Genetics Flashcards
Single gene mutations: Base substitution (3)
Silent mutation: change in base pair, but same protein
Nonsense mutation: changes that result in a stop codon
Missense mutation: changes that affect amino acid produced by codon
Single gene mutations:
Indels
- Frameshift mutation: Alters the reading frame significantly if deletions don’t occur in multiples of 3 –> results in a completely different sequence of amino acid which completely alters the protein or result in a downstream stop codon
- If indels occur in multiples of 3, then it will truncate the protein but might maintain some semblance to original protein
Autosomal dominant pedigree
- Vertical transmission
- Passed from fathers and mothers to sons and daughters
- Male-to-male transmission (i.e. no X-linked features)
- If 1 parent has the disease, 50% chance offspring will have disease
Autosomal dominant pedigree:
- Penetrance, expression, mosaicism, de novo
- Penetrance: black or white –> complete penetrance vs incomplete penetrance (= “skipped” generation); the ability of a known disease-causing genotype to exhibit the disease phenotype
- Expressivity: same genotype, but variable (always present) phenotype, differing severity of disease, complete penetrance
- Mosaicism: more than 1 genotype in different cells; suspect gonadal mosaicism if normal parent and 2 or more affected offspring
- De novo: spontaneous mutation
Autosomal recessive pedigree
- Disease is seen in siblings in single generation
- Males and females equally affected
- Fathers and mothers can each transmit an abN allele
- Parents of affected person are usually carriers/unaffected
- Risk for 2 heterozygotes to have an affected child is 1/4, carrier risk for a sibling is 2/3, wildtype homozygous (i.e. normal child) 1/3
- Consanguinity increases the risk of AR conditions
2/3 rule
- If there is an AFFECTED offspring, the risk of the sibling being a carrier is 2/3
- -> But beware, the 2/3 rule only applies to siblings of an affected individual.
- Therefore, the carrier risk of a person with WITHOUT an affected sibling will be 2/4 = 1/2
How do you work out the incidence of a recessive condition?
Square the carrier frequency and multiply by 4
E.g. Friedrich ataxia has carrier frequency of 1/100
Incidence = (100x100)x4 = 1 in 40,000
How do you work out carrier frequency in a recessive condition?
Opposite of incidence!
- Divide incidence by 4 and square root of that number
X-linked inheritance
- X-linked recessive:
- -> 1/4 risk of an affected male child in each pregnancy from female carrier
- -> All daughters of a male with an X-linked dz = obligate carrier
- X-linked dominant:
- -> 1/2 risk of an affected male child in each pregnancy from female carrier
X-inactivation
- Females have 2 X chromosomes and only 1 X is active in any one cell due to X-inactivation
- X-inactivation process is usually random –> 50:50 split between maternal and paternal inherited X-chrom being active in 1 cell
Non-random X-inactivation
- Skewed X-inactivation: e.g. 90:10 instead of 50:50
- A female carrier would mainfest condition if X-inactivation is non-random and skewed towards abnormal X
- Can result in X-linked recessive disease and can protect from X-linked dominant disease
Anticipation
- Seen in triplet repeat disorders
- Disease gets worse over successive generations due to increase in repeat numbers
Mitochondrial inheritance
- Mitochondrial DNA is only maternally inherited
- Affected mother can pass down to both son and daughter
- An affected male will not pass down mutated mitochondrial gene to their offspring
- Heteroplasmy: some mitochondria have mutations and others don’t in a cell
Mitochondrial bottleneck
- Not all mitochondria are replicated equally to daughter cells during oogenesis
- Mitochondrial load of each daughter cell dictates likelihood of dz (difficult to predict)
E.g. asymptomatic Mo can have profoundly dz child - Cannot use maternal mutant load to predict foetal mutant load
Mitochondrial vs X-linked inheritance
- No male to male transmission
- X-linked: sons are affected, daughters are less severely affected
- Mitochondrial: sons and daughters are equally affected and descendants of affected male cannot have the dz
Autosomal dominant: homozygote
- Usually heterozygote (AD dz are caused by mutation in only 1 copy of gene)
- Homozygote AD are usually genetically lethal
How can a female offspring have the disease phenotype in an X-linked recessive inheritance?
- If father has the disease (Xa,Y) and mother is a carrier (Xa,x)
- Skewed X-inactivation
Imprinting
- Parent of origin!!! is important
- Imprinting silences gene expression
–> Maternally imprinted gene = gene is inherited from mother is silent and the gene from father is expressed
and vice versa - Imprinting of an abnormal allele switches off the mutation –> no disease
- Imprinting is reset in each generation: methyl tags stripped during gametogenesis, imprinting pattern rewritten in ovaries/testes in before passing down to offspring
Imprinting “pedigree” example explanation
- Remember: imprinting disorder and imprinting pedigrees are different things
- Imprinting disorder = abnormality in imprinting process
- Imprinting pedigree = normal imprinting process, but inheritance of mutated gene
Paternally imprinted gene example:
- Female offspring (K) has: Ai,a –> mutated allele imprinted so not expressed (from father)
- Imprinting is reset during gametogenesis: gamete has a chance of having A or a
- If K passes down A, this mutated gene will no longer be silenced because it is a PATERNALLY imprinted gene and it’s the mother (K) passing it down
- K’s offspring will have the disease phenotype
Imprinting pedigree: maternally imprinted genes
Maternal imprinting:
- All affected persons inherit mutated gene from father (so there is half a chance that his offspring will have dz)
- No affected children from females
- Mothers with mutated genes silence it when they pass it on to offspring
- Half the children of a male will express the dz
- Imprinting is reset when passed onto next generation
Imprinting pedigree: paternally imprinted genes
Paternal imprinting
- All affected persons inherit mutated gene from mother (so there is half a chance that her offspring will have dz)
- No affected children from male
- Fathers with mutated gene silence it when passing it onto their offspring
- Half the children of a female will express the dz
- Imprinting is reset when passed onto next generation
Pedigree tips
- Always remember genetic material halves when you go down by 1 generation
- Do a bloody punnett square to figure out risk (e.g. XLR - male dz is 1/2)
- In recessive pedigree, multiply by punnett square factor of 1/4 if working out risk of recessive dz
- In XLR pedigree, if gender is not known, need to multiply final risk by 1/2 = chance of being male
Transcription factors
Regulates binding of RNA polymerase = initiates transcription of DNA into RNA
Risk of gonadal mosaicism
Low - 1-3%
Mutations that are most likely to cause non-functional or truncated protein?
Frameshift mutation (indels not in multiples of 3) Nonsense mutation (stop codon)
Acrocentric chromosomes and Roberstonian translocations
- 13, 14, 15, 21,22
- -> Very short p arms with non-essential genetic information
- Robertsonian translocations involve balanced translocation of acrocentric chromosomes
Chromosomal disorders:
- Aneuploidy (abnormal number)
- Structural: translocations, inversions
- Gain or loss of part of chromosome: missing or duplicated genetic material
Non-disjunction
- Failure of homologous chromosomes to separate in anaphase I
- Failure of sister chromatids to separate at meiosis II
- Gives rise to nullisomic and disomic gametes
Aetiology of Trisomy 21
95% free trisomy 21: 47XY or XX,+21
- Maternal nondisjunction: meiosis I 65%, meiosis II 23%
- Paternal nondisjunction: meiosis I 3%, meiosis II 5%
- 3% mitotic nondisjunction: mosaic - modified phenotype, trisomic zygote or normal zygote
5% translocation (Robertsonian) Down syndrome
- Need to perform karyotype as a CGH array will miss T21 due to translocation
- No maternal age effect, risk of recurrence
- Problem arise at gametogenesis
Nuchal translucency
Associated with monogenic disorders and aneuploid states
When do microdeletions occur?
During meiosis
- Error in meiotic recombination
Trinucleotide repeat expansion
- Repeats below certain length are stable in meiosis and mitosis
- Above threshold length, repeat number is unstable with bias toward expansion with each DNA replication
- Size of expansion is proportional to AGE of onset OR SEVERITY
- Liability to expand is related to gender of transmitting parent
Anticipation
Earlier onset in subsequent generations
Trinucleotide repeat disease
- Fragile X - (CGG)n –> >200 in 5’UTR
- Myotonic dystrophy - (CTG)n –> >50 in 3’UTR
- Friedriech’s ataxia - (GAA)n –> >200, intronic
Imprinting: Angelman’s syndrome
Loss of maternally derived allele which is required for normal development, paternal allele should be imprinted
- 70% deletion of maternally derived 15q12
- 2% paternal uniparental disomy
- 10% UBE3A mutation
Imprinting: Prader-willi syndrome
Loss of paternally derived allele which is required for normal development, maternal allele should be imprinted
- 70% have deletion of paternally derived 15q11-12
- 25% maternal uniparental disomy
Retinoblastoma
- Incomplete penetrance
- Autosomal dominant inheritance
- Other malignancies are associated with the disease
Mosaicism
- Mutations that arise post-zygotically
- 2 or more genetically different cell lines in an individual, derived from single zygote
Somatic mosaicism
- Not relevant to inherited disease as it affects somatic cells
- High-level somatic mosaics may express an altered phenotype e.g Mosaic Turner or T21
Gonadal mosaicism
- Arises in germline cells –> mutation-bearing gametes
- Substantial proportion of autosomal dominant or X-linked diseases arise from new mutations
- May get a clone of gametes in a phenotypically normal parent that carry the mutation
Conventional Karyotype
- Visually analyses whole chromosomes
- Detects aneuploidy, large chromosomal imbalances, balance and unbalanced chromosomes
- Cannot detect microdel/dups, DNA sequence changes
FISH
- Fast test, uses DNA probes for specific targets e.g. individual chromosome, chromosomal region, gene
- Detect presence/absence of SPECIFIC DNA sequences on chromosomes e.g. Williams, trisomies, monosomies (need to “fish” for specific targets)
CGH (comparative genomic hybridisation) assay
- Dosage
- Compare DNA (genome) from 2 sources: test sample and control sample - look at gain/losses of DNA content –> difference in genetic material (loss/gain)
- Molecular karyotype: virtual karyotype from array of many thousand tagged DNA probes
- Detects: microdeletions and microduplications, monosomies and trisomies, variations that may not be clinically significant
- Cannot detected balanced chromosomal changes/rearrangements, ploidy abnormalities e.g. triploidy
SNP (single nucleotide polymorphism) array
- Dosage
- Variation in a single nucleotide at a specific locus (submicroscopic level), genome wide test of chromosomal dosage
- Can detect: CNVs with genotype abnormalities, allelic imbalance, chimerism, uniparental disomy, long continuous stretches of homozygosity = consanguinity, mosaicism up to 7%
- -> Allelic imbalance = whether 2 allelic copies of single base pair are homozygous or hetero e.g. UPD, mutated tumour suppressor gene
Sanger sequencing
- Spelling changes
- Determine exact sequence of bases and compare to reference sequence
- E.g. sequence of Marfan gene (FBN1)
- Can detect: single gene mutations
- Cannot detect: exonic deletions/duplications
Single gene sequencing
- Spelling changes
- Next generation sequencing
- Sequences many genes simultaneously
- Can detect changes of a single base within a gene, cannot detect outside gene of interest
Other genetic tests
- Triplet repeat analysis: 1) PCR sizing, 2) Southern blot
- -> PCR can only detect up to certain # of rpts
- -> Southern blot sizes full range of expansion
- Methylation-sensitive MLPA: identify methylated targets
Southern blot vs Western blot
- Southern blot: for DNA testing, DNA fragments separated by size e.g. deletion of an allele, triplet repeats
- Western blot: for protein, proteins separated by size, stained with antibodies to target protein e.g. dystrophin staining for DMD
Whole genome/exome sequencing
- Can detect missing DNA or sequence changes in multiple genes
- Useful for genetically heterogeneous conditions
- Cannot detect triplet repeats or methylation defects
Consanguinity
- Increased risk of autosomal recessive disease
- Risk of having a child born with a major congenital problem is approximately x2 the background population risk
What increases the risk of methylation disorders?
IVF pregnancies
- Increases risk of methylation defects by x4
