Download Gene Disorders1（Saffen）

Medical Genetics:
Single Gene Disorders
Lecturer: David Saffen. Ph.D.
Laboratory for Molecular Neuropsychiatric Genetics
Department of Cellular and Genetic Medicine
School of Medicine, Fudan University
[email protected]
Outline
A. Historical Background
B. Patterns of inheritance
C. Genetic mutations
D. Prenatal diagnosis
A. Historical Background
• Gregor Mendel
• Archibald Garrod
• Thomas Hunt Morgan
• Linus Pauling
Gregor Mendel
Established the rules of inheritance of discrete
traits in plants, providing the foundation for the
discovery of the gene and the establishment of
the modern science of genetics
Mendel’s Laws:
Law of Segregation:
Each individual possesses two factors (alleles) for a
given trait, which “segregate” during the formation of
gametes in such a manner that each gamete contains
only one of the factors (alleles). Progeny subsequently
receive one factor (allele) from their father and one
factor (allele) from their mother
Law of Independent Assortment:
Factors (alleles) for distinct traits are inherited
independently, i.e. the inheritance of a factor (allele) for
one trait does not Influence the inheritance of a factor
(allele) for a second trait.
1822-1884; German-speaking
Augustinian friar in Brno, Silesia
(currently Czech Republic)
Archibald Garrod
Postulated that recessive metabolic disorders resulted from
the inheritance of a defective enzyme from each parent.
Garrod’s tetrad: alkaptonuria, cystinuria, pentosuria, albinism
1857- 1936; British physician
Professor Oxford University;
Published Inborn Errors of
Metabolism” in 1908
Urine samples from patient
with alkaptonuria. Left (freshly
voided); right (after 24 h at RT)
Cystinuria
(caused by defects in the SLC3A1
and SLC7A9 transporter genes)
Xylulose accumulates in the urine
of patients with pentosuria.
(caused by L-xylulase deficiency)
Albinism
(caused by a deficiency of tyrosinase, a enzyme
required for the synthesis of melanin)
Thomas Hunt Morgan
Working with Drosophila, established that
gene are carried on chromosome and form the
functional basis of heredity: essentially establishing
the modern science of genetics
Tan Jiazhen
(谈家桢)
“Father of modern
genetics in China”
Link with
Fudan
University:
1909-2008
1866- 1945; American Geneticist
Professor Columbia and California
Institute of Technology;
Nobel Prize: Physiology or Medicine 1933
Linus Pauling
First to demonstrate of the molecular basis
of a genetic disease, sickle cell anemia: essentially
establishing the field of molecular genetics
Sickle-like appearance of
red blood cell isolated from
sickle cell anemia patient
(left) compared to normal
red blood cell (right).
Electrophoresis of CO-hemoglobin isolated from
normal Individual (a) or individuals heterozygous (b) or
homozygous (c) for hemoglobin mutation.
1901-1994; American quantum
chemist and biochemist.
Professor at the California Institute
of Technology & Stanford University
Nobel Prizes: Chemistry 1954;
Peace 1962; Published:
Itano I et al, “Sickle Cell Anemia,
a Molecular Disease”
Science 110, 1488-1490, 1949
B. Patterns of inheritance within pedigrees
Autosomal dominant
Penetrance and expressivity
Autosomal recessive
Consanguinity and inbreeding
Co-dominant
Incompletely dominant
X-linked dominant
X-linked recessive
Y-linked
Probands
and
pedigrees
“Punnett squares”
Genotype = combination
of alleles at a specific locus
A
Sperm
A-allele
Sperm
a-allele
Eggs
A-allele
AA
aA
Eggs
a-allele
Aa
aa
Sperm
A-allele
Sperm
a-allele
Eggs
A-allele
AA
aA
Eggs
a-allele
Aa
aa
a
A = normal (major) allele
a = mutated (minor) allele
unaffected
affected
Autosomal dominant
inheritance
A = normal (major) allele
a = mutated (minor) allele
Sperm
A
Sperm
a
Eggs
A
AA
Aa
Eggs
A
AA
Aa
1/2 of offspring
affected
Sperm
a
Sperm
a
Eggs
A
aA
aA
Eggs
A
aA
aA
all offspring
affected
Sperm
a
Eggs
A
AA
aA
Eggs
a
Aa
aa
3/4 of offspring
affected
Sperm
a
Sperm
a
Eggs
A
aA
aA
Eggs
a
aa
aa
all offspring
affected
Sperm
A
Sperm
a
Sperm
a
Eggs
a
aa
aa
Eggs
a
aa
aa
all offspring
affected
Example: Neurofibromatosis type 1 (NF1)
An autosomal dominant disorder caused by
inactivation of one copy of the neurofibromin gene (NF1) located at 17q11.2.
Incidence of NF1 = ~1/3500 births; 80% of mutations are paternal in origin.
Aa
de novo mutation
inherited from
father
Aa
AA
AA
AA
1/2 of offspring
affected
Sperm
A
Sperm
a
Eggs
A
AA
Aa
Eggs
A
AA
Aa
Aa
1/2 of offspring
affected
A = normal (major) allele
a = mutated (minor) allele
Penetrance and expressivity
Penetrance: the probability that a genetic variant will have a detectable
phenotype (this is an all-or-nothing classification):
Variable penetrance: describes variants with less than 100% penetrance
Expressivity: the severity of expression of the phenotype
Variable expressivity: describes phenotypes that vary among individuals
with the same genotype
Expressivity of neurofibromatosis type 1 phenotype
Café-au-lait spots
(black arrows)
And cutaneous
neurofibroma
(white arrow)
Disseminated
cutaneous and
subcuntaneous
neurofibromas
Lisch nodules
(iris hamartomas)
Distended eye due to
pressure from tumor
on optic nerve
Autosomal recessive inheritance
Aa
Aa
aa
aa
A = normal (major) allele
a = mutated (minor) allele
Sperm
A
Sperm
a
Eggs
A
AA
aA
Eggs
a
Aa
aa
1/4 of offspring
affected
Sperm
A
Sperm
a
Eggs
a
Aa
aa
Eggs
a
Aa
aa
1/2 of offspring
affected
Sperm
a
Sperm
a
Eggs
a
aa
aa
Eggs
a
aa
aa
all offspring
affected
Example: Cystic fibrosis (CF)
An autosomal recessive disorder caused by mutations in the CF
transmembrane regulator gene (CFTR) located at 7q31.2.
Large differences in frequency of CFTR mutations in different populations:
~1/25 among Northern Europeans; ~1/500 in Asian populations
Symptoms include: abnormal chloride ion transport in exocrine tissues leading
to the accumulation of mucus in lungs, sinuses, intestines, pancreas and male
reproductive tract. Accompanying bacterial infections and inflammation cause
tissue damage and organ failure. Expression of CF symptoms is highly variable.
CBAVD =
congenital absence of
vas deferens
Lung from cystic
Fibrosis patient
Consanguinity
and inbreeding
1.0
Aa
Aa
Aa
0.0
0.5
0.5
Probabilities that an individual
harbors one or two copies
of the A1 allele
Aa
0.25
0.25
aa
0.0625 = 1/16
F = probability that
a homozygote has
received both alleles
at a locus from the
same ancestor; i.e.
that the alleles are
identical-by-decent
(IBD)*
*Note: alleles that produce the same phenotype, but at not known to be IBD are termed identical-by-state (IBS).
Example: Xeroderma pigmentosum (XP)
A rare, autosomal recessive disorder caused by mutations in
genes encoding enzymes required for repair of ultra violet
light-damaged DNA. Eight subtypes have been defined,
based upon mutations in different genes. The classical form
is caused by mutations in the XP complementation group A
gene (XPA) located at 9q22.3, which encodes a “zing finger”
protein required for nucleotide excision repair. The inability to
repair damaged DNA gives rise to malignant melanoma and
basal cell and squamous cell carcinomas.
Prevalence in US and Europe: ~1/1,000,000; prevalence in
Japan ~1/100,000; 20% of cases derive from offspring of
marriages between first cousins.
Co-dominant inheritance
Example: the ABO blood types are determined by three variants of the
alpha 1-3-galactosyltransferase gene (ABO), located at 9q34.2.
The “A” variant produces the “A” antigen on the surface of red
blood cells by adding an N-acetylgalactosamine residue to a cell surface
glycoprotein called H-antigen. Similarly, the “B” variant produces “B” antigen
by adding a D-galactosamine residue to H-antigen. By contrast, the “O” variant
is inactive, resulting in red blood cells with unmodified H-antigen on the cell surface.
Variants A and B are dominant with respect to the O variant,
but co-dominant with respect to each other.
A
B
O
A
A
AA
AB
AO
B
B
AB
BB
BO
AB
O
AO
BO
OO
O
Incompletely dominant inheritance
[homozygotes more severely affected than heterozygotes]
Example: Acondroplasia, the most common
form of dwarfism, is caused by specific
mutations in the fibroblast growth factor
receptor subtype 3 gene (FGFR3), located
at 4p16.3. Two mutations: 1138G>A (~98%)
and 1138G>C (~1-2%) account for 99% of
cases. These are gain-of-function mutations
that change the amino acid sequence of FGFR3
In such a way that causes the receptor to
become constitutively active.
The incidence of acondroplasia is 1/15,000 to
1/40,000 in all ethnic groups. De novo mutation
Of 1138G occur exclusively in the paternal germ
Line and the frequency increases with age (>35
years). Homozygous achondroplasia is lethal.
Note: when modeling the contributions of genetic variants to a disease, the variants are
often assumed to have additive effects: homozygotes carrying a liability variant are
assumed to be roughly two-fold more severely affected than heterozygotes or
two-fold more likely to be diagnosed with the disease.
X-linked dominant inheritance
with male lethality
Disorder is observed in ~50% of daughters of affected mothers;
Males die during prenatal period. Expressivity in affected females
Varies with underlying pattern of X-inactivation
Example: Rett syndrome
Xq28: methyl CpG binding protein 2 gene (MECP2) gene
Prevalence among females: 1/10,000 – 1/15,000. rarely observed in 47, XXY males.
Mutations in MEPC2 are thought to interfere with transcriptional silencing and
epigenetic regulation of genes in regions of methylated DNA, leading to inappropriate
activation of gene expression. Symptoms include small brains with cortical and cerebellar
Atrophy without loss of neurons (smaller cells with fewer dendritic branches); motor
disabilities; stereotypic hand-wringing and circulating hand-mouth movements, epilepsy, autism
DNMT1 = DNA (cytosine-5) methyltransferase 1
HDAC = histone deacetylase
X-linked recessive inheritance
Female carrier: May be unaffected
or suffer variable symptoms depending
upon pattern of X inactivation
Example: Hemophilia A and B
[Xp28 (F8=cofactor) and Xp27.1-p27.2 (F9= protease)]
Incidence: ~1/5000 (F8) and ~1/100,000 (F9) newborn males
Severity of symptoms depends on residual Factor VIII or IX activity:
severe (<1%); moderate (1%-5%); mild (5%-25%); Clotting factor replacement has
extended life expectancy from 1.4 year in early 1900’s to 65 years today.
Y-linked inheritance
Example: azoospermia caused by deletions
in AZF regions of the Y-chromosome
Normal testis
Sertoli cell only testis
Locus heterogeneity
Example: Charcot-Marie-Tooth Neuropathy
39 CMT
risk loci
Disease
modifier genes
Example: cystic fibrosis
Gene
Pulmonary
Function
(FEV1)
Pseudomonas
aeruginosa
acquisition/
colonization
ADIPOR2
++
IFRD1
+
ILS
+
MBL2
++
Liver
Disease
++
MSRA
+
-
-
TCF1I2
TBFB1
Diabetes
+
EDNRA
SERPINA1
Intestinal
Obstruction
+
+
++
-
+
Ref: Cutting GR, Modifier genes in Mendelian disorders: the example of cystic fibrosis, Ann NY Acad Sci 1214, 57-69, 2010
Founder mutations and the risk of
genetic disorders in isolated populations
Example: Tay-Sachs disease (recessive inheritance)
Multigenerational
pedigree
demonstrating
common
remote
common
ancestors
in Cajun
population
*
*
*
*
*
*
*
**
*
*
*
*
*
*
*
*
*
*
**
*
**
*
**
*Heterozygous for hex A a-subunit exon 11 insertion; **Homozygous for hex A a-subunit exon 11 insertion
*Heterozygous for G to A transition in spice donor site in intron 9 of hex A a-subunit
Maintenance of deleterious mutations in the
population: Heterozygote advantage
Prevalence of Malaria (left) and sickle-cell disease (right) in Africa
Recessive genetic disorders with
suspected heterozygote advantage
Disorder
Heterozygotes
resistant to:
Sickle-cell anemia
Malaria
Thalassemia
Malaria
Primaquine/fava bean-induced hemolysis
(glucose-6-phosphate dehydrogenase deficiency)
Malaria
Cystic fibrosis
Cholera
Tuberculosis
Chronic obstructive lung disease (emphysema)
cirrhosis of liver
(a1-antitrypsin deficiency)
Tuberculosis
C. Genetic mutations
• Point mutations
Coding sequence mutations
Mutations affecting RNA splicing
Promoter mutations
• Indels
• Repeat expansions
Intergenerational “anticipation”
Missense mutations
Example: sickle-cell disease
Note: this is an example of a
gain-of-function mutation
Nonsense mutations and
nonsense-mediated mRNA decay (NMD)
Examples: Tryptophan-to-stop codon mutation in PAX3
and nonsense mutations in PAX10
PAX3
PAX10
NMD: complete loss-of-function
(Waardenburg syndrome: hearing
loss, pigmentation abnormalities,
Hirschsprung disease)
Mutant “gain-of-function” proteins
(Severe neurological deficits)
Nonsense mutations and
nonsense-mediated mRNA decay (NMD)
Examples: Tryptophan-to-stop codon mutation in PAX3
and nonsense mutations in PAX10
PAX3
PAX10
NMD: complete loss-of-function
(Waardenburg syndrome: hearing
loss, pigmentation abnormalities,
Hirschsprung disease)
Mutant “gain-of-function” proteins
(Severe neurological deficits)
Mutations affecting RNA splicing
Exon
Intron
*
CFTR (CF transmembrane conductance regulator)
Novel, deleterious splice site: frame-shifted aa
sequence containing
termination codons
**
**
*MITF = microphthalmiaassociated transcription factor
(mutations cause Waardenburg
syndrome type 2)
**SMN1 survival of motor neuron 1
SMN2 survival of motor neuron 2
(mutations in SMN1 cause spinal
muscular atrophy)
Promoter mutations
Example: clotting factor IX (Leyden)
Small insertions and deletions (indels)
Example: Frame-shift mutation in Tay-Sachs disease
In the absence of hex A activity
GM2 ganglioside accumulates in
the brain, causing neurological
damage and death by age 2 to 4.
Insertion of
four nucleotides
into exon 11 of
hexosaminidase A gene
shifts the reading frame and
introduces a premature
stop codon
The rate of de novo mutations
increase with father’s age
Ref: Kong A et al, Rate of de novo mutation and the importance of
father’s age to disease risk, Nature 488, 471-475, 2012
Repeat expansions
Huntington disease
Progressive and fatal
neurodegenerative
disorder that produces
uncontrolled movements
cognitive deficits and
emotional disturbances.
All areas of the brain affected,
with particularly extensive
damage to striatum (caudate
nucleus and putamen)
Dominant inheritance, with
symptoms typically appearing
In middle age.
Currently ~ 15,000 HD patients
In US, with an additional 75,000
Pre-onset heterozygotes.
Age 50
Proposed mechanism of repeat expansion
Inter-generational “anticipation”:
progressive increase in repeat length and
decrease in age of onset in an HD pedigree
Ref: Ranen et al, American Journal Human Genetics 57, 593-6022, 1995
Catalog of Mendelian disorders
Mendelian Inheritance in Man
http://www.ncbi.nlm.nih.gov/omin/
To date, causative genetic variants for approximately
3,000 Mendelian disorders have been identified
D. Prenatal diagnosis of genetic disorders:
Amniocentesis and chorionic villus sampling (CVS)
Note: fetal blood can be directly obtained from the umbilical cord (cordocentesis).
Non-invasive methods
for prenatal diagnosis
Note: AFP = alpha-fetoprotein
Non-invasive genetic tests
PLoS One. 2012;7(5):e38154. doi: 10.1371/journal.pone.0038154. Epub 2012 May 29.
Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis
using targeted massively parallel sequencing of maternal plasma DNA.
Liao GJ, Chan KC, Jiang P, Sun H, Leung TY, Chiu RW, Lo YM.
Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of
Health Sciences, The Chinese University of Hong Kong, Shatin,
New Territories, Hong Kong, China.
Science Translational Medicine. 2012 Jun 6;4(137):137ra76.
Noninvasive whole-genome sequencing of a human fetus.
Kitzman JO, Snyder MW, Ventura M, Lewis AP, Qiu R, Simmons LE, Gammill HS, Rubens
CE, Santillan DA, Murray JC, Tabor HK, Bamshad MJ, Eichler EE, Shendure J.
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
References and further reading
RI Nussbaum, RR McInnes and HF Willard,
“Thompson & Thompson Genetics in Medicine,
Edition 7,” 2007, Saunders Elsevier, Philadelphia, PA;
ISBN: 978-1-4160-3080-5 (Chapters 7 and 15)
T Strachan and A Read, “Human Molecular Genetics,
4th Edition,” 2011, Garland Science, New York, New York
ISBN: 978-0-815-34149-9 (Chapter 13)