the A and B loci. The proportion of recombined gametes amongst the gametes transmitted is known as the “recombination fraction”. 1- The loci A and B are on different chromosome pairs θ = number of recombined gametes/number of gametes transmitted Assuming that the crossing-over event for a pair of chromosomes follows Poisson’s law, and knowing that a parental gamete has zero or an even number of crossings-over, whereas a recombined gamete has an odd number, we can show that the frequency of recombined gametes is always equal to or lower than that of the parenteral gametes and so 0 ≤ θ < 1/2 If θ = 1/2, then all the gamete types have the same probability and the alleles at the loci A and B loci are transmitted independently. Loci A and B are therefore said not to enhibit genetic linkage. This is the situation if A and B are on different pairs of chromosomes, and also if A and B are one the same pair, but at some distance from each other. However, if θ < 1/2, then the two loci are genetically linked. For a couple of which the genotypes at the A and B are known, the probability of observing the genotypes of the offspring depends on the value of θ. Let us assume the following crossing: Figure 1 In this case, the four gametes all have the same probability: 1/4. 2- The loci A and B are on the same chromosome pairs Here we have to distinguish between two possible situations: the alleles A1 and B1 may be on the same chromosome within the pair, in which case A1 and B1 are said to be "coupled"; or they may be on different chromosomes, in which case A1 and B1 are said to be in a state of "repulsion". Figure 2 For instance, let us suppose that A1 and B1 are "coupled". Four types of gametes are still produced. Figure 5 Therefore, such a couple can have 4 types of offspring Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 324 Genetic Linkage Analysis Clerget-Darpoux F Take a family of which we know the genotypes at the A and B loci of each of the members. Let L(θ) be the liklihood of a recombination fraction 0 ≤ θ < 1/2 L(1/2) be the liklihood of θ = 1/2, that is of independent segregation into A and B. The lod score of the family in θ is: Z(θ) = log10 [L(θ)/L(1/2)] Z can be taken to be a function of θ defined over the range [0,1/2]. Lod score of a sample of families The liklihood of a value of θ for a sample of independent families is the product of the liklihoods of each family, and so the lod score of the whole sample will be the sum of the lod scores of each family. Figure 6 Assuming that there is gamete equilibrium at the A and B loci, in parent 1 there is a probability of 1/2 that alleles A1 and B1 will be coupled, and a probability of 1/2 that they will be in repulsion. (1) A1 and B1 are coupled, so the probability that parent (1) provides the gametes A1B1 and A2B2 is (1θ)/2 and the probability that this parent provides gametes A1B2 and A2B1 is θ/2. The probability that the couple will have child of type (1) or (2) is (1-θ)/2, and that of their having a type (3) or type (4) child is θ/2. The probability of finding n1 children of type (1), n2 of type (2), n3 of type (3) and n4 of type (4) is therefore [(1- θ)/2]n1+n2 x (θ/2)n3+n4 (2) A1 and B1 are in a state of repulsion, so the probability that parent (1) provides the gametes A1B2 and A2B1 is (1-θ)/2 and the probability that this parent provides gametes A1B1 and A2B2 is θ/2. The probability of the previous observation is therefore: (θ/2)n1+n2 x[(1-θ)/2]n3+n4 So in the end, with no additional information about the A1 and B1 phase, and assuming that the alleles at the A and B loci are in a state of coupling equilibrium, the probability of inding n1, n2, n3 and n4 children in categories (1), (2), (3), (4) is: p(n1,n2,n3,n4/θ)=1/2{[(1 θ)/2]n1+n2 x (θ/2)n3+n4 + (θ/2) n1+n2 x [(1-θ)/2] n3+n4} So the liklihood of θ for an observation n1, n2, n3, n4 can be written: L(θ/n1,n2,n3,n4)=1/2 {[(1-θ)/2]n1+n2 (θ/2)n3+n4 + (θ/2) n1+n2 [(1-θ)/2] n3+n4} Special case: number of children n= 1 Regardless of the category to which this child belongs L(θ) = 1/2 [(1-θ)/2] + 1/2 [θ/2] = 1/4 The liklihood of this observation for the family does not depend on θ. We can say that such a family is not informative for θ. Informative families An "informative family" is a family for which the liklihood is a variable function of θ. One essential condition for a family to be informative is, therefore, that it has more than one child. Furthermore, at least one of the parents must be heterozygotic. Definition: if one of the parents is doubly heterozygotic and the other is: - A double homozygote, we have a backcross - A single homozygote, we have a simple backcross - A double heterozygote, we have a double intercross I- 3. Test for linkage Several methods have been proposed to detect linkage: "U scores", were suggested by Bernstein in 1931, "the sib pair test" by Penrose in 1935, "likelihood ratios" by Haldane and Smith in 1947, "the lod score method" proposed by Morton in 1955 (1). Morton’s method is the one most commonly used at present. The test procedure in the lod score method is sequential (Wald, 1947 (2)). Information, i.e. the number of families in the sample, is accumulated until it is possible to decide between the hypotheses H0 and H1: H0: genetic independence θ = 1/2 and Hl: linkage of θ1 0 ≤ θ1 < ½. The lod score of the θ1 sample Z(θ1) = log10 [L(θ1)/L(l/2)] indicates the relative probabilities of finding that the sample is Hl or H0. Thus, a lod score of 3 means that the probability of finding that the sample is Hl is 1000 times greater than of finding that it is H0 ("lod = logarithm of the odds"). The decision thresholds of the test are usually set at -2 and +3, so that if: Z(θ1) 3 H0 is rejected, and linkage is accepted. Z(θ1) ≤ -2 linkage of θ1 is rejected. -2 < Z(θ1) < 3 it is impossible to decide between H0 and Hl. It is necessary to go on accumulating information. For the thresholds chosen, -2 and +3, we can show that: The first degree error, α < 10-3 The second degreee error, β < 10-2 The reliability, 1-ρ > 0.95 ∀ θ1 The power, P(θ) > 0.80 ∀ θ1 if the true value of θ < 0.10 I- 2. Definition of the "lod score" of a family Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) Figure 7 325 Genetic Linkage Analysis Clerget-Darpoux F Details about the principle underlying the test are to be found in Wald (2), and the justification for criteria -2 and +3 in Morton (1). In fact, what is being tested is not a single value of θ1 relative to θ = 1/2, but a whole set of values between 0 and 1/2, with a step of various size (0.01 or 0.05). If there is a value of θ1 such that Z(θ1) = 3: linkage is concluded to exist. Figure 10 The proposed test has the advantage of being very simple, and of providing protection against falsely concluding linkage. However, some criticisms can be levelled, not only against the criteria chosen (Chotai (3)), but also against the entire principle of using a sequential procedure (Smith (4)). The number of families typed is, indeed, rarely chosen in the light of the test results. Figure 8 If there is a value of θ1 such that Z(θ1) = -2 The linkage is excluded for any θ ≤ θ1 If ∀ θ -2 < Z(θ) < 3, no conclusion can be drawn, the sample is not sufficiently informative. Figure 9 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 326 Genetic Linkage Analysis Clerget-Darpoux F configuration, weighting it by the probability of this configuration, and knowing the phenotypes of individuals in A and B. Knowledge of the genetic parameters at each of the loci (gene frequency, penetration values) is therefore necessary before we can estimate θ (Clerget-Darpoux et al (5)). It is obvious that calculating the lod scores, despite being simple in theory, is in fact a lengthy and tedious business. In 1955, Morton provided a set of tables giving the lod scores for various values of θ for a disease locus and a marker locus for nuclear families with sibling sizes of 2 to 7. However, the situations envisaged were very restrictive. In particular, it was assumed that the disease was determined by a dominant or recessive completely pentrating rare gene. "LIPED" written by Ott in 1974 (6) was the pioneering software in linkage analysis. It is able to carry out this calculation, in an extensive pedigree for any values of q, f1, f2, f3 and for penetration as a function of age. The "Linkage" program of Lathrop et al, 1984 (7,8) is the one most often used for gene mapping. It can be used to carry out multipoint analysis. All the software we have described is based on the same recursive algorithm, r (Elston and Stewart), which means that it can be used to investigate pedigrees of any size, but that it envisages all the possible haplotypical combinations of markers, and is therefore limited by the number of markers to be taken into account. In contrast, "Genehunter" (9), which is based on a Markov chain principle, is limited not by the number of markers taken into consideration in the analysis, but by the size of the family structure. The very recently developed software package "Allegro" (10) can apply information from a large number of markers and extended family structures. Analysis of gene linkage has made it possible to construct a gene map by locating the new polymorphisms relative to one other on the genome. The measurement used on the gene map is not the recombination fraction, which is not an additive datum, but the gene distance, which we will define below. I- 4. Estimation of the recombination fraction If the test, on a sample of the family, has demonstrated linkage between the A and B loci, then one may want to estimate the recombination fraction for these loci. The estimated value of θ is the value which maximizes the function of the lod score Z, and this is equivalent to taking the value of θ for which the probability of observing linkage in the sample is greatest. I- 5. Recombination fraction for a disease locus and a marker locus Let us assume we are dealing with a disease carried by a single gene, determined by an allele, g0, located at a locus G (g0: harmful allele, G0: normal allele). We would like to be able to situate locus G relative to a marker locus T, which is known to occupy a given locus on the genome. To do this, we can use families with one or several individuals affected and in which the genotype of each member of the family is known with regard to the marker T. In order to be able to use the lod scores method described above, what is needed Figure 11 is to be able to extrapolate from the phenotype of the individuals (affected, not affected) to their genotype at locus G (or their genotypical probability at locus G). What we need to know is: 1. the frequency, g0 2. the penetration vector f1, f2,f3 f1 = proba (affected /g0g0) f2 = proba (affected /g0G0) f3 = proba (affected /G0G0) It will often happen that the information available for the marker is not also genotypic, but phenotypic in nature. Once again, all possible genotypes must be envisaged. As a general rule, the information available about a family concerns the phenotype. To calculate thelikelihood of θ, we must envisage all the possible genotype configurations at each of the loci, for this family, writing the likelihood of θ for each Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) I- 6. Linkage analysis for three loci : the phenomenon of interference (V. Bailey, 1961) Now let us consider three loci A, B and C. Let the recombination fraction between A and B be θ1, that between B and C be θ2 and that between A and C be θ3. Figure 12 327 Genetic Linkage Analysis Clerget-Darpoux F Let us consider the double recombinant event, firstly between A and B, and secondly between B and C. Let Rl2 be the probability of this event. If the crossings-over occur independently in segments AB and BC, then: Rl2 = θ1θ2 If this is not the case, an interference phenomenon is occurring and Rl2 = C θ1 θ2 where C 1 If C < 1 the interference is said to be positive; and crossings-over in segment AB inhibit those in segment BC. If C >1 the interference is said to be negative; and crossings-over in segment AB promote those in segment BC. Let us consider the case of a triple heterozygotic individual. Such an individual can provide 8 types of gametes. x(θ) = -1/2 Log (1-2θ) is an additive measurement. It is known as the genetic distance, and is measured in Morgans. It can be shown that x measures the mean number of crossings-over. Test for the presence of interference Let us consider a sample of families with the genotypes A, B and C. Let Lc be the greatest likelihood for θ1, θ2, θ3 and L1 the greatest likelihood when we impose the constraint C=1 (i.e. θ3 = θ1 + θ2 - 2θ1θ2) Then -2 Log (Ll/Lc ) follows a χ2 pattern, with one degree of freedom. I- 7. References Figure 13 Figure 14 1. Morton NE. Sequential tests for detection of linkage. Am J Hum Genet 1955; 7: 277-318. 2. Wald A. Sequential analysis. New York: Wiley,1977. 3. Chotai J. On the lod score method in linkage analysis. Ann Hum Genet 1984; 48: 359-378. 4. Smith CAB. Some comments on the statistical methods used in linkage investigations. Am J Hum Genet 1959; 11: 289-304. 5. Clerget-Darpoux F.; Bonaïti-Pellié C, Hochez J. Effects of mispecifying genetic parameters in lod score analysis. Biometrics 1986; 42: 393-399. 6. Ott, J. Estimation of the recombination fraction in human pedigrees: Efficient computation of the likelihood for human linkage studies. Am J Hum. Genet 1974; 36: 363386. 7. Lathrop GM, Lalouel, J. Easy calculations of lod scores and genetic risks on small computers. Am J Hum Genet 1984; 36(2): 460-465 8. Lathrop GM; Lalouel JM; Julier C; Ott J. Multilocus linkage analysis in humans. Detection of linkage and estimation of recombination. Am J Hum Genet 1985; 37: 482-498. 9. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES. Parametric and Nonparametric Linkage Analysis: A Unified Multipoint Approach. Am J Hum Genet 1996; 58: 1347-1363. 10. Gudbjartsson DF, Jonasson K, Frigge M, Kong A. Allegro, a new computer program for multipoint linkage analysis. Nature Genet 2000; 25: 12-13 11. Bailey N. Introduction to the mathematical theory of genetic linkage. London: Oxford University Press, Amen House,1961. 12. Ott, J. Analysis of human genetic linkage. Johns Hopkins University Press, 1985. 13. Morton NE. The detection and estimation of linkage between the genes for elliptocytosis and the Rh blood type. Am J Hum 1956; 8: 80-96. 14. Smith CAB. Testing for heterogeneity of recombination fractions in human genetics. Ann Hum Genet 1963; 27: 175-182. Figure 15 We can write that θ3 = θ1 + θ2 -2 R12 θ3 = θ1 + θ2 -2 Cθl θ2 If C = 1 θ3 = θ1 + θ2- 2θ1θ2 The recombination fraction is a non-additive measurement. However, we can write (1-2θ3) = (1-2θ1)(1-2θ2) if x(θ) = k Log (1-2θ) then we have x(θ3) = x(θ1) + x(θ2) and for k = -1/2, x(θ)∼θ for small values of θ. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) IIGenetic localization heterogeneity of The analysis of genetic linkage can be complicated by the fact that mutations of several genes, located at different places on the genome, can give rise to the same disorder. This is known as genetic heterogeneity of localization. One of the following two tests is used to identify heterogeneity of this type, the "Predivided 328 Genetic Linkage Analysis Clerget-Darpoux F sample test" or the "Admixture Test". The first test is usually only appropriate if there is a good family stratification criterion or if each family individually has high informativity. II- 3. Generalization of the "admixture test" In some single-gene diseases, several genes have been shown to exist at different locations. This is true, for example of multiple exostosis disease, for which 3 genes have been identified successively on 3 different chromosomes. The "admixture test" is then extended to determine the proportion of families in which each of the three genes is implicated (Legeai-Mallet et al, 1997), and the possibility that there is a fourth gene. The three locations on chromosomes 8, 19 and 11 were reported as El, E2 and E3, and the proportions of families concerned as αl, α2 and α3 respectively. α4 was used to represent the proportion of the families in which another location was involved. For each family i of the sample, the likelihood was calculated using the observed segregation within the family of the markers available in each of the three regions, according to the clinical status of each of its members. Li(El, E2, E3,αl, α2, α3/Fi) = αl (L(E1/Fi)/L(El=1/2/Fi)] + αl(L(E2/Fi)/L(E2=1/2/Fi)] + α3 [L(E3/Fi)/L(E3=1/2/ Fi)]+ α4. For all the families L(El, E2, E3,αl, α2, α3/ ΠFt) = i Li(El, E2, E3,αl, α2, α3 / Fi) Each αi can be tested to see if it is equal to 0, and then the corresponding non nullα i and Ei values are estimated. It is also possible to calculate the probability that the gene implicated is at El, E2 or E3 for each of the families in the sample. The post hoc probability makes use of the estimated αi proportions, but also the specific observations in this family. The sample investigated has been shown to consist of three types of families: in 48% of families, the gene is located on chromosome 8, in 24% of them on chromosome 19, and in 28% of families the gene is located on chromosome 11. There was no evidence of a fourth location in this sample. The post hoc probabilities of belonging to one of these 3 sub-groups were then estimated: the probability that the gene implicated would be on chromosome 8 was over 90% for 5 families, that it would be on chromosome 19 for 3 of them, and that it would be on chromosome 11 for 4 families. For the other families, the situation was less clear-cut: the post-hoc probabilities are similar to the ad hoc probabilities because of the paucity of information provided by the markers used. II- 1. The "Predivided sample test" This test is intended to demonstrate linkage heterogeneity in different sub-groups of a sample of families. The aim is to test whether the genetic linkage between a disease and its marker(s) is the same in all sub-groups. These groups are formed ad hoc on the basis of clinical or geographical criteria etc.... Let us assume that the total sample of families has been divided into n sub-groups (it is possible to test for the existence of as many sub-groups as families). θi denotes the true value of the recombination fraction of subgroup i. We want to test the null hypothesis H0: θ1= θ2= θ3= …= θn against the alternative hypothesis Hl: the values of θi are not all equal. Therefore, the quantity Figure 16 follows a χ distribution2 with (n-l) degrees of freedom. The homogeneity of the sample for linkage with a typeI error of the sample for linkage with a type I error equal to α if Q is above the critical threshold χ2(n-l) corresponding to α. II- 2. The "Admixture Test" Unlike the previous test, the "admixture test" is not based on an ad hoc subdivision of the families. It is assumed that among all the families studied genetic linkage between the disease and the marker is found only in a proportion α of the families, with a recombination fraction θ < 1/2. In the remaining (l-α) families, it is assumed that there is no linkage with the marker (θ=1/2). For each family i of the sample, the likelihood is calculated Li(α, θ) = α Li(θ) + (l-α) Li(1/2), where Li(θ) is the likelihood of θ for family i. The likelihood of the couple, (α, θ) is defined by the product of the likelihoods associated with all the families: L(α,θ)= Πi Li(α,θ). We test to find out whether α is significantly different from 1 by comparing Lmax(α = l,θ), the maximized likelihood for θ assuming homogeneity, and Lmax(α,θ), the maximized likelihood for the two parameters α and θ (nested models). Then variable Q =2[Ln Lmax (α,θ) —Ln Lmax (α= 1,θ)], follows a χ2 distribution with one degree of freedom. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) II- 4. References 1. 329 Legeai-Mallet L, Margaritte-Jeannin P, Clerget-Darpoux F et al. Genetic heterogeneity of hereditary multiple exostoses. Hum Genet 1997; 99: 298-302. Genetic Linkage Analysis Clerget-Darpoux F 2. Morton N. The detection and estimation of linkage between the genes for elliptocytosis and the Rh blood type. Am J Hum Genet 1956; 8: 80-96. 3. Smith CAB. Testing for heterogeneity of recombination values in human genetics. Ann Hum Genet 1963; 27: 175182. III- Statistical properties method of lod scores of The conditions of application which underlie these properties: sequentiality, segregation of a simple single-gene disease in nuclear families, in which all the members are genotyped for a genetic marker, and the non-ambiguity of the test is not confirmed in practice. The table below shows the change in these conditions of application. We discuss here the impact of these changes on the statistical properties. the III- 1. The test procedure The test procedure used in the method of lod scores is sequential (Wald, 1947). The amount of information, i.e. the number of families is accumulated in the sample, until it is possible to decide between the H0 and H1 hypotheses: H0: genetic independence θ = ½ and H1: linkage to θ1, 0 ≤ θ1 < 1/2 The value of the lod score of the sample in θ1 z(θ1) = log10 [L(θ1)/L(1/2)] indicates the relative probabilities of observing the sample as H1 or H0. Thus, a lod score of 3 implies that the probability is 1000 times greater of observing the sample as H1 rather than H0 ("lod=logarithm of the odds"). The decision thresholds of the test are usually set at -2 and +3, so that if: Z(θ1) 3 H0 is rejected and linkage is concluded Z(θ1)≤ 2 linkage is rejected for θ1. -2 < Z(θ1) < 3 it is impossible to decide between H0 and H1. It is necessary to go on accumulating information. For the -2 and +3 thresholds selected, it can be shown that: The first degree error α < 10-3 The second degree error β < 10-2 The reliability 1-ρ > 0.95 ∀θ1 The power P(θ) > 0.80 ∀θ1 if the true value of θ < 0.10 III- 1.1. Impact of non-sequentiality In general, one is working on a sample of families of a fixed size. This problem of non-sequentiality was raised by Smith (1959) and investigated by Chotai (1984) and Guihenneuc (1991), who have shown that the type-1 error of the test was not increased, but on the contrary reduced. Furthermore, the power will obviously depend on the size the sample. It also depends on the parameters of the genetic model (penetrations, frequency of the morbid allele, degree of dominance), of the types of family analysed (nuclear or extensive families), the informativity of the markers, of what is known about the phase of the alleles at the disease locus and the marker locus, and of the value of the recombination fraction between these two loci. If one knows all about the genetic model of the transmission of the disease and its parameters, the greater the power of the method, the easier it is to detect the presence of recombination between the disease locus and a marker locus, in other words, the genotype of each of the two loci, but also the haplotype, i.e. the combination of 2 alleles from each locus on the same chromosome segment are easily identifiable from the phenotype. At the disease locus, the genotype can be deduced unambiguously from the phenotype if there is a rare dominant gene with total penetrance for the heterozygote and zero penetrance for the normal homozygote (no phenocopy). The power diminishes as the degree of dominance and the penetrance decline, and the gene frequency and proportion of phenocopies increase (Ott, 1991). Figure 17 Figure 18 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 330 Genetic Linkage Analysis Clerget-Darpoux F At the marker locus, this power is greater the higher the degree of heterozygotism, or in other words, the more polymorphic the marker. If we consider the two loci together, the amount of knowledge about the haplotype transmitted is greater if there are a large number of generations. Finally, the proximity of the two loci increases the power of detection of the genetic linkage. Multipoint linkage analysis, which uses several reference markers near to each other on a given chromosome segment, increases the power of the method by increasing the informativity of the meioses. In general, it is used to pinpoint the location of a morbid locus once it has been established that genetic linkage is present. III- 1.2. Maximization of the lod score over the [0, 1/2] interval (Ref: Génin E., Ann Hum Genet,1995,59:123-132) However, in practice, the test is never carried out for a single value of θ1, but is done as follows: the lod score is calculated for various values of θ1, the maximum lod score Zmax is calculated and the test is applied to Zmax .A criterion of +3 or even less, is used to conclude that linkage is occurring, based on the argument that risk remains sufficiently small. The probability of the posthoc non linkage is never calculated. The fact of considering an alternative hypothesis by using the maximum lod score, Zmax (which amounts to testing H0: θ = 1/2 versus H1: θ < 1/2) actually reduces the reliability of the test considerably. Thus, the probability ρ that there is no linkage when a Zmax of + 3 has been obtained can be as high as 16.4%; i.e. more than three times the probability calculated by Morton (1955). for a dominant disease in a sample of nuclear families with two children). Reliability =1-ρ. The example of the conflicting results obtained for Alzheimer’s disease is a good illustration of the usefulness of calculating the probability of linkage post hoc. Alzheimer’s disease is a form of dementia characterized by loss of memory and of cognitive function. Only a few families have multiple cases, but within this sub-group of families, the distribution of the patients is compatible with the hypothesis of the intervention of a dominant mutation on an autosomal gene. Analyses of genetic linkage by the method of lod scores were therefore carried out to localize the gene involved. In 1987, a maximum lod score of +2.46 was obtained using a marker of chromosome 21 in a large genealogy with numerous members affected (family FAD4), and this at first led people to conclude that the mutation responsible was located on chromosome 21 (St Georges-Hyslop et coll. 1987). For many years, research into this disease was therefore focused on this chromosome. Five years later however, several different teams provided a very significant demonstration of linkage with chromosome 14 markers. The very high lod scores that were obtained showed that most of the early familial forms were due to a mutation of a chromosome 14 gene 14 (Schellenberg et coll. 1992, St Georges-Hyslop et coll. 1992). In particular, in the case of family FAD4, a lod score of +5.21 was obtained with markers for this region. In view of the observations obtained for chromosome 21 markers in FAD4, the post-hoc probability that there was no linkage was 1/3. It is likely that if this calculation had been done in 1987, the existence of a mutation on chromosome 21 in this family would have looked less convincing. Furthermore, it has now been shown that the gene implicated is located on chromosome 14. III- 1.3 References The table below shows the probability that linkage does not exist as a function of the Zmax obtained. 1. 2. 3. 4. Génin E, Martinez M, Clerget-Darpoux F. Posterior probability of linkage and maximal lod score. Ann Hum Genet 1995; 59: 123-132. Schellenberg GD, Bird T, Wijsman E et al. Genetic linkage evidence for a Familial Alzheimer's disease locus on chromosome 14. Science 1992; 258: 668-671. St Georges-Hyslop PH, Haines J, Rogaev E et al. Genetic evidence for a novel familial Alzheimer's disease locus on chromosome 14. Nature Genet 1992; 2: 330-334. St Georges-Hyslop PH, Tanzi RE, Polinsky RJ et al. The genelic defect causing Alzheimer's disease maps on chromosome 21. Science 1987; 235: 885-890. III-2. Genotype information III-2.1. Ambiguity in phenotype-genotype relationships at the disease locus The original lod score method was applied to the study of nuclear families (the parents and their children), and this made it easy to deduce the genotype at each of the loci for each member of the family. Since it is the Figure 19 The relationship between ρ and Zmax depends on the type of family structure and the determinism of the disease (in this case the calculation has been carried out Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 331 Genetic Linkage Analysis Clerget-Darpoux F are linked by the constraint of the value of the prevalence of the disease within the population. III-2.2. Ambiguity in the marker genotype To calculate a lod score between a disease locus and a marker locus, it is necessary to take into consideration all the possible genotypical configurations at each of the loci and to write the probabilities of these configurations. If some individuals have not been genotyped for the genetic marker, the probability of each possible genotype must be calculated. To do this, is will be necessary to specify the allele frequencies of the marker. Any error in thee allele frequencies, in particular the under-estimation of the frequency of an allele in the patients, artificially increases the values of the lod score and can therefore lead to a false conclusion that there is genetic linkage (false positives) (Ott, 1991 ; Freimer et al, 1993; Knapp et al, 1993). In increasingly frequent use of very extensive genealogies, in which only individuals of the last generation are typed, alls for great caution in interpreting positive results. III-2.3. Gamete disequilibrium between alleles at the disease locus and at the marker locus An association between a susceptibility gene and a marker can lead to bias in the estimation of the recombination fraction. In particular, the "lod scores" method specifies that there must be no selection for the marker in the sample. However, in a context of an association, selection based on the status of the patient implicitly involves selection for a marker. Furthermore, the calculation assumes that the probability for each genetic combination is equal in the parents, and this is not true if there is an association. In the analysis, failing to take into account the disequilibrium existing between disease alleles and marker alleles, induces a very great under-estimation of the "lod score" (in other terms, a marked reduction in the power of the linkage test) and a very slight under-estimation of the recombination fraction (Clerget-Darpoux, 1982). phenotypes that can be observed this means that the phenotype/genotype correspondence was known. In particular, when the analysis was carried out between a "disease" locus and a "marker" locus, the disease was assumed to involve a single gene, due to a rare allele of an autosomal gene, or linked to gender, with complete penetrance (probability of being affected equal to 1 for people carrying one copy of the allele for dominant diseases, of two copies for recessive diseases). Gamete equilibrium was also assumed to exist between the alleles at the "disease" locus and the "marker" locus. The method, the properties of which were fully established on the basis of these hypotheses, has been extended over the past twenty years to more varies and complex situations, but without questioning its underlying properties. In particular, it is applied to diseases of which the determinism is less or even totally unknown, which are studies in large genealogies, of which some of the members have an unknown phenotype. This leads us to investigate the power of the test using various models and its robustness to modeling errors. It should be stressed that the "lod score", which is thought of above all as a function of the recombination fraction and used to estimate this variable, also depends on the value of the genetic parameters at the disease locus, i.e. the frequency of the alleles at this locus and the penetrances (probabilities of being affected) associated with each of these genotypes. We evaluated the effects that an error in these parameters produced in the linkage test and in estimating the recombination fraction (Clerget-Darpoux et coll, 1986,1992,1993). - Loss of power: The power of detecting linkage can be very severely reduced if there is an error concerning the relative penetrance of each of the genotypes: i.e. concerning the ratio of probabilities of being affect in those who carry two copies of the morbid allele, those who have a single copy and those who do not carry it at all, "the phenocopies". - False exclusion of linkage: The robustness of the method to false specifications of the values of the parameters is not symmetrical with regard to the two hypotheses being tested. We have shown that the lod score is always, greatest for the correct values of the parameters and that it can be considerably reduced if these have been wrongly specified. As a consequence, an error in the values of the parameters does not lead to a false conclusion of linkage although it can wrongly lead to the exclusion of linkage. This is particularly the case if the proportion of phenocopies is underestimated. - Bias in the recombination fraction: The estimation of the recombination fraction is very sensitive to any error in the value of any of the parameters. In addition, the effects of the errors on the gene frequency and on the penetrance values are usually additive, because in most studies these parameters Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) III-3. The problem of multiple tests One of the difficulties encountered in the statistical interpretation of the analyses of the genetic linkage of complex diseases arises in fact from the fact that in general and with a varying degree of explicitness, the data are subjected to multiple tests: several clinical classifications, several genetic markers, several models, several samples. It is quite clear that the discontinuation criteria usually used in the lod score test no longer have the same statistical significance when several tests are applied simultaneously to the same sample or to several samples. E. Thompson (1984) has investigated this problem in the case of a disease involving a single gene for which the genetic linkage is tested using several markers located on different chromosomes (and therefore independent). 332 Genetic Linkage Analysis Clerget-Darpoux F The situation is much more complex for multifactorial diseases, because the multiplicity of the tests has several types of impact and these are not independent (Clerget-Darpoux et coll, 1990). Multiple tests could be taken into account by readjusting the discontinuation criterion of the lod scores test. However, on the one hand, it is not always clear from the publications which tests have actually been carried out, and on the other, this can make the test too conservative. This is why we think that the replication strategy should be favored. If a positive result is replicated for a new sample (using the same classification, the same marker, the same transmission model) this provides a reliable threshold of significance. III-4. References 4. Clerget-Darpoux F, Babron M.C., Bonaïti-Pellié C. Assessing the effect of multiple linkage tests in complex diseases. Genet Epidemiol 1990; 7: 245-253. 5. Clerget-Darpoux F, Bonaïti-Pellié C. Strategies based on marker information for the study of human diseases. Ann Hum Genet 1992; 56: 145-153. 6. Clerget-Darpoux F, Bonaïti-Pellié C. An exclusion map covering the whole genome: a new challenge for genetic epidemiologists ? Am J Hum Genet 1993; 52: 442-443 7. Freimer NB, Sandkuijl LA, Blower SM. Incorrect specification of marker allele frequencies : effect on linkage analysis. Am J Hum Genet 1993; 56: 1102-1110. 8. Guihenneuc C, Prum B, Clerget-Darpoux F, Bonaïti-Pellié C. Remarques sur la méthode du lod score en génétique. Pub Inst Stat Univ Paris 1990; 35: 19-37. 9. Knapp M, Seuchter SA, Bauer MP. The effect of misspccifying allele frequencies in incompletely typed families. Genet Epidemiol 1993; 10: 413-418. 1. Chotai J. On the lod score method in linkage analysis. Ann Hum Genet 1984; 48: 359-378. 10. Morton NE. Sequential tests for the detection of linkage. Am J Hum Genet 1955; 7: 277-318. 2. Clerget-Darpoux F. Bias of the estimated recombination fraction and lod score due to an association beween a disease gene and a marker gene. Ann Hum Genet 1982; 46: 363-372. 11. Ott J. Analysis of human genetic linkage, 2nd ed ition. John Hopkins University Press, 1991. 3. 12. Smith CAB. Some comments on the statistical methods used in linkage investigations. Am J Hum Genet 1959; 11: 289-304. Clerget-Darpoux F, Bonaïti-Pellié C, Hochez J. Effects of misspecifying genetic parameters in 1od score analysis. Biometrics 1986; 42: 393-399. 13. Wald A. Sequential analysis. New York: Wiley, 1947 This article should be referenced as such: Clerget-Darpoux F. Genetic Linkage Analysis. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):323-333. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 333 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Educational Items Section Consanguinity Robert Kalmes, Jean-Loup Huret Institut de Recherche sur la Biologie de l'Insecte, IRBI - CNRS - ESA 6035, Av. Monge, F-37200 Tours, France (RK); Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Educ/ConsangID30039ES.html DOI: 10.4267/2042/37916 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology I- Definition II- Coefficient of consanguinity of an individual II- 1.Formulation II- 2.General formula III- Consanguinity of a population IV- Self-fertilization V- Generalization V- 1. Genotype frequencies at equilibrium V- 2. Properties of consanguinity VI- Human population VII- Genetic counselling VIII- Rare alleles - Common alleles VIII-1. Exercice VIII-2. Practical consequences IX- Consanguinity - Heterozygotism - Isogenetic line X- Multiallele system X- 1 Exercice: Consanguinity for a locus and three alleles I- Definition II- Coefficient of consanguinity of an individual A subject is in a situation of consanguinity if, for a given locus, (s)he has two identical alleles, per copy of one and the same ancestor gene. The coefficient of consanguinity (Cc or F) is the probability that the two allele genes that an individual has at a locus are identical by descendance. → This assumes that a common ancestor (A) is shared by the parents, F and M, of the individual, I studied. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) II- 1.Formulation First, look for the common ancestor (or common ancestors) on the genealogical tree. Then, calculate the probabilities; for example: 334 Consanguinity Kalmes R, Huret JL value of F = 1/16, and 1.5% a value of F = 1/32; what is the consanguinity of this population? Answer: α= (2.5 X 1/8) + (2 X 1/16) + (1.5 X 1/32) = 0.484% IV- Self-fertilization This means that each genotype is fertilized exclusively by itself (a situation that is possible in maize (corn), but not in Drosophila, or in Man). In a population of plants, underHW in Go, which is then put in a situation of self-fertilization: Figure 1 A possesses alleles a1 and a2. It transmits to the greatgrandparents GGP: • either identical alleles (a1 and a1 or: a2 and a2) → proba: 1/2 • or different alleles (a1 and a2 or: a2 et a1), but... if A itself exhibits consanguinity (with a coefficient of consanguinity FA), then a1 and a2 have a probability FA of being identical, and A transmits a1 and a2 with a proba 1/2, i.e. FA x 1/2 Overall, A transmits the identity with a proba: 1/2 + 1/2 FA, or: 1/2 (1 + FA) Note: FA can be equal to zero. Each generation i has a proba 1/2 of transmitting this allele to i+1; therefore a proba (1/2)n after n generations; or (1/2)p to go from GGP1 to I and (1/2)m to go from GGP2 to I, if f and m are the number of links linking the father and mother respectively to the common ancestor (here p = m = 3). Therefore: FI = (1/2)p+m+1(1+FA) ... And, if there are several common ancestors (not consanguinous with each other), a sum Σ, addition of the various consanguinities, gives us the: AA Aa aa Go 0.25 0.50 0.25 self-fertilization AA X 1 X1/4 G1 Aa aa aa X1/2 X1/4 0.25 0.125 0.25 AA Aa X1 0.125 0.25 aa etc... What is the frequency Hn of the heterozygotes in generation n? Hn = 1/2 Hn-1 → Hn = (1/2)nHo; tends towards zero. Dn = Dn-1 + 1/4 Hn-1 Rn = Rn-1 + 1/4 Hn-1 → at the equilibrium of self-fertilization: Deq = Do + 1/2 Ho; Heq = 0; Req = Ro + 1/2 Ho Being under HW in Go, Do = p2; Ho = 2pq; Ro = q2 → Deq = p2 + 1/2 2pq = p2 + pq = p (p +q) = p; similarly for Req → II- 2.General formula Genotype frequencies at equilibrium: Deq = p Heq = 0 Req = q FI = Σ(1/2)p+m+1(1+FAi) Note: FA is negligible in man and at the level of the individual, but may not be in Drosophila, particularly in an entire population. Genealogy studies are indispensable for determing consanguinity; see: Genealogy and Coefficient of Consanguinity, Exercices. V- Generalization Genotype III- Consanguinity of a population The mean coefficient of consanguinity is equal to the mean of the various individual coefficients weighted by the frequencies of the various types of crosses between related individuals. To evaluate this, an inventory is compiled for the individuals of the different types of crossings between related individuals, and they are classified on the basis of the value of Fx. EQUATION α = Σ Fifi where fi is the frequency of the subjects with consanguinity Fi. Example: a population in which 6% are consanguin, and among these: 2.5% have a value of F = 1/8; 2% a Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) AA AA Aa aa General case panmixia selffertilization 0 <= F <= 1 F=0 F=1 allozygotism + autozygotism p2(1-F) + pF 2pq(1-F) q2(1-F) + qF p2 2pq q2 p 0 q Thus, any population (and this includes a consanguin population) will behave as though: • one fraction (1-F) was developing in panmixia • one fraction F was developing in self-fertilization F being the mean coefficient of consanguinity of the population. F=0 in panmixia, F=1 in self-fertilization. The genotype frequencies at equilibrium will be: 335 Consanguinity Kalmes R, Huret JL F(AA)eq = p2(1 - F) + pF = p2 - p2F + pF = p2 + Fp (1 - p) = p2 + Fpq; similarly for F(aa); thus: Note: the exact equation q2+ pqCc is replaced by the approximation: q x Cc. This is applicable to human genetics (genetic counselling) if/because q is very small. V- 1. Genotype frequencies at equilibrium EQUATION: F(AA)eq = p2 + Fpq F(Aa)eq = 2pq(1 - F) F(aa)eq = q2 + Fpq Exercice 1: Parents first cousins; for a mutant gene with recessive autosomal transmission with frequency q = 1/100 (example of phenylketonuria, one of the most common recessive autosomal diseases): what is the risk in the general population? What is the risk that I could be affected? Answer: For the general population: q 2 = 1/10 000 For I, it is, according to the equation: q x Cc = 1/100 x 1/16 = 1/1 600 Note: the risk of a recessive autosomal disease in the individual I, relative to the general population, is increased by the factor: q x Cc / q 2 = Cc / q here = 6.25 (or, if we use the accurate equation (q2+ pqCc) / q 2 = 7.19) EQUATION: The risk that a consanguin subject will be homozygotic for the allele a is: F(aa) = q2 + Fpq Another demonstration of the relations F(AA) = p2 + Fpq, F(Aa) = 2pq(1 - F), et F(aa) = q2 + Fpq is given in: Genetic Constitution of Consanguin Populations. Are the allele frequencies altered? F(A) = D + H/2 = p2 + Fpq + 2pq(1 - F)/2 = p2 + Fpq + pq - Fpq = p2 + pq = p(p + q) = p → invariable; therefore: V- 2. Properties of consanguinity Exercice 2: same exercice, but for a frequency q = 1/10 000 of the mutant gene.br Answer: For the general population: q 2 = 1/100 000 000 For I, it is, according to the equation: q x Cc = 1/10 000 x 1/16 = 1/160 000 The risk for individual I relative to the general population, is increased by a factor Cc / q here = 625 or, if we use the accurate equation, q2+ pqCc / q 2 = 626 (the rarer the allele, the better the approximation q x Cc). Consanguinity: • modifies the genotype frequencies. We can see an increase in the frequency of homozygotes and a reduction in that of heterozygotes. • does not modify the allele frequencies VI- Human population It is usual within the human population for there to be several common ancestors (e.g. below: AM and AF male and female ancestors, parents of GP 1 and 2). In practice, the equation is simplified to: EQUATION CcI = Σ(1/2)p+m+1 Example: Parents first cousins: p=2; m=2; Σ is the sum of 2 terms, since there are 2 possibilities of having identical alleles: via AM and via AF (i.e. 2 common ancestors); so, Answer: Fi = (1/2)2+2+1 + (1/2)2+2+1 = 1/16 VIII- Rare alleles-Common alleles VIII-1. Exercice Consider a gene A of which the recessive allele a has a freqency F(a) = q = 0.5 and a gene B of which the recessive allele b has a freqency F(b) = q = 0.0001, a fairly usual frequency for a morbid allele, calculate the frequency/risk of being recessive homozygote(s) for each of these two genes 1. according to Hardy-Weinberg (HW) 2. for a consanguin child whose parents are firstcousins 3. compare Answer: 1. According to HW: • F(aa) = q2 = (0.5)2 = 0.25 • F(bb) = q2 = (0.0001)2 = (10-4)2 = 10-8 2. for a consanguin child whose parents are firstcousins: • Σ(1/2)p+m+1= (1/2)5 + (1/2)5 = (1/2)4 = 0.0625 • F(aa) = q2 + Fpq = (0.5)2 + 0.0625 X 0.5 X 0.5 = 0.2656 Figure 2 VII- Genetic counselling For a deleterious mutant recessive autosomal allele (rare by definition) with a frequency q, the risk that a consanguin child will be homozygotic for this allele is: q x Cc whereas it is q2 for the children of nonconsanguin parents. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 336 Consanguinity Kalmes R, Huret JL • F(bb) = q2 + Fpq = (10-4)2 + 0.0625 X 1 X 10-4 = (1 + 625)10-8 = 626 X 10-8 3. comparison: the increase in the frequency (risk) of homozygotism due to the consanguinity will be F(consang.)/F(under HW), i.e.: • for the common allele: 0.26256 / 0.25 = 1.06, slight increase • for the rare morbid allele: 626 X 10-8/10-8 = 626 !!! A sample of 400 individuals is examined. The numbers of the various genotypes are as follows. A1A1 32 1. 2. VIII-2. Practical consequences 4. A2A2 57 A2A3 90 A3A3 125 Answer: 1. The allele frequencies are estimated by counting the alleles. Thus, for allele A1 for example: frequency of A1 = ((2 x 32) + 36 + 60) / (2 x 400) = 0.20 = p similarly: frequency of A2= 0.30 = q; frequency of A3 = 0.50 = r 2. The proportions of panmixia are in fact those indicated by the Hardy-Weinberg law. a. Theoretical frequencies of the genotypes according to the Hardy-Weinberg law IX- Consanguinity - Heterozygotism Isogenetic line In the human species, the percentage of heterozygotic loci, calculated from enzymatic polymorphism, has a value H = 0.067. We can take it that there are 30000 structural genes and in consequence 2010 genes in the heterozygotic state in the human genome (30000 x 0.067 = 2010). If an individual results from an uncle-niece cross: this individual will be more "homogenous" than his or her parents, because of the increased consanguinity, the percentage of his/her hetero-zygotic genes falls from 2010 to 1759 genes (2010 x 7/8) since Fi = 1/8 (1/8 of genes are identical as a result of consanguinity). Consequences: If regular consanguin crosses are made (for example brother/sister crosses in mice), at each generation: → Fi tends towards a value of 1, → the individuals will become totally homozygotic. Within each familly, all the individuals will be identical in the genetic sense of the word. Exactly the same genome. Exactly the same genes. This leads to the concept of the isogenetic line. A1A1: p2 = 0.202 A1A2: 2 pq = 2 x 0.20 x 0.30 A2A2: q2 = 0.302 A1A3: 2 pr = 2 x 0.20 x 0.50 A3A3: r2 = 0.502 A2A3: 2 qr = 2 x 0.30 x 0.50 with p, q, r: the respective frequencies of the alleles A1, A2 and A3. b. Theoretical numbers A1A1: A2A2: A3A3: c. 0.202 x 400 =16 36 100 A1A2: A1A3: A2A3: 48 80 100 Comparison of the theoretical numbers and the actual numbers found by a chi-squared test of conformity χ2 = (32 - 16)2/16 + .....+ (125 - 120)2/100 = 50 dd1 = 6 - 2 - 1 = 3; to a 5% threshold, [[chi]]2 calculated is greater than the value given in the table (7.815) and is therefore highly significant. Consequently the proportions of the genotypes do not comply with those of the Hardy-Weinberg law, the hypothesis of panmixia can be rejected. 3. Consanguinity has the effect of increasing the frequency of homozygotes and of reducing that of heterozygotes, relative to the proportions given by the Hardy-Weinberg law. This is indeed what we find. Consequently, consanguinity can account for X- Multiallele system The genotype frequencies at equilibrium for every AiAi homozygote and every AiAj: heterozygote will be: F(AiAi) = pi2(1 - F) + piF F(AiAj) = 2pipj(1 - F) X- 1 Exercice: Consanguinity for a locus and three alleles In a population of a diploid species with separate sexes and separate generations, we are dealing with a triallele autosomal locus (three possible allele states: A1, A2 and A3). Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) A1A3 60 Estimate the allele frequencies. Can we assume that we have the proportions of panmixia in the sample? Knowing that there is no selection, no mutation, no migration, no drift (large population), can consanguinity account for the difference? What are the theoretical proportions of the various genotypes, knowing that the mean coefficient of consanguinity is F? Estimate the value of F from the proportions of the sample. 3. In other words, the increase is: (q2 + Fpq)/q2 = 1 + Fp/q • when p = q: → = 1 + F ≅ 1 • when q is rare, p ≅ 1 → = 1 + F/q ≅ F/q, with Fmax = 0.25 (incest), F is often of the order of 1 to 5 X 10-2 and q = 10-3 or 10-4, therefore a risk increased by a factor of 10 to 103, which is generally the case for recessive diseases. Isolates, with a high level of consanguinity, allow unusual diseases to emerge. A1A2 36 337 Consanguinity Kalmes R, Huret JL the significant differences between the previous theroretical and actual numbers. For the whole population, the theoretical genotype frequencies are: This article should be referenced as such: Kalmes R, Huret JL. Consanguinity. Atlas Cytogenet Oncol Haematol. 2002; 6(4):334-338. A1A1: (1- F) p2 + Fp A1A2: 2 pq (1 - F) A2A2: (1 - F) q2 + Fq A1A3: 2 pr (1 - F) A3A3: (1 - F) r2 + Fr A2A3: 2 qr (1 - F) 4. The frequency of A1A2 can be used simply to calculate F: frequency of A1A2 = 2 pq (1 - F) 36/400 = 2 x 0.20 x 0.30 (1 - F) therefore: 1 - F = 0.75 F = 0.25 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 338 Genet Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Educational Items Section Genealogy and Exercices Coefficient of Consanguinity, Robert Kalmes Institut de Recherche sur la Biologie de l'Insecte, IRBI - CNRS - ESA 6035, Av. Monge, F-37200 Tours, France (RK) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Educ/ConsangGenealEng.html DOI: 10.4267/2042/37915 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology This genealogy indicated by arrows is based on the fact that every arrow starts at the ancestor and leads to the offspring. In general, each individual is crossed by two arrows. If only one parents is shared, then only one arrow is shown in the genealogy. GENEALOGY Establishing the genealogy of an individual X, consists of identifying the individuals who share part of their genetic inheritance with X, because they are ancestors, collaterals or descendants (collaterals: brothers, halfbrothers, cousins, uncles, nephews, etc ....). Representation: there are several ways of representating genealogies, in addition to the usual method used in human genetics, and these may be more convenient when one is studying Drosophila for example (see below). COEFFICIENT OF CONSANGUINITY To calculate Fx, what we have to do is: - Identify the parents of X (father and mother). - Identify all the individuals in the genealogical tree that are common ancestors of the father and mother of X and who are the only individuals who can have transmitted two identical alleles to X. - An individual will be considered to be a common ancestor if, starting from one of the two parents of X are going back up the hereditary path from the supposed common ancestor, it is then possible to come back down again to the second parent of X without breaking the sequential line of parenthood. - In fact, each sequential line of parenthood describes the Mendelian transmission of genes, and this means that it can never pass more than once through the same individual, nor change direction anywhere except in the only common ancestor that it contains. - Two lines of parenthood are different if the ordered sequences of the individuals that compose them differ, even if in only one place. - Several different lines of parenthood can pass through the same common ancestor. Figure 1 A and B are the parents of E and F, who are in turn the parents of H. C and D are the parents of G. C and his/her offspring, G, are the parents of I, who, mated with H, gives X. Figure 2 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 339 Genealogy and Coefficient of Consanguinity, Exercices Kalmes R Individual B : Descendant of a cross between half-siblings, Only one line of parenthood. Example 1: Brother - sister cross Figure 6 Figure 3 Individual C: Descendant of an uncle — niece cross, 2 lines of parenthood. FC = 1/8 The parents of X (father and mother) are P and M. A is a shared ancestor since P ---- A ---- M. P-A-M is a line of parenthood with two links of parenthood. Here p + m = 2. B is also a shared ancestor, since P ---- B ---- M. P-BM is a line of parenthood with two parenthood links. Here p + m = 2. Therefore, FX = _ (1/2 ) p+m+1 (1 + F Common ancestor) gives here: FX = ((1/2 ) 3 (1 + FA )) + ((1/2 ) 3 (1 + FB )) Note: If, in a genealogy, it is not possible to find out whether a common ancestor is also consanguine, by convention it is assumed that (s)he is not. This is applied to A and B, and so, FA = 0 and FB = 0 → FX = (1/2 ) 3 + (1/2 ) 3 = 2 (1/2 ) 3 = 1/4 Some examples: Calculation of the coefficients of consanguinity of individuals derived from various types of crosses (the common ancestors are not related to each other). Figure 7 Individual D: Descendant of a cross between first cousins 2 lines of parenthood FD = 1/16 Figure 8 Individual E: Descendant of a cross of cousins derived from first cousins, 2 lines of parenthood. FE = 1/64 Figure 4 Individual A: Line of parenthood Descendant of a brother—sister cross, 2 lines of parenthood. FA = 1/4 Figure 9 This article should be referenced as such: Kalmes R. Genealogy and Coefficient of Consanguinity, Exercices. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):339-340. Figure 5 Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 340 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Educational Items Section Genetic Constitution of Consanguine Populations Robert Kalmes, Jean-Loup Huret Institut de Recherche sur la Biologie de l'Insecte, IRBI - CNRS - ESA 6035, Av. Monge, F-37200 Tours, France (RK); Genetics, Dept Medical Information, UMR 8125 CNRS, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France (JLH) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Educ/ConsangPopuEng.html DOI: 10.4267/2042/37917 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Let us consider the case of a diallele gene, A1 and A2, with a frequency of p and q in the parents. Knowing that the children’s consanguinity is equal to F, if a child is selected at random, what is the probability that (s)he will be A1A1? The two copies of gene A in this child may be: The same by inheritance, an event with a probability of F. - or not be the same by inheritance, an event with a probability of (1 - F) In the first case, the probability that the first copy of gene A will be A1, is equal to p, the frequency of A, in the parents, and the probability that the second copy will also be A1, is equal to 1, as both copies of the gene are the same by inheritance. If the first one is A1, then the second will also be A1. In the second case, the probability that the first copy of gene A will be A1 is equal to p, the frequency of A1 in the parents, and the probability that the second copy will also be A1 is still equal to p, because we are in a situation in which the two copies of the gene are not "the same by inheritance": if the first is A1, the second is not automatically A1: it will only be A1 if it is selected again, with a probability p. Hence the frequency of the genotypes A1A1 in the children: frequency(A1A1) = Fp +(1-F)p2 The same logic, with A2 and q replacing A1 and p, gives us the expected frequency of the A2A2 genotype in the children: frequency(A2A2) = Fq + (1-F)q2 What is the frequency that a randomly selected child will be an A1A2 heterozygote? Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) The two copies of the gene A, present in this child may be: the same by inheritance, an event with a probability of F; or not be the same by inheritance, the opposite event, with a probability of (1-F). In the first case, the probability that the first copy of gene A, A1, is equal to p, the frequency of A1 in the parents, but the probability that the second copy will be A2 is equal to 0, because we are in a situation in which both copies of the gene are "the same by inheritance"; if the first is A1, then the second is A1 too. In the second case, the probability that the first copy of gene A is A1 is equal to p, the frequency of A1 in the parents, and the probability that the second copy will be A2 is equal to q, because here we are in a situation in which both copies of the gene are not "the same by inheritance": although it would also be possible for the first to be A2 and the second A1, again with a probability pq. Hence the frequency of the A1A2 genotypes in the children: frequency(A1A2) = (1-F)2pq These genotype frequencies are, after being developed and factorized: frequency(A1A1) = p2+ Fp(1-p) = p2+Fpq frequency(A1A2) = 2 pq(1 - F) frequency(A2A2) = q2 + Fq(1 - q) = q2 + Fpq This article should be referenced as such: Kalmes R, Huret JL. Genetic Constitution of Consanguine Populations. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):341. 341 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Educational Items Section Prenatal Diagnosis Louis Dallaire Centre de Recherche, Hôpital Ste-Justine, Montréal, H3T 1C5, Canada (LD) Published in Atlas Database: June 2002 Online updated version: http://AtlasGeneticsOncology.org/Educ/PrenatID30055ES.html DOI: 10.4267/2042/37918 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2002 Atlas of Genetics and Cytogenetics in Oncology and Haematology Introduction I- Families at risk I- 1. Advanced maternal age I- 2. Recurrence of numerical and structural chromosomal anomalies I- 3. Fragile X syndrome and mental retardation I- 4. Chromosomal instability I- 5. Hereditary metabolic diseases I- 6. Neural tube defects II- Foetal Ultrasonography II- 1. Ultrasonography II- 2. Cardiac ultrasonography II- 3. Markers suggesting the presence of a birth defect II- 4. Foetal defects detected by ultrasound during the second trimester of pregnancy II- 4.1. Nervous system anomalies II- 4.2. Cardiovascular defects II- 4.3. Thoracic anomalies II- 4.4. Gastro intestinal malformations II- 4.5. Urogenital malformations II- 4.6. Musculo skeletal malformations II- 4.7. Other anomalies III- Techniques to obtain foetal tissues III- 1. Amniocentesis III- 2. Chorionic villus sampling (CVS) III- 3. Cordocentesis III- 4. Foetoscopy III- 5. Fetal cells in maternal circulation IV- Congenital anomalies due to single gene defects V- Maternal serum markers V- 1. Neural tube defects V- 2. Trisomy 21 or Down syndrome VI- Fluorescence in situ hybridization (FISH) VII- Future perspectives VII- 1. In utero treatment VII- 2. Preimplantation diagnosis VII- 3. Preconception screening Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 342 Prenatal Diagnosis Dallaire L couples at risk to envisage a pregnancy since an alternative is now offered to them. Introduction Prenatal diagnosis answers the need to detect early in pregnancy a number of foetal anomalies and genetic diseases. The prenatal diagnosis of genetic diseases has become widely available for pregnancies at risk in the last three decades. In 1976 results of three multicentric studies, realized in America and Europe, confirmed that the tests performed on amniotic fluid cells (amniocytes) were reliable and that the amniocentesis done during the second trimester was a low risk procedure both for the mother and her foetus. Approximately 3% of viable foetuses would be born with a severe anomaly. We now feel the impact of prenatal diagnosis on the incidence of severe defects at birth since a number of them will be diagnosed as early as the end of the first trimester. If a woman is known to be at risk to conceive a child with a genetic disease a prenatal diagnosis could be indicated. Knowing the nature of the anomaly to be detected, this diagnosis can be realized in ultrasonography, with or without the study of amniotic fluid cells or other foetal tissues. Before any intervention or use of an invasive procedure is attempted, the sine qua non rule of prenatal diagnosis is to make sure that the genetic disease, likely to be present, is detectable and that there is a possibility to show or exclude this defect by testing the foetal tissues. Prenatal diagnosis allows I- Families at risk I- 1. Advanced maternal age Women who are 35 or more at delivery have a higher risk of giving birth to an infant with a chromosomal defect due to a non disjunction. This increased risk is due in part to ovum aging. This risk increases with age (fig1) and frequently involves a trisomy 21 (Down syndrome) that is the most frequent autosomal anomaly. Trisomies 13 and 18 and sex chromosome defects, XXY and XXX are frequently observed in children born to mothers in this age group. Among countries where prenatal diagnosis is available selection criteria for the availability of prenatal diagnosis is variable and amniocentesis will generally be offered to pregnant women aged 35 or more at the time of delivery. The availability of preventive medical measures for pregnant women may include a screening test for trisomy 21 by testing for maternal serum markers ( see serological markers). This screening test, to some extent, may allow the identification of women more at risk of bearing a trisomic child and, if the test was negative, reassure those who would elect not to have an amniocentesis. Figure 1 - Maternal age and incidence of trisomy 21 at birth. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 343 Prenatal Diagnosis Dallaire L Familial chromosomal translocation: one of the parents is carrier of a balanced chromosomal translocation and according to: 1- the type of translocation, 2-the importance of the segments involved, 3- the segregation of chromosomes in meiosis, there is variable risk frequency: - of spontaneous miscarriage due to a major imbalance of the chromosomal complement - to give birth to an affected infant with a viable chromosomal defect - that the foetus be a normal carrier like one of his parents - and the foetus may have a normal karyotype. When an individual is found to have a structural aberration the rule is to obtain the karyotype of his parents and if necessary of the siblings: first to find the origin of the defect and second to inform family members of the reproduction risk if themselves are normal physically but carriers of a translocation (fig 2). I- 2. Recurrence of numerical and structural chromosomal anomalies All chromosomal defects (see also: Chromosomes abnormalities ) resulting from a division error, or non disjunction, can reoccur in more than 1% of cases in a subsequent pregnancy and this risk can be very high for a woman in the 30 years or less age group. At the age of 20 the risk of trisomy 21 is approximately 1/2000, 1/1200 at 25, 1/900 at 30, 1/400 at 35, 1/100 at 40 and 1/40 at 45 years of age. This phenomenon also implies that the aneuploidy can involve chromosomes other than the one diagnosed initially. For instance a woman who had conceived a child with a trisomy 21 could, in a subsequent pregnancy, bear a child with a trisomy 13 or 18, or even a sex chromosome anomaly XXX or XXY. It is also possible that a trisomy involving other autosomes be non viable and result in an early miscarriage. Figure 2 - Partial family tree of a translocation 4;18. (>60) at the Xq27.3 locus. If a child is affected, his mother can be a carrier (we then speak of pre-mutation) Of the syndrome and she is expected to have an amplification of triplet CGG in the range of 60 to 200. The amplification inhibits the expression of gene FMR1. Individuals of both sexes can be affected but males are generally more severely affected. If there is a positive family history of X linked mental retardation a molecular study may allow the detection We also suggest to karyotype couples who have a personal or familial history of repeated foetal losses or birth of children with mental retardation with or without malformations or dysmorphism. Individuals with a Fragile X syndrome (see also: Dysgonosomies and related syndromes) have a peculiar facies and mental retardation of variable severity. The chromosomal study reveals a reduced density of the chromatin in region Xq28. The genetic defect was identified as an abnormal CGG triplet amplification Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 344 Prenatal Diagnosis Dallaire L of a Fra X syndrome and if indicated a prenatal diagnosis could be offered. during the first 4 weeks of embryogenesis. The intake of folic acid as soon as a pregnancy is planned, and for the first two months has reduced the incidence and recurrence of the neural tube defects. It is highly recommended when there is a family history of neural tube defect to monitor a pregnancy in ultrasonography to make sure that both foetal cranium and rachis are normal. In families at risk it is very important to encourage the intake of folic acid as soon as a woman plans a pregnancy or cease all means of contraception. Spina bifida aperta: opening of the tissues over the bone defect with or without extrusion of the meninges; it is occulta if the skin is normal. Anencephaly: closure defect of the cranial vault. The skull defect may be limited to a region of the cranium and be variable in size; we then refer to an encephalocele Open lesions of the neural tube and cranium induce an elevation of alpha-foetoproteins in amniotic fluid and subsequently in maternal serum. If there is a history of previous or familial microcephaly a family study will help determining if this is a hereditary defect: autosomal dominant or recessive. Ultrasound examinations of the developing foetus may facilitate the follow up of the head biparietal diameter and circumference, but only severe growth deficiencies will likely be detected. I- 4. Chromosomal instability Some syndromes, called chromosome instability syndromes manifest an unstable chromosomal structure. We cite here as exemples Fanconi disease characterized by anemia, growth delay, skeletal anomalies and Bloom syndrome characterized by anemia, dwarfism and light hypersensitivity. Both have increased chromosomal breakages and affected individuals are predisposed to cancer. These diseases have an autosomal recessive mode of inheritance and the recurrence risk is 25 % after the birth of an affected child. Chromosomal exchanges are frequent in Fanconi disease while sister chromatin exchanges are observed in Bloom syndrome. Using appropriate techniques for the culture of foetal cells and special staining techniques for the chromosomes, these syndromes can be diagnosed prenatally when the parents have been shown to be heterozygous or normal carriers. However the demonstration of specific mutations in those rare diseases is not always feasible. If a prenatal diagnosis is requested one can count on the molecular study of foetal cells only if parental mutations have been identified prior to the procedure. I- 5. Hereditary metabolic diseases a. Metabolic disease diagnosed in a child and finding of an enzyme deficiency or a mutation that could be detected in a subsequent pregnancy. b. Known metabolic disease: the study of the parents show that they are both carriers (heterozygous) and that they have a 25% risk of conceiving an affected child like in cystic fibrosis. Due to the high gene frequency of this disease screening programs to detect carriers are now being offered in some high risk populations. II- Foetal Ultrasonography I- 6. Neural tube defects Cardiac ultrasonography, that allows examination of great vessels and heart chambers, is done usually around the 20th week of pregnancy. II- 1. Ultrasonography Ultrasonography (Fig 3) makes use of ultrasounds to study tissues and organs. It is applied from the first trimester but it is only during the second trimester that one can best evaluate foetal morphology and preferably around the 18th week of gestation. II- 2. Cardiac ultrasonography Neural tube defects have a multifactorial etiology and their incidence is widely variable. They used to be more frequent in the British Isles, Canada, China and other countries like Hungaria with an incidence of 5/1000 births and a recurrence risk of 5%. In France and United States the incidence was more like 1/1000 with a low recurrence risk. It has been shown, first in Great Britain, that the intake of folic acid may help the closure of the neural tube and lower the recurrence frequency in high risk pregnancies. Closure of the neural tube takes place Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) II- 3. Markers suggesting the presence of a birth defect Ultrasonographic markers are variations observed during the ultrasound session that will alert the examiner to the possibility of an abnormal foetal development or a genetic disease. 345 Prenatal Diagnosis Dallaire L Figure 3 - Fœtal ultrasound at 16 weeks of gestationThose markers can reveal for example the possibility of a chromosomal anomaly such as a trisomy 21, 13, 18, or a chondrodysplasia. II- 4. Foetal defects detected by ultrasound during the second trimester of pregnancy ULTRASOUND MARKERS SUGGESTING THE PRESENCE OF A FOETAL ANOMALY • Abdominal calcifications (meconial peritonitis) • Bladder hypertrophy (urethral valve) • Bone hypodensity (hypophosphatasia) • Cerebral ventricles increased (hydrocephaly) • Cono-truncal defect or defect of the heart common trunk, manifested as a tetralogy of Fallot or a vascular defect (Di George, and velo-cardio-facial syndromes secondary to a deletion - del 22q11-) • Cranial vault ossification defect (anencephaly) • Cystic hygroma (Turner syndrome, 45X) • Double buble in the gastric region (duodenal atresia) • Endocardial cushion defect, or of the primary cardiac septum, described as an atrium septal defect (trisomy 21) • Facial hypoplasia and cleft lip ( trisomy 13 holoprosencephaly) • Fractures (osteogenesis imperfecta) • Increased number of choroidal cysts ( trisomy) • Increased volume of cerebral ventricles (hydrocephaly) • Lemon sign, lemon shape head (spina bifida) • Long bones shortening (bone dysplasia) • Nucal skin folds increased (trisomy 21) • Persistant flexed fingers (trisomy 18 arthrogryposis) • Polydactyly (trisomy 13; Ellis Van-Creveld syndrome) • Pterygium colli (Turner syndrome; pterygium multiple) • Stomach unseen (oesophageal atresia) • Thoracic deformity (skeletal dysplasia) Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) II- 4.1 Nervous system anomalies • Anencephaly • Cyst of the posterior fossa • Encephalocele • Facial dysplasia • Holoprosencephaly (cerebral ventricle and facial anomalies) • Hydrocephaly • Microcephaly • Myelomeningocele • Porencephaly ( cystic lesions of the brain) • Rachischisis (significant vertebral closure defect) • Spina-bifida II- 4.2 Cardiovascular defects • Arythmia • Pericardial fluid collection • Septal defect • Situs inversus • Valvular defect • Vascular anomalies • Ventricular hyperplasia • Ventricular hypoplasia II- 4.3 Thoracic anomalies • Atresia of the oesophagus • Diaphragmatic hernia • Pleural effusion • Intrathoracic cysts II- 4.4 Gastro intestinal malformations • Absence of abdominal muscles • Ascites • Cystic lymphangioma 346 Prenatal Diagnosis Dallaire L • Diaphragmatic hernia • Intestinal atresia • Laparoschisis (para-umbilical extrusion of abdominal viscerae) • Mesenteric cyst • Omphalocele (umbilical hernia of abdominal viscerae) • Umbilical cord tumor (chorioangioma) II- 4.5 Urogenital malformations • Hydronephrosis • Hydroureter • Polycystic kidneys • Renal agenesis • Teratoma • Urethral valve II- 4.6 Musculo skeletal malformations • Arthrogryposis • Bone dysplasias • Club foot • Fractures • Limb palsy • Limb reduction defect • Mineralization defect • Pterygium colli • Pterygium multiple II- 4.7 Other anomalies • Acardiac monster • Amniotic band • Cystic lesions • Siamese twins • Teratomas • Tumors diagnostic clinics perform amniocenteses between the 14th and 16th week of pregnancy. Studies have shown an increased loss of amniotic fluid if the amniocentesis done before the 12th week and there is a risk of skeletal anomalies in particular of club feet secondary to oligoamnios. According to the age of pregnancy from 10 to 30 ml of fluid are obtained during the procedure ( fig 5). Foetal cells from the upper digestive system, urinary tract, skin and membranes are found in the fluid and recuperated by centrifugation of the specimen. They are then kept in culture for a period of 5 to10 days in a culture medium to which calf serum has been added. Cellular multiplication is then sufficient and allows the preparation of microscopic slides allowing the numerical and structural studies of the metaphasic chromosomes. Treatment of chromosomes during the slide preparation reveals segments of different intensity or banding patterns. Those bands reflect a variable ratio of AT;GC nucleotides on the chromatids and help to identify chromosome pairs. III- 2. Chorionic villus sampling (CVS) The biopsy or aspiration of chorionic villi by the vaginal route (fig 6) yields foetal cells, several of which are in the process of dividing and can be analysed during the hours following the procedure. There is a risk of miscarriage and maternal cell contamination of the specimen thus leading a number of clinicians to abandon this procedure done before the 12th week of pregnancy. Reduction limb defects have been reported if the CVS is done towards the end of the first trimester. In special circumstances when the risk of genetic disease is high as for instance in hereditary metabolic diseases or if one of the parents is carrier of a balanced chromosomal translocation, this technique has the advantage of reaching a diagnosis around the 11th or 12th week of gestation. III- Techniques to obtain foetal tissues III- 1. Amniocentesis The amniocentesis (fig 4) is early if done around the 12th week of gestation. Today several prenatal Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 347 Prenatal Diagnosis Dallaire L Figure 4 - Illustration of the amniocentesis procedure . Figure 5 - Illustration of the chorionic villus sampling procedure.III- 3. Cordocentesis introducing a tube with optic fibres through the abdomen and the uterus allowing to biopsy the foetus or proceed to surgical interventions. For security reasons this invasive technique is not a routine procedure and is rarely utilized except in development programs. Blood can be obtained from the foetal cord under ultrasound guidance. If at the end of second trimester there is an urgent need to confirm a diagnosis or to avoid extraordinary measures if there is there is a threat of premature labor and the foetus is found to be abnormal This procedure will allow a short term chromosomal analysis from lymphocytes or an enzyme study. The rapid cytogenetic study could also confirm or exclude a chromosomal defect previously found in the amniocytes. This approach can also be useful to delineate mosaicism like for instance a trisomy 20 which usually has a favourable outcome or identify a chromosomal marker confined to annexial tissues. Cordocentesis has been used to study severe immunological disorders by measuring adenosine deaminase and doing T cells analysis. III- 5. Fetal cells in maternal circulation The presence of foetal cells in the maternal blood stream could give us some information of the chromosomal complement and the foetal genotype. Research in this direction has been initiated several years ago but up to date has yielded meagre results on the efficacy of this non invasive procedure. Several difficulties are encountered: the low frequency of nucleated cells mean to isolate them, their identification and genetic analysis. The venue of FISH technique and other means to identify abnormal chromosomal complements, and the PCR (polymerase chain reaction) for molecular analysis have recently convince III- 4. Foetoscopy Foetoscopy is a technique that allows to visualize the foetus around the end of the second trimester, by Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) 348 Prenatal Diagnosis Dallaire L researchers not to abandon this avenue which could be a great asset to the prenatal diagnosis of genetic disease. VI- Fluorescence in situ hybridization (FISH) Fluorescense in situ hybridization makes use of molecular probes marked in fluorescence that correspond to a gene or DNA sequence and showing a bright signal under UV microscope at a specific locus on a chromosome. First the FISH technique can apply to interphasic cells readily obtained at amniocentesis and confirm the presence of an euploid or aneuploid complement like for chromosomes X, Y, 13, 15, 18, 21. This technique also applies to chromosomal markers that can be detected in amniocytes with the help of FISH. The technique can also be used to identify the origin of supernumerary segments or confirm the loss of specific sequences or a deletion on a given chromosome. IV- Congenital anomalies due to single gene defects Several congenital malformations have a hereditary origin and their mode of transmission can be autosomal dominant, recessive or X linked. Some syndromes could be identified during the second trimester of pregnancy if a major anomaly is detected at ultrasound ( like bone dysplasias). However if there is a history of congenital anomaly of unknown etiology but seen in a previous pregnancy, the mother could be reassured at ultrasound if she is pregnant again. This measure applies for instance in cases of omphalocele and laparoschisis for which the risk of recurrence is low. V- Maternal serum markers Serological markers are normal proteins found in the maternal circulation and if their level is abnormal it will allow the detection of some foetal pathologies early in pregnancy. The screening efficacy is increased if both procedures foetal ultrasonography and marker studies are completed simultaneously. V- 1. Neural tube defects Alpha-1 foetoprotein (AFP) constitute 20% of circulating foetal proteins and its level varies with foetal age at the time it is measured (fig 6). An increase of AFP in the amniotic fluid will reflect on the maternal serum level and may alert to the presence of an open neural tube defect. A higher than normal level in the amniotic fluid may be due to a skin lesion unseen at ultrasound or may be due to foetal demise. Figure 6 - Amniotic fluid AFP values during the second trimester. V- 2. Trisomy 21 or Down syndrome VII- Future perspectives AFP may also lead to suspecting a foetal trisomy 21 if the maternal level is low according to the maternal age around the 16th week of pregnancy. A triple test is the combination of three maternal serum markers: human chorionic gonagotrophin (hCG), oestriol (uE3) and AFP. The measure of these proteins at a given maternal and gestational ages, may give an approximate risk figure that the foetus is trisomic (21). The sensibility of this test is 60% and more based on criteria used for the evaluation. An early screening procedure based on the nucal translucensy, hCG and a placental protein PAPP-A, is available in some clinics from the end of the first trimester to the 13th week of pregnancy. Nucal translucency corresponds to the nucal tissue thickness. A measure over 3 mm is considered suspicious at 12 weeks of pregnancy. This screening procedure has a 80% sensibility for trisomy 21 and can suggest the presence of other pathologies. An abnormal result will be validated by a chromosomal study. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) VII- 1. In utero treatment The in utero treatment is limited to fluid aspiration for instance in bladder hypertrophy secondary to an urethral valve, and in some thoracic or abdominal fluid collections. Other surgical procedures have been completed like the insertion of a catheter in the bladder, correction of certain heart defects, to name the most common. The finding of an abdominal wall defect (ex: omphalocele) allows time for planning the mode of delivery and alert neonate specialists and pediatric surgeons to an immediate intervention at birth to prevent systemic complications. As part of indications for medical fœtal therapy, fœtal arythmia can be corrected via a maternal medication approach. Finally a restrictive phenyl-alanine diet, prescribed as soon as a phenyl-cetonuric woman plans a pregnancy, will prevent foetal complications and 349 Prenatal Diagnosis Dallaire L especially a microcephaly and severe mental retardation in the child. The prenatal diagnosis of some metabolic diseases like galactosemia or leucinosis will allow to plan ahead if the foetus is sick and prescribe restrictive metabolic milk for the infant to prevent early complications secondary to abnormal metabolites. For X linked diseases fœtal sexing is recommended before proceeding to a molecular diagnosis. VII- 3. Preconception screening Preconception screening is a recent avenue in the field of prevention. It implies the detection of gamete anomalies and more specifically at the ovum level. Recent publications refer to preconception diagnosis by studying the first polar body in maturing ova: polar bodies reflect the chromosomal complement and genotype of the ovum that could be used in the in vitro fertilization. In a recent literature report, a normal ovum was selected from a mother known as a carrier of a dominant gene for a severe form of Alzheimer disease. It was reported that this ovum free of mutation was used for the in vitro fertilization and a normal infant was carried to term. The route is then traced for diagnostic interventions based on gamete studies, but ethic dilemmas will surge from any attempt to manipulate germinal cells. VII- 2. Preimplantation diagnosis Preimplantation diagnosis is defined as the analysis of a cell taken from a fertilized egg at, for instance, the eight cell stage. It was introduced as an assisted procreation technique in 1989 but it still considered a research and development procedure. We do not know yet if it is a secure and reliable procedure although to date but according to literature reports a few dozens infants born after this technique seem to have a normal development. A limited number of laboratories in Europe and America have the facilities and the knowledge to offer this test as a diagnostic procedure. To date this technique has been attempted in more than one hundred pregnancies at risk and especially in mucoviscidosis, Duchenne muscular dystrophy, hemophilia A, alpha and beta thalassemia, bulbar atrophy, Lesch Nyhan syndrome, incontinentia pigmenti, Huntington disease, myotonic dystrophy. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4) This article should be referenced as such: Dallaire L. Prenatal Diagnosis. Atlas Genet Cytogenet Oncol Haematol. 2002; 6(4):342-350. 350 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Instructions to Authors Manuscripts submitted to the Atlas must be submitted solely to the Atlas. Iconography is most welcome: there is no space restriction. The Atlas publishes "cards", "deep insights", "case reports", and "educational items". Cards are structured review articles. Detailed instructions for these structured reviews can be found at: http://AtlasGeneticsOncology.org/Forms/Gene_Form.html for reviews on genes, http://AtlasGeneticsOncology.org/Forms/Leukaemia_Form.html for reviews on leukaemias, http://AtlasGeneticsOncology.org/Forms/SolidTumour_Form.html for reviews on solid tumours, http://AtlasGeneticsOncology.org/Forms/CancerProne_Form.html for reviews on cancer-prone diseases. 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