Finding Disease Related Genes Flashcards
Define linkage disequilibrium
Genes that are non-randomly inherited
What causes linkage disequilibrium
Physical linkage of genes Functional interactions (even on diff chroms)
Define haplotype
Regions of high linkage disequilibrium ie inherited together
What’s the LOD score
The logarithm of the ratio of 2 loci of:
The odds they’re Linked w a specified recombination fraction : the odds they’re not linked
Describe ways cytogenetically can detect disease related genes
Bkpts of balanced rearrangements Deletion/ duplication Positional cloning Chromosome walking Chromosome jumping
How can balanced rearrangement cause disease
Submicroscopic del-/ dup
Disruption of gene at breakpoint
Position effect
X-autosomal translocation
What’s positional cloning
Method to ID gene solely on approx chromosomal location
Linkage mapping
Chromosome abns
Linkage disequilibrium
Describe chromosome walking
Common method used it produce clones covering a RoI
Start with known makers @ each end of RoI
Use marker to probe genomic library to ID other clones that share sequence- ie tile RoI extending out until entire region is covered
Very slow method
Issues: high % rrpt sequences- non specific binding
Describe chromosome jumping
Restriction digest DNA - fragment ~80-130kb in size
Ligate to a marker and circulise DNA (now far DNA is near marker)
Digest with 2nd ER- cuts junction DNA
Ligate into a vector- use as probe in chromosome jumping to ID further positions of RoI
Genes within cloned genomic reign IDd using cDNA library
If probe hybridises to cDNA- can deduce sequence
How do you perform autozygosity mapping
ID family/cohort w. Homogeneous phenotype
Genotype large # SNPs/ microsatellite (genome)
ID regions of homozygosity in affected ppl
Use bioinformatics to for this (IBD Finder)
Fine map using polymorphic markers to differentiate homo from auto
ID candidate gene and sequence
Name four ways can find a disease related gene
Cytogenetics
Autozygosity mapping
Linkage
WES/WGS
What’s the coefficient of inbreeding
The probability a child for a consanguineous family is homozygous for a specific gene from a common ancestor
F= 16 for 2nd cousins
What factors affect autozygosity mapping
informative affected and unaffected ppl in the cohort
Frequency of allele in population (Lower freq- more likely its autozygous).
Degree of relatedness (further away= small regions of IBD Therefore more significant if share IBD) (greater chance 2nd allele entered family resulting in homozygosity).
Phenotypic heterogeneity: essential phenotype are accuarte so looking for same diseas
What’s linkage
The tendency for genes /markers to be inherited together as they’re located nearby on the same chromosome
What’s linkage based on
Because meiotic recombination is random the smaller distance between two loci the more chance they’ll be inherited together
Use markers to track inheritance of an unidentified gene
What’s parametric linkage
The probability a gene is linked to a marker when studied though their LOD scores
Need to know relationship between phenotype and genetic similarities
What’s no parametric linkage
Studies the probability of an allele being IBD with itself
Not appropriate for finding genes involved in common diseases
Not a precise model
What LOD score means the loci are linked or not
+ score (>3) = linkage likely
- score (-2): unlikely
How do you carry out linkage mapping
Use markers across genome in families
Use computer programmes to ID regions with high LOD scores
Fine map candidate region with densely packed markers to find candidate genes
Sequence genes to look for mutations
If analysing affected siblings using linkage what would you be looking for
AD traits: affected sibs would share 1 haplotype for RoI
AR traits: affected sibs would share 2 haplotype a for RoI
Random inheritance sibs would share: 0,1,2 alleles (1/4, 1/4, 1/2)
If investigating an AR trait by WES who would you test
Affected siblings: shared variants/ compound heterogeneity
If investigating an X-linked recessive trait by WES who would you test
Two remotely related male family members
If investigating an dn AD trait by WES who would you test
Trios
Affected proband and unaffected mum and dad
What complex traits is WES being used to investigate
Diabetes
Autoimmune disorder: lupus
