medical genetics 3 and 4- mitsouras Flashcards
how to calculate the risk for unrelated parents to have affected offspring for autosomal recessive disorder
Probability child affected=
(Probability mom carrier) x (Probability dad carrier) x 1/4= 2pq x 2pq x 1/4
how to calculate the risk for unrelated parents to have an offspring who is a carrier for autosomal recessive disorder
Probability child carrier=
(Probability mom carrier) x (Probability dad carrier) x 2/4=2pq x 2pq x 2/4
penetrance and expressivity
fraction of individuals with same genotype that show expected phenotype
- Fully penetrant => phenotype always expressed when genotype is present - Incompletely penetrant => phenotype expressed in a fraction of individuals when genotype is present - Measured across individuals of same genotype NOT within an individual - Expressed as a percentage of individuals that express expected phenotype (ex. 80% penetrant for incomplete & 100% for complete)
Expressivity: range of phenotypes produced by same genotype
- Phenotype is variable among individuals of same genotype
what is locus heterogeneity and which disease do we frequently describe with locus heterogeneity?
mutations in different loci (genes) produce same phenotype/disorder
ex:BRCA1 & BRCA 2 in familial breast and ovarian
what is mutational heterogeneity and which disease do we frequently associate with it?
Mutational heterogeneity: different mutations (alleles) in same locus (gene) produce disease phenotypes of different severity
ex: Cystic fibrosis
what is anticipation? and which type of diseases is it used to describe?
anticipation: Progressively earlier age of onset & severity of symptoms
- Correlates with number of repeats
used in trinucleotide repeat disorders such as huntingtons and fragile x
these disorders occur due to a slippage of the DNA polymerase during the replication of gametes
-if the # of repeats> threshold==> disease phenotype
Describe how mitochondrial disorders are transmitted and some of the most frequent
Mitochondrial disorders:
- Mutations in mitochondrially encoded genes
- Mother to child transmission (ALL children of affected mother are affected)
- Father does not transmit
- Mitochondrial genes involved in energy metabolism
- Clinical symptoms in muscle, heart, CNS
Mitochondrial genes encode for a lot of proteins of the ETC–> mutations often result in problems in organs with high energy requirements
- Number of mutant mitochondria within a cell has to exceed a threshold (80%) for disease manifestation (threshold=# affected can affect the ability of the cell to produce energy)
- Homoplasmy: all mitochondria within a cell have identical sequence (WT or mutant)
- Heteroplasmy: mixture of wild-type & mutant mitochondria within a cell
- Heteroplasmy contributes to wide variability of symptoms in mitochondrial disorders
Define multifactorial inheritance, liability and risk
Multifactorial traits are when genes and the environment interact to result in greater phenotypic diversity
-Risk is disease susceptibility conferred by genes alone
-Liability encompasses ALL factors affecting disease development: genes & environment (G X E)
Liability distribution of population is continuous variable with normal distribution
There is a discrete liability threshold for disease development
Disease development is result of “bad” genes and “bad” environment
–>lifestyle changes can delay or even prevent disease
Relatives of affected individual have more risk genes & higher incidence of disorder than general population (familial vs population incidence)
- Risk increases the closer the familial relationship (1st vs 2nd vs 3rd degree) because amount of DNA shared increases
- ->the liability curve shifts to the right (because of increased risk) so more persons are affected at threshold.
using candidate gene association studies: If statistically significant association between specific mutations in variant genes and disease then variants are involved in disease (causative variants) = “susceptibility loci”
what are the different types of SNPs?
Single nucleotide polymorphisms
single base pair changes that are bi-allelic (the minor allele must be > 1% to be a SNP)
cSNPs:
Silent SNP: often the 3rd codon position will not change the AA coded for
Synonymous cSNP:
Substitution of BP will result in the same type of aa
(ex: acid for acid or hydrophobic for hydrophobic–> doesn’t change the function of the protein much)
non-synonymous results in substitution with different type of aa, acidic with hydrophobic etc)–> often cause disease
how can SNPs be used in the identification of disease genes?
o Non-coding SNPs can be used as markers for association studies to identify disease genes due to their linkage (close proximity) to genes. –> to identify susceptibility loci
o Can be causative agents for disease or causes of non-disease phenotypic variation (differences in drug metabolism, drug response); these are cSNPs.
Sanger DNA Sequencing
- Uses chain terminating nucleotide analogs.
- Size fractionation by gel electrophoresis and then read sequence.
- Use when mutation is unknown & to identify unknown mutations
- Can identify/detect SNPs/point mutations, deletions, insertions etc
- Expensive & time consuming but highly accurate (used in BRCA1/BRCA2 testing)
covers single gene
Exome Sequencing
- Use to identify unknown mutations
- Sequence all human exons with single assay on an array.
- Whole-genome coverage.
- Expensive but quick.
- Used to identify genes for syndromes (kabuki syndrome)
–> uses next generation sequencing (NGS)
Microarray Hybridization
- Use primarily to identify unknown mutations/changes (can also be used for known)
- Compare control DNA vs. patient DNA.
- Get different colors depending on presence of genes.
- Screen entire genome or transcriptome with single assay
- Expensive
- Used for a variety of applications: detect chromosomal abnormalities (array CGH), gene expression changes (expression arrays), genotyping/GWAS (SNP arrays)
control DNA labeled green and pt DNA labeled red. if yellow–> [pt DNA]=[control]
if red–> [pt]> [control]–> trisomy
if green –> [pt]< [control] –> deletion
Southern Blotting
- Use when mutation is known
- Used for the detection of relatively larger rearrangements (insertions, deletions, duplications etc)
- Used for single gene.
- Used frequently for triplet repeat expansion disorders.
pt DNA–> size fractionation by gel electrophoresis–> labeled probe for mutation of interest–> determine size (MW) of fragments hybridizing probe detecting mutation and interpret the pt’s genotype
PCR Amplification
- PCR is a way to rapidly amplify desired segment of patient DNA
- After PCR amplification additional method is needed to screen for mutation in patient (sequencing, RFLP)
- Have to know the mutation.
used to amplify a region of pt DNA–> need an additional method (RFLP) to screen for the mutation in the pt.
