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Genetic risk in sarcoma
INTERNATIONAL SARCOMA
KINDRED STUDY
ISKS ISKS
Global
PARTICIPANT
Local Study Centres
INDIA
FRANCE
USA
Tata Memorial
Hosp
Centre Claude
Berard
Huntsman
Cancer Inst
UK
CANADA
Marsden & UCLH
Vancouver Hosp
Biospecimens
Laboratory
Database
Biospecimens
Laboratory
Database
Biospecimens
Laboratory
Database
Biospecimens
Laboratory
Database
Biospecimens
Laboratory
Database
Global Study Centre
CENTRAL
Biospecimens
Laboratory
Database
ISKS GLOBAL STEERING
COMMITTEE
NZ
Christchurch
Hosp
APPROVED PROJECTS
AUSTRALIA
PeterMac
Royal Prince Alfred
Prince of Wales
Princess Alexandra
Wesley
Royal Adelaide
Hollywood Private
ISKS families

645 families
207 no family history, 51 uninformative

387 families with cancer history
TP53 related syndromes
9 Classic Li Fraumeni Syndrome
58 Chompret LFL
19 Birch LFL
279 Eeles LFL
Other sarcoma related syndromes
1 familial schwannomatosis
1 neurofibromatosis
2 Gorlin’s syndrome
15 other striking pedigrees
Other cancer syndromes
1 breast cancer, 2 colorectal cancer
Screening for heritable cancer genes in
sarcoma
NBN
37/105 (27%) patients
carrying 50 cancer
predisposition alleles
MRE11A
RAD50
ATM
FANC
A-C/E-G/L/M
BRCA1
PALB2
BRCA2
BRIP1
FANC
I/D2
RAD51
CHEK2
TP53
Screening for heritable cancer genes in
sarcoma
6/106
NBN
38/106 (27%) patients
carrying 50 cancer
predisposition alleles
RAD50
2/106
(0)
2/106
FANC
A-C/E-G/L/M
2/106
BRCA1
BRCA2
FANC
I/D2
PALB2
BRIP1
BARD1
RAD51
2/106 1/106
(0)
MRE11A
(0)
ATM/
ATR
CHEK2
TP53
7/106
(0)
(19/580)
TP53 wild-type by MLPA and HRM/Sequencing
*
*
*
*
*
*
TP53 wild-type by MLPA and HRM/Sequencing
Whole exome
sequencing
Genes of interest
Affected
M #1 K #2
0.25
0
0.17
0
0.89
0
0.9
0
0.86
0
F
0
0
0
0
0
M
0
0
0
0
0
ID
rs121434596
.
.
.
.
MAF
.
.
.
.
.
Effect
NS
NS
FS
NS
FS
GeneName
NRAS
RUNX1
PTEN
TP53
BAX
GeneDesc
neuroblastoma RAS viral oncogene homolog
runt-related transcription factor 1
phosphatase and tensin homolog
tumor protein p53
BCL2-associated X protein
AA
13
122
105
178
38
Change COSMIC
G/V
52
G/R
157
.
941
H/D
2980
.
3
349
2655
1897
95
V/M
S/P
R/W
D/N
3
41
15
7
R/W
5
0.97
0.34
0.88
0.57
0.51
0.38
0.43
0.48
0.43
0.48
0.46
0.47
0
0
0
0
rs3730947
.
.
rs61753720
.
.
.
0.005 NS
NS
NS
NS
LIG1
MLL2
ABCA1
NBN
ligase I, DNA, ATP-dependent
myeloid/lymphoid or mixed-lineage leukemia 2
ATP-binding cassette, sub-family A
nibrin
0.54
0.39
0.48
0
rs144307645 .
NS
HOXC6
homeobox C6
67
0.45 rs8191664
0.4 rs139525250 .
0.07 NS
NS
NEIL2
EXT2
nei endonuclease VIII-like 2
exostosin 2
257 R/Q
270 S/L
0.34
0.56
0.45
0.43
0
0
.
4
Genes of interest
Affected
M #1 K #2
0.25
0
0.17
0
0.89
0
0.9
0
0.86
0
F
0
0
0
0
0
M
0
0
0
0
0
ID
rs121434596
.
.
.
.
MAF
.
.
.
.
.
Effect
NS
NS
FS
NS
FS
GeneName
NRAS
RUNX1
PTEN
TP53
BAX
GeneDesc
neuroblastoma RAS viral oncogene homolog
runt-related transcription factor 1
phosphatase and tensin homolog
tumor protein p53
BCL2-associated X protein
AA
13
122
105
178
38
Change COSMIC
G/V
52
G/R
157
.
941
H/D
2980
.
3
349
2655
1897
95
V/M
S/P
R/W
D/N
3
41
15
7
R/W
5
0.97
0.34
0.88
0.57
0.51
0.38
0.43
0.48
0.43
0.48
0.46
0.47
0
0
0
0
rs3730947
.
.
rs61753720
.
.
.
0.005 NS
NS
NS
NS
LIG1
MLL2
ABCA1
NBN
ligase I, DNA, ATP-dependent
myeloid/lymphoid or mixed-lineage leukemia 2
ATP-binding cassette, sub-family A
nibrin
0.54
0.39
0.48
0
rs144307645 .
NS
HOXC6
homeobox C6
67
0.45 rs8191664
0.4 rs139525250 .
0.07 NS
NS
NEIL2
EXT2
nei endonuclease VIII-like 2
exostosin 2
257 R/Q
270 S/L
0.34
0.56
0.45
0.43
0
0
.
4
Genes of interest
Affected
M #1 K #2
0.25
0
0.17
0
0.89
0
0.9
0
0.86
0
F
0
0
0
0
0
M
0
0
0
0
0
ID
rs121434596
.
.
.
.
MAF
.
.
.
.
.
Effect
NS
NS
FS
NS
FS
GeneName
NRAS
RUNX1
PTEN
TP53
BAX
GeneDesc
neuroblastoma RAS viral oncogene homolog
runt-related transcription factor 1
phosphatase and tensin homolog
tumor protein p53
BCL2-associated X protein
AA
13
122
105
178
38
Change COSMIC
G/V
52
G/R
157
.
941
H/D
2980
.
3
349
2655
1897
95
V/M
S/P
R/W
D/N
3
41
15
7
R/W
5
0.97
0.34
0.88
0.57
0.51
0.38
0.43
0.48
0.43
0.48
0.46
0.47
0
0
0
0
rs3730947
.
.
rs61753720
.
.
.
0.005 NS
NS
NS
NS
LIG1
MLL2
ABCA1
NBN
ligase I, DNA, ATP-dependent
myeloid/lymphoid or mixed-lineage leukemia 2
ATP-binding cassette, sub-family A
nibrin
0.54
0.39
0.48
0
rs144307645 .
NS
HOXC6
homeobox C6
67
0.45 rs8191664
0.4 rs139525250 .
0.07 NS
NS
NEIL2
EXT2
nei endonuclease VIII-like 2
exostosin 2
257 R/Q
270 S/L
0.34
0.56
0.45
0.43
0
0
.
4
Comparison of the germ cell tumor
and the myelodysplasia
Sept
2007
GeneName
molog
NRAS
LONP2
P,
OR10P1
member 1
xDMBX1
1
LIG1
PTEN
BAX
TP53
Feb
2008
Chr Cytoband
Effect
GeneDesc AA
Change GCT
Chrvariant
Cytoband
Call Effect
MDS variantAACall C
neuroblastoma
1
p13.2
RAS viral
NSoncogene13
homolog G/V
1 0p13.2 Absent NS 0.25
13 Het
lon
16 peptidase
q12.1 2, peroxisomal
STOP
278
R/*
160.41
q12.1
Het STOP0.58
278Het
olfactory
12 q13.2
receptor, family
NS 10, subfamily
122 P, member
D/N 1 120.47
q13.2
Het
NS 0.44
122Het
diencephalon/mesencephalon
1
p33
FS
homeobox
337-338 1
.
1 0.57
p33
Het
FS 0.42 337-338
Het
ligase
19 q13.33
I, DNA, ATP-dependent
NS
phosphatase
10 q23.31 and tensin
FShomolog
BCL2-associated
19 q13.33
X protein
FS
tumor
17 p13.1
protein p53
NS
349
105
38
178
V/M
.
.
H/D
190.63
q13.33
100.39
q23.31
190.55
q13.33
170.38
p13.1
Het
Het
Het
Het
NS
FS
FS
NS
0.97
0.9
0.86
0.9
349
Hom
105
Hom
38Hom
178
Hom
NEJM, 1990, 322:1425
JNCI, 1990, 82:221
Clonal i(12p) in both mediastinal GCT
and leukemia
Co-expression in leukemic cells of
cytokeratin and monocytic markers
DNA Ligase 1
•
K #2: somatic mutation in LIG1 (T311M, Condel/PolyPhen2 pathogenic)
– Retention of paternal LOF allele (V349M)
•
Functions in DNA replication and the base excision repair process
– Neil2 involved in BER
– Interacts physically with Nbn
•
Mutations in LIG1 result in immunodeficiency and increased sensitivity to DNAdamaging agents
•
Associated with increased cancer risk
– Compound heterozygoyte died of lymphoma age 19
– Variants associated with lung cancer risk
•
Gene targeting in mice
– Required for development
– Associated with anemia
Osteoporosis
M #1 K #2 Fa
0.41
1
0.4
0.44 0.43
0
Mo Gene
Description
0.34 FRZB frizzled-related protein
0.49 LRP5 low density lipoprotein receptor-related protein 5
Effect AA Change OMIM Variant
NS
200
R/W
1
605083
NS
1036
R/Q
3
.
dbSNP
Clinical
MAF
pathogenic
0.0461
.
.
Acknowledgements
Rainbows for Kate Foundation
ISKS participants and families
ISKS Australia Steering Committee
ISKS Global Steering Committee
ISKS Australia
Mandy Ballinger
Jess McDonald
Kim Riddell
Belinda Zielony
Jasmine Mar
Kate Crough
Kate Mahendran
kConFab/ISKS RNs
Allison Wicht
Vicki Fennelly
kConFab
Heather Thorne
Eveline Niedermayr
Linda Williams
Lana Djandjgava
Carla Osinski
Peter Mac
Paul James
Gillian Mitchell
Mary-Anne Young
Ella Thompson
Ian Campbell
Richard Tothill
Maria Doyle
Jason Ellul
Jason Li
RUNES
Rapid Understanding of Nucleotide variant Effect Software
Novelty
ENSEMBL
HGMD
dbSNP
Splice effect
Translation impact
Consolidate
ACMG category
Affected genes/transcripts/proteins
NCBI gene
Reference and variant codons
Reference and variant AA
HGVS nomenclature
SIFT/POLYPHEN2/BLOSUM/Condel
dbSNP rsID/MAF
ClinVar cross reference
HGMD cross reference
Splicing/translational effect
OMIM cross reference
Frameshift
Domain mapping
Mutations cross reference
Mouse Genome Database
DECIPHER cross reference
STEPHEN KINGSMORE, CENTER FOR PEDIATRIC GENOMIC MEDICINE
KANSAS CHILDREN’S MERCY HOSPITAL
ACMG classification
Category
Description
Criteria
1
Previously reported and recognized
cause
HGMD variant disease mutant
dbSNP pathogenic clinical significance
2
Novel, pathogenic
Loss of initiation, premature or disrupted STOP, whole
gene deletion, frameshift, essential splice disruption
3
Novel, may be pathogenic
Non-synonymous, in-frame indel, polypyrimidine tract
disruption, other splice site variants
4
Novel, probably not pathogenic
All variants not in categories 1-3, synonymous, dbSNP
MAF>0.02
5
Known neutral
-
6
Association with disease, but not
expected to be pathogenic
-
Maternal
14
18
16
Paternal
16
29
26
Neither
Both
(het)
9
15
2
None homozygous
14
1
16
Nijmegen Breakage Syndrome
Autosomal recessive Fanconi anemia phenotype
•Radiosensitivity
•Cancer predisposition
-50% incidence <15 years
-lymphoid malignancies
-brain tumors
-rhabdomyosarcoma