Genetics Flashcards
Exome
Protein coding genes represent 1-2% of genome (3 billion base pairs, 22-25k genes)
Polymorphism
iv. Differences that occur at a frequency of > 1% in a population are often referred to as polymorphisms
Chromatin
DNA and protein (histones) packaged to form a coiled structure
Form chromosomes
DNA bases
- Purines = adenine + guanine
2. Pyrimidines = cytosine + thymine (Ys)
Chromatid
One copy of the duplicated chromosome
Chromosome sizes
Largest -> smallest, therefore chromosome 1 = biggest (not including sex chromosomes)
Mitochondrial DNA
i. Consists of 37 genes, 13 of which encode proteins
ii. No introns
iii. 93% of mitochondrial genome is coding DNA (nuclear 2%)
iv. This genetic material is maternally inherited (sperm mitochondria are in the tail)
RNA
i. Peptide (protein) via intermediate messenger RNA (mRNA)
1. Complementary to strand of DNA
2. Contains uracil instead of thymine
3. Travels to the ribosomes and is translated into a protein (see below)
ii. Directly for ribosomal RNA (rRNA) – involved in translation
iii. Directly for transfer RNA (tRNA) – involved in translation
a. mRNA – messenger RNA contains genetic information and is a copy of portion of DNA. Functions to carry genetic information from DNA out of nucleus into cytoplasm for translation
b. rRNA – ribosomal RNA is structural component of ribosomes. Doesn’t contain genetic material
c. tRNA – functions to transport amino acids to the ribosomes during protein synthesis
d. snRNA – complexes with protein producing small nuclear ribonucleoproteins (snRNP). Act to modify RNA transcript
Promoter region
5’ ie upstream of the first exon – often TATA box (5’ TATAA 3’)
1. Recruit RNA polymerase factors and transcription factors
Codon
i. Sequence of bases along the mRNA is read in groups of 3 (triplets) called codons
ii. Each codon specifies an amino acid and ultimately the sequence of the amino acids along a peptide
iii. There are 43 (64) possible codon combinations - 61 specify amino acids + 3 specify stop signals
1. Redundancy present
2. AT(U)G = methionine = start codon
3. TAA, TAG, TGA = stop codons
iv. Modifying the first nucleotide position more likely to change the AA
Transcription
a. Messenger RNA is transcribed from the DNA – occurs in the nucleus
b. Transcription is initiated by attachment of RNA polymerase to the promoter site
i. Regulatory proteins/ transcription factors bind to region to either repress or activate transcription
c. Antisense strand of DNA read 3’ to 5’ by RNA polymerase
i. mRNA is then synthesized in a 5’ 3’ direction
d. Same structure as DNA except that uracil replaces thymine
e. A 7-methylguanosine ‘cap’ is added to the 5’ end of RNA and several hundred adenine bases are added to the 3’ end after transcription (polyA tail)
Translation
a. mRNA is then translated into amino acid sequence at the ribosomes – occurs in the cytoplasm
b. Each codon (3 bases) = one amino acid
c. Every codon is recognized by a transfer RNA with complementary anticodons and bind corresponding amino acid
d. Post translational modifications – such as glycosylation – can occur
DNA replication/enzymes
a. Helicase opens up the DNA at the replication fork.
b. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.
c. Topoisomerase works at the region ahead of the replication fork to prevent supercoiling.
d. Primase synthesizes RNA primers complementary to the DNA strand.
e. DNA polymerase III extends the primers, adding on to the 3’ end, to make the bulk of the new DNA.
f. RNA primers are removed and replaced with DNA by DNA polymerase I.
g. The gaps between DNA fragments are sealed by DNA ligase
Complementary DNA
Synthesised from single stranded RNA via reverse transcriptase
Mitosis
a. The production of 2 identical daughter cells produced from a single parent cells
b. DNA replication occurs during interphase of S phase of the cell cycle – prior to mitosis
c. Consists of prophase, metaphase, anaphase and telophase
d. Prophase = pair
i. Chromosomes condense and become visible
ii. Centrioles form and move towards opposite ends of the cell
iii. Nuclear membrane dissolves
iv. Mitotic spindle forms from centrioles (spindle fibres made of microtubules)
v. Spindles attach to each sister chromatid at kinetochore
e. Metaphase = middle
i. Centrioles complete their migration to poles
ii. The chromosomes line up in the middle of the cell
f. Anaphase = apart
i. Spindles (microtubules) attach to kinetochores begin to shorten - exerts force on sister chromatids that pulls them apart
iv. This ensure each daughter cell gets identical sets of chromosomes
g. Telophase = two
i. Chromosomes decondense
ii. Nuclear envelope forms
iii. Cytokinesis reaches completion, creating two daughter cells
Meiosis
a. The process of cell division to form four haploid cells (eg gametes)
b. Two cell divisions involved
c. Females = begins in fetal life, completed with ovulation
d. Males = occurs over a few days
e. Meiosis I = homologous chromosomes pair
i. Prophase I = homologous chromosomes pair
ii. Metaphase I anaphase I telophase I
iii. Recombination occurs in this stage = exchange between homologous chromosomes
iv. In oogenesis, one daughter cell receives most of the cytoplasm and becomes the egg, the other becomes the first polar body
f. Meiosis II
Ovum development
c. Complete the first stage of prophase I by fifth month of development to form 1-2 million oocytes (92 chromosomes)
d. After puberty, the oocyte divides (completes meiosis I) to form a large ovum and a small polar body (46 chromosomes)
e. Secondary oocyte undergoes a second meiosis
f. Meiosis is completed only if the ovum is fertilized
Non disjunction
i. Failure of homologous chromosomes in meiosis I / sister chromatids in meiosis II to separate during anaphase
ii. Results in aneuploidy (unequal number of chromosomes in each cell)
iii. Occurs more commonly in female gametogenesis – in eggs
iv. Increasingly common with age
Variant vs mutation
- Variants = alteration to DNA sequence
- Mutation = disease-causing variant
- Variants contribute to natural phenotypic differences between individuals
- 5x106 variants between individuals (1-2%)
- Variants responsible for evolutionary changes
Single gene mutation
- Definition = affect a single base (point mutation), a small number of bases, or very large sequences
- Classification
a. Base substitutions
a. Base substitutions
i. Silent = changes that do not affect the amino acid production by a codon
ii. Nonsense = changes amino acid to produce a stop codon abolish protein production (eg. thalassaemia)
iii. Missense = changes amino acid and alters the protein (eg. sickle cell)
b. Deletions/ insertion
i. These can alter reading frame which would result in a completely different sequence of amino acid, and completely alter the protein or result in a downstream STOP codon = frameshift mutation
Chromosomal abnormalities
- Key points
a. Chromosomal abnormalities occur in 1-2% of live births, 5% of still births and ~50% of early fetal losses
ii. 50% of all miscarriages due to fetal aneuploidy
iii. Chromosome abnormalities are uncommon at birth, but common at conception
iii. Acrocentric chromosome – when short arm contains insignificant genetic material – chromosomes 13, 14, 15, 21, 22 (involved in Robertsonian translocations) -> negligible effect of lost material
a. Gain/loss of an entire chromosome (= aneuploidy)
i. Aneuploidy = abnormal number of chromosomes
ii. Eg. Trisomy - T13, T21, T18 compatible with embryogenesis
- monosomy incompatible with life (except turner)
2. Classification
a. Ploidies = multiples of the 23 chromosome set
b. Somy = copies of individual chromosomes
- Sex chromosome aneuploidy
a. X inactivation – only one X chromosome is expressed in each cell
b. 47,XXY – asymptomatic
c. 47,XYY – fertility and reproduction issues; can lead to atypical presentations of X-linked disorders
d. 47, XXY – Klinefelter
i. With each X chromosome beyond normal number – IQ drops 10-20 points
ii. Most common cause primary male hypogonadism
e. 45, X – Turner
b. Structural abnormalities (= translocation, inversion)
i. Rearrangement of whole or part of chromosomes
ii. Caused by chromosomal breakage during crossing over
iii. May be balanced or unbalanced – balanced typically has no phenotype
iv. Eg. Translocation, inversion
c. Gain/loss of part of chromosome (= microduplication/ deletion)
i. Eg. 22q22
b. Deletions <5 Mb – NOT visible on conventional karyotype
- microdeletions: William, DiGeorge
- duplications: Charcot Marie Tooth type 1
Copy number variations (CNV)
= submicroscopic genomic differences in the number of copies of one or more sections of DNA that result in DNA gains or losses
i. Outcome varies = pathogenic, disease susceptibility, disease resistance, silent
Contiguous gene disorder
= when deletion + duplication of several genes in the same chromosomal region each play a role in the resulting clinical features
Inversion
= single chromosome is broken, at two points, piece is inverted and joined back
a. Pericentric = breaks are in 2 opposite arms of the chromosome and include the centromere
b. Paracentric = occur only in one arm
c. Carriers are phenotypically normal, but are at increased risk of miscarriages (paracentric) and abnormal offspring (pericentric)
Deletions
= loss of chromosome material, which can be terminal (ends of chromosomes) or interstitial
a. Often associated with mental retardation
b. Most common deletions are distal
c. Can be detected with FISH or microarray
Insertions
= piece of chromosome is broken and incorporated into a break in another part of chromosome
a. Can occur between 2 or 1 chromosome
b. Insertions are RARE
c. Carriers are at risk of having offspring with deletions/ duplications of the inserted segment
Ring chromosome
a. Ends of a chromosome are deleted + ends joined to form a ring
b. Can have normal phenotype/ congenital abnormalities depending on amount loss
Clinical genetics definitions
- Genotype = genetic constitution of an organism
- Phenotype = physical characteristics
- Locus = position of a gene on the chromosome
- Allele = an alternative variant of a particular gene
• Homozygous = at a particular locus there are two copies of the same allele
• Heterozygous = at a particular locus there are two different alleles
• Hemizygous
o Only carrying one copy of a genomic region due to deletion or altered function of the corresponding region on the other chromosome
o Males – a mutation in any gene on the X chromosome
o Female – a mutation in any gene on the X chromosome ONLY if Turner’s syndrome
• Compound heterozygote = at a particular locus there are two different mutations
• Polymorphism = where there are at least two, or more, relatively common alleles of a gene in the population (>=1%)
o Eg. Different alleles of genes responsible for ABO blood groups
- Dominant = a phenotype is dominant if the trait can be seen in individuals who are heterozygous for an allele (ie only need one copy); NOTE: may not be inherited, can be de novo and so severe that the individual dies and does not pass on the allele
- Recessive = a phenotype is recessive if the trait is seen only individuals homozygous for the disease (ie need two copies)
- Codominant = a phenotype is co-dominant when the effects of both alleles are seen in the heterozygote
• Penetrance = proportion of people with a genotype who develop disease (black + white)
o For some disorders penetrance is 100% eg. NF-1, CF
o For other disorders lower penetrance eg. BRCA1, polydactyly
• Expressivity = how the phenotype is expressed in a different individual (shades of grey)
o Some disorders the expressivity is similar eg. NF-1 (variable), CF (consistent), HOCM/DCM
• Genetic heterogeneity = multiple genes converge on same phenotype
o Allelic heterogeneity = where different mutations of the same gene exist to cause the same phenotype (eg multiple mutations of the CFTR exist, causing the phenotype of CF)
o Locus heterogeneity = where multiple genes can be mutated in various ways to cause the same phenotype
Eg. LQT syndrome can result from genetic mutations in different sodium and potassium channels
Eg. ID, hearing loss, retinitis pigmentosa, epilepsy
• Digenic inheritance = disease caused by co-inheritance of mutations at two distinct loci (rare)
• Mosaicism = more than one genotype in different cells o Point mutation or chromosomal abnormality o Germline (gonadal) vs constitutional (somatic)
Mendelian vs non Mendelian inheritance
Mendelian
• Refers to the collection of patterns of expression of physical traits over two or more generations that follows the rules of parental-to-offspring transmission (autosomal or sex-linked, dominant or recessive), that Mendel first described
• Patterns attributable to the action of single genes
• Most clinically recognizable for rare, highly penetrant, monogenic diseases
EG: AD, AR, XD, XR, YD
Non-Mendelian
• Many instances of familial clustering of rare traits but pattern of inheritance does not follow Mendel’s laws
• Inheritance can appear to be non-Mendelian
o Multiple genes impact on phenotype expression
o Despite a disorder being monogenic additional factors impact the concordance between genotype + phenotype
EG: Incomplete penetrance, Sex-limited expression, Imprinting, Multigenic inheritance, Anticipation, Mitochondrial inheritance
Autosomal dominant traits
- Key points
a. Phenotype is dominant if the trait can be seen in individuals who are heterozygous for an allele
b. Common to have de novo mutations – occur and can create case without FHx – E.g. Noonan’s - Examples = NF1, Marfan, PCKD, TS, vWD, OI, hereditary spherocytosis, familial hypercholesterolaemia, HD, myotonic dystrophy, acute intermittent porphyria, hereditary haemorrhagic telangiectasia, Noonan syndrome
- Inheritance
a. If one parent affected 50% of children will inherit - Pedigree
a. Equal numbers of affected males and females
b. Vertical transmission of phenotype (>1 generation)
c. Male to male transmission occurs (this excludes X linked) + female to female transmission
d. Skipped generation may be due to incomplete penetrance
e. Most common form of inheritance (think: reproductive fitness) - Exceptions
a. De novo mutations
iii. The more severe the disorder, the more common de novo mutations are (those with severe disorders less likely/ never procreate – called low/zero fecundity)
iv. Examples - Achondroplasia 80% de novo
b. Gonadal mosaicism
Autosomal recessive traits
- Key points
a. Phenotype is recessive if the trait is only seen in individuals who are homozygous for the allele
b. Both parents need to be carriers
c. More severe than autosomal dominant (unlikely to reproduce with most AR conditions)
d. Less likely to be due to new mutations as need 2 new mutations of the same gene
e. Fewer variables within families
f. Heterozygotes typically not affected and asymptomatic but can have late effects – mild disease in adults
g. Consanguinity increases risk of AR conitions - Examples = deafness, albinism, Wilson disease, sickle cell disease, thalassemia, haemochromatosis, PKU, alpha-1-antitrypsin deficiency (+ other IEM), CF, Friedreich ataxia, homocystinuria
- Pedigree
a. Horizontal appearance of phenotype especially among siblings
b. Equal number of males and females
c. Consanguinity (mating of related individuals) may be present
d. Heterozygotes are carriers, and are generally healthy - Note
a. Biallelic phenotype = 2 different mutations
i. More likely if there is high prevalence in the community, usually due to low severity disease
b. Pseudo-dominant conditions
i. Recessive conditions in more than one generation by bad luck
ii. Pedigree looks dominant but is actually AR
iii. More common with common and less severe disorders (eg haemacrhomatosis)
Hardy Weinberg equation
o The allele and genotype frequencies in the population
o p2 + 2pq + q2 = 1
o Represents frequency of alleles in population in one gene
P = incidence of one allele
Q = incidence of second allele
p2 = number of unaffected individuals in a population (assume 1 for rare AR condition) = homozygous for allele 1
q2 = incidence of disorder = homozygous for allele 2
2pq = carriers = heterozygous for the 2 alleles
o Example = If the incidence of Tay Sachs in 1 in 10,000 Q2 = 1/10,000 Q = 1/100 P2 = 1 P = 1 2pq = 2 x 1 x 1/100 = 2/100 = 1/50 Therefore carrier frequency is 1/50
X-linked recessive traits
- Key points
a. Common to have de novo mutation
b. Female carriers may have mild phenotype OR be completely healthy
i. 50% of females with fragile X have ID - Examples = DMD, Fragile X, haemophilia A, adrenoleukodystrophy, X-linked hypohidrotic ectodermal dysplasia, G6PD, Fabry disease, ocular albinism, colour blindness, CGD
- Inheritance
a. Male with disorder
i. All female daughters are carriers
ii. None of sons inherit
b. Female carriers
i. 1/4 chance of having an affected child
ii. Males – 50% affected (ie. 25% chance of having affected male)
iii. Females – 50% carrier - Pedigree
a. Absence of father-son transmission
b. Affected males much more common; all their daughters are obligate carriers
Ratio of affected/hemizygous males to carrier/heterozygous females 2:1
Lyonisation and skewed X inactivation can lead to symptoms in female - rare, and usually more mild
Female dystrinopathy
- DMD/similar phenotype in females to males is RARE
- female dystrinopathies occur d/t:
1. Turner XO
2. Translocations b/w X and autosomal chromosomes
3. Skewed X inactivation
4. Homozygous mutations in dystrophin gene
X linked dominant traits
- Key points
a. Less common clinically
b. Phenotype consistently in females and males
i. If not lethal for males – males will have the more severe phenotype
ii. If lethal for males – only females will be affected
c. Common to have de novo mutations - Examples = X-linked hypophosphataemic rickets, incontentia pigmenti (males lost as miscarriages)
- Inheritance
a. Affected males
i. 100% daughters affected
ii. 0% sons affected
b. Affected females
i. 50% sons affected
ii. 50% daughters affected – less severe - Pedigree
a. As common in females and males HOWEVER often lethal in males
Penetrance and expressivity
- Key points
a. Terms that describe how the disease genotype correlates with clinical phenotype
b. Alterations in penetrance or expressivity can make monogenic traits appear to be transmitted in a non-Mendelian pattern - Penetrance
a. Penetrance = proportion of individuals who carry the causative genotype who manifest disease (0-1)
b. For most disorders, complete penetrance is the exception and not the rule
c. Classification
i. Full penetrance = genotype status predicts development of disease; can be reliably used for genetic counselling (HD, TaySachs)
ii. Incomplete penetrance = penetrance values of <1, in which expression of disease NOT always observed among individuals who carry the disease associated genotype
iii. Variable penetrance = penetrance levels that change across ethnic groups of within families (BRCA1) - Expressivity
a. Expressivity refers to clinical or phenotypic differences of disease manifestation when the condition is present
b. Common among diseases which effect multiple organ symptoms
Pleiotropy
- Pleiotropy = ability of variants in a single gene to produce more than one or multiple phenotypic effects, often in different tissues or organs
a. Distinct from variable expressivity, which describes how two individuals with the same pathogenic variant (or combination of variants) can manifest different phenotypic effects or different degrees of disease expression despite identical genotypes - Example = Marfan syndrome - pathogenic FBN1 variants can cause cardiac manifestations (aortic dilatation and rupture), ocular manifestations (ectopia lentis and severe myopia), and connective tissue findings (joint hyperextensibility and arachnodactyly)
Anticipation
- Key points
a. Anticipation = phenomenon in which successive generations display accelerated, earlier-onset, or more severe disease manifestations
b. Often first recognized in the most severely affected offspring – milder disease forms in parents/grandparents - Examples
a. Trinucleotide repeat expansion
b. Short telomere syndrome eg. dyskeratosis congenita
Mosaicism
- Key points
a. Mosaicism = state of having two populations of genetically distinct cells in an individual who arose from a single fertilized egg
b. Occurs due to several mechanisms in the developing blastocyst or embryo
c. Usually caused by mitotic non-disjunction
d. Events that occur later during development affect a smaller proportion of cells and a more limited number of cell lineages
e. Classic feature is hypomelanosis of Ito (Blaskhoid hypomelanosis)
i. Congenital skin disorder affected M+F
ii. Associated with chromosomal mosaicism + translocation
iii. Patterned, hypopigmented macules over the body surface in demarcated whorls, streaks and patches
iv. Often associated with: ID, seizures, microcephaly, muscular hypotonia
- Inheritance
a. Individuals with mosaicism can only transmit the variant to the next generation if it is present in the gametes. - Diagnosis – can be made on microarray + next generation sequencing
- NOTE
a. Chimerism = uncommon state of having two or more populations of genetically distinct cells due to fusion of two or more fertilized egg
Mitochondrial inheritance
- Key points
a. Mitochondrial inheritance = traits due to genetic variation in the mtDNA rather than the nuclear genome - Mitochondrial inheritance
a. Exclusively inherited through maternal line (ie. from egg)
b. Heteroplasmy = more than one type of mitochondria (affected or unaffected by the variant) in each cell
c. Females with a mitochondrial variant who exhibit heteroplasmy will pass on varying numbers of affected or unaffected mitochondria to their eggs -> substantial variation in the contribution of the mitochondrial variant to each offspring - Mitochondrial diseases
a. 1000-2000 mitochondrial cell
b. Mitochondrial failure -> cell injury
c. Disease commonly affects brain, heart, liver, muscle, renal, endocrine, respiratory - Pedigree
a. All a mother’s children affected
b. No descendants of an affected male have the disease - Mitochondrial vs X linked
a. No male to male in either
b. X linked = males affected exclusively (or more severely) than females
c. Mitochondrial = males and females affected to the same extent
d. Mitochondrial = no descendants of an affected male have the disease, whereas this can happen in X linked conditions
Sex limited expression
• The expression of some traits, regardless of their chromosomal location, can be restricted to one sex, likely due to critical physiologic, anatomic, or hormonal differences
• Examples
o Male pattern baldness – can be inherited as AD trait
o Familial male precocious puberty – variants of GNAS1 gene
o Juvenile hypertrophy of breast – limited to females
Multigenic disorders
- Key points
a. Caused by the combined effects of >1 gene – multigenic or complex disease - Classification
a. Digenic
i. Pathogenic variants at two distinct loci required for disease to manifest
ii. Many exhibit classic AR inheritance pattern
iii. Example = digenic form of retinitis pigmentosa, Usher syndrome
b. Triallelic
i. Rare type of inheritance that requires three gene variants for disease to manifest - Two pathogenic variants at one locus and one additional variant at a different locus
- Example = Bardet-Biedl
a. Most individuals homozygous or compound heterozygotes for a pathogenic variant in one gene consistent with AR
b. Families described in which three variants in two genes segretgate with the disease phenotype
Polygenic disorders
- Key points
a. Characterised by familial clustering, but non-Mendelian patterns
b. Due to multiple genes with small effects
d. Examples = DM, CVS disease, asthma, MS etc - Characteristics
a. Similar rate of recurrence among all first-degree relatives
b. Identical twin risk is not 100%, but is more than sibling risk
c. Often susceptibility alleles in non-coding regions (SNPs) - SNPs
a. Occur every 1/300 base pairs
b. Most common type of genetic variation
c. Each individual has 10 million SNPs
d. Usually in non-coding regions
f. Often used in association studies – Genome Wide Association Study (GWAS)
Translocation pedigrees
- May be inherited from a carrier or appear de novo
- Carriers of a reciprocal translocation are phenotypically normal, with an increased risk for miscarriage and bearing affected children
• Pedigree o Males = females o Multiple miscarriages o Parents unaffected o Offspring 2/6 normal (50% carrier) 1/6 unbalanced = affected 3/6 non-viable = miscarriage
Epigenetics and imprinting
- Definitions
a. Epigenetics = alteration of gene expression (rather than DNA itself)
i. Transcribed genes need to be accessed by transcription factors, and so the chromatin is more open
ii. Methylation of cytosines in promoter region contributes to ‘silencing’ of genes
b. Imprinting = epigenetic marking of a gene based on its parental origin and results in monoallelic expression
i. For imprinted genes, expression is determined by the parent of origin of the chromosome
ii. Exception NOT the rule – 1% genome is imprinted
c. Mechanism of imprinting is usually due to parental specific methylation of CpG-rich domains AND modification of histone proteins
d. This is reset during gamete formation
i. Genetic imprinting occurs early in the formation of eggs/sperm
ii. Imprinting then occurs again in the next generation when that person produces his/her own eggs/sperm ie. maternal or paternal imprint is sex specific in relation to the parent the allele is inherited from NOT the offspring
iv. Father passes on paternally imprinted genes
v. Mother passes on maternally imprinted genes
- Imprinting disorders
a. Imprinting disorders occur when there are INAPPROPRIATELY two active copies or two inactive copies of the imprinted gene (ie. group of disorders based on inappropriate gene dosage)
i. Eg. normal maternal imprinting – you are relying on the paternal copy to work – therefore if something goes wrong with the paternal copy there is a problem
c. Maternal vs paternal imprinting
i. Maternal imprinting = maternal gene silencing (and paternal gene expression) – a maternally imprinted gene means that when inherited from the mother it is NOT expressed, and vice versa
d. Imprinting silences one gene
a. Imprinting = DNA sequence will be normal, but the relevant allele is switched off methylation testing required
Uniparental disomy
= both genes are inherited from the one parent (maternal UDP = two maternal copies)
i. Is the presence of two chromosomes/ two alleles inherited from one parent
ii. Effect of this varies, can result in:
1. An imprinting type disorder
2. Uncovering of autosomal recessive disorder
iii. Is usually maternal, due to non-disjunction during meiosis
1. Error in meiosis I two copies of material from the same grandparent (uniparental isodisomy)
2. Error in meiosis II one copy of material from each maternal grandparent (uniparental heterodisomy)
iv. This means the maternal gamete has an extra set of chromosomes, with uniparental disomy arising due to fertilization with nullisomic gamete OR trisomic rescue (most common)
v. Note that the terminology is the opposite to imprinting:
1. Maternal UPD = two copies of maternal chromosomes, absence of paternal genes
2. Paternal UPD = two copies of paternal chromosomes, absence of maternal genes
c. Uniparental disomy = FISH or SNP array
i. NOTE: SNP detects some but not all UPD
ii. Can do specific UPD studies
Prada Willi syndrome
- PWS and Angelman syndrome occur due to absence of monoallelic expression of key genes at 15q12
- Some genes in this location are only active on the paternal copy, and some on the maternal copy
- Absence of PATERNALLY functioning genes
- Deletion on paternal 15 – OR both 15s are maternal
• Mechanism
o 70% paternally derived deletion of 15q12
o 25% maternal UDP 15 - increasing due to increasing maternal age
o <1% imprinting defect
Paternal imprinting = silencing
• Key features o Floppy baby (hypotonia) o Voracious appetite (hyperphagia) - most common syndromic form of obesity o Obesity, short stature o Moderate ID o Hypogonadism, cryptorchidism - hypopigmentation vi. Depigmentation of the skin or eyes relative to familial background in 30-50% - small hands and feet
Other features:
- neuro/psych: OCD, epilepsy (25%)
- facies: almond shaped eyes
i. Premature adrenarche (pubic and axillary hair), but other secondary sexual characteristics are delayed or incomplete
- Investigations
a. Methylation analysis: detects all cases
b. Microarray abnormal in deletions + and some UPD
c. Deletions can also be detected via FISH
d. In practice, PWS panels will perform karyotype, methylation studies FISH + microsatellite probes for maternal uniparental disomy - Treatment
a. Growth hormone
i. Does not require formal GH deficiency testing
ii. Subsidized in genetically confirmed PWS until the age of 18 years
v. Require sleep study prior to use
vi. Contraindications: uncontrolled DM, respiratory compromise, severe sleep apnoea (IGF-1 stimulates adenotonsillar hypertrophy)
vii. Series of increased fatality seen initially within commencement of GH treatment, usually related to severe OSA + intercurrent URTI - Prognosis
a. Mortality up to 3%, average age of death is 33.2
Angelman syndrome
- PWS and Angelman syndrome occur due to absence of monoallelic expression of key genes at 15q12
- Some genes in this location are only active on the paternal copy, and some on the maternal copy
- Absence of MATERNALLY functioning genes (UBE3A)
- Deletion on maternal 15 – OR both 15 are paternal
• Mechanism o 70% maternally-derived deletion of 15q12 o 5-10% UBE3A mutation o 5% patUDP15 o 3% imprinting defect o 10-20% unknown
• Key features
o Severe ID
o Lack speech + inappropriate laughter - behavioural “happy puppet”
o Unsteady gait/ataxia
o Epilepsy
- postnatal microcephaly, delayed and disproportionate
- hand flapping
- seizures in 80%, and abnormal EEG even in absence of seizures
- Investigations
a. Methylation testing of 15q11.2-13 (will pick up 70%)
b. UBE3A single gene sequencing (will pick up 10%)
BWS and Russel Silver syndrome - difference
- BWS and Russel-Silver syndrome are caused by the same gene (11p15) – location of IGF-2 (paternally expressed growth factor)
- Usually only the paternal copy is active
- Loss of maternal copy (eg. paternal UDP) = paternal over-expression = BWS (big)
- Loss of paternal copy eg. imprinting defect, both copies maternal imprint = paternal under-expression = Russel silver (small)
Beckwith Weiderman syndrome
- Absence of MATERNAL gene
- Disrupting imprinting of 2 neighbouring domains on 11p15 (paternal allele growth promoting, maternal allele growth suppressing)
- Key point = association with IVF (loss of IC2 methylation)
c. Overactivity of IGF-2 (growth factor)
d. Imprinted genes = IGF2, gene H19 (involved in IGF2 suppression), WT1 (Wilms tumour gene), many others
• Mechanism
o 50% loss of methylation at mat IC2 on 11p
o 20% paternal UPD 11
o 5% gain of methylation at mat IC1 on 11p
o 5-10% CDKN1C mutation
• Key features o Overgrowth disorder o Macrosomia, neonatal hypoglycaemia o Hemihypertrophy o Macroglossia, visceromegaly o Predisposition to embryonal malignancies (Wilms, hepatoblastoma, neuroblastoma) - screening every 3mo - exomphalos - ear creases/pits - naevus flammeus - cognitively can be normal, mild-mod ID
- Investigations
a. Methylation testing – diagnostic
b. SNP array is abnormal in rare microdeletions/duplications and some patUDP11 - Prognosis
a. Generally good prognosis if survive past infancy
i. Apnoea/cyanosis may occur -> 21% infant mortality
b. Follow-up tumours with USS and AFP
i. Nowadays JUST do USS every 3/12 until age 8 years
Russel-Silver syndrome
• Absence of PATERNAL gene
• Mechanism
o 50-60% 11p methylation defect
o <10% maternal UPD7
o Rest unknown
• Key features
o Short stature
o IUGR
o Asymmetry
o Triangular face (prominent forehead, pointed chin)
o Macrocephaly (preserved HC despite IUGR)
- hemihypertrophy as well
- clinodactyly (bending/curving of finger)
- Investigations
a. Methylation testing 11p
b. UPD7 studies (DNA from parents)
c. May detect UPD7 on SNP array - Treatment
a. GH treatment effective
Imprinting pedigree features
- For imprinting it is the gender of the parent of origin of the gene that matters – NOT the gender of the child
- Equal number of males and females
• Key points
o No affected children from the gender that is imprinted (no affected children from females if maternal imprinting, no affected children from males if paternal imprinting)
o Imprinting is reset when passed to the next generation
o If a pedigree shows a disorder inherited from both male and female parents, it cannot be an imprinting disorder
• Maternal imprinting = genes inherited from the mother are switched off
o Mutation in a maternally imprinted gene will result in the condition in
HALF of the children of a male with a mutation
NONE of the children of a female with the mutation (mutation imprinted)
• Paternal imprinting = genes inherited from the father are switched off
o Mutation in paternally imprinted gene will result in the condition in:
HALF of the children of a female with the mutation
NONE of the children of a male with the mutation
Trinucleotide Repeat Expansion Disorder
b. Classification
i. Normal range (stable range in mitosis and meiosis)
ii. Intermediate (mutable) range / permutation repeat size is unstable but does not result in a phenotype
iii. Full mutation
c. Allele expansion often dependent on gender of transmitting parent
i. Maternal = myotonic dystrophy, FRAX, Friedreich ataxia (lager repeats)
ii. Paternal = CAG repeat disorders such as HD, SCA (smaller repeats)
ii. CANNOT use the repeat size to predict phenotype with accuracy eg. myotonic dystrophy prenatal, HD predictive test
- Classification
a. Repeat Codon CAG (glutamine) = polyglutamine, e.g. HD, SMA
b. Non-CAG, e.g. FRAX, FA, myotonic dystrophy
