AMB14 Flashcards
(14 cards)
what are SNPs, indels and microsattelites mostly due to?
not mutagens but errors by DNAP
what are the most common kind of SNP
transtion mutations
purine to purine
pyrimindine to pyrimidine
what are the aims of the international hapmap
develop a haplotype (set of DNA variations that tend to be inherited together) map of the human genome to describe common patterns of human genetic variation.
what does the hapmap project focus on? why may this be unhelpful
common snps >1%
most sequences of interest e.g. disease resistance are rare.
describe affymetrix
uses hybridisation stringency to detect single bp differences between probe and oligos and genomic DNA
single bp mismatch wont hybridise
DNA chip: 2 million markers in one chip, duplicates built into chips, etched onto surface.
fluroesces if complementary to that allele
describe illumina
uses primer extention to detect bp differences
detect which bp gets incorperated telling you which allele you have.
describe infinium probe design
3’ end of primer is positioned adjacent to the SNP site, or non polymorphic site.
extention of the primer incorperates a biotin nt or a dinitrophenyl labelled nt.
C and G nt are biotin labelled
A and T dnp labelled
how is GWAS used to identify gene
- family who are related and show phenotype of interest + case cntrol
- high throughput whole genome genotyping to look for association between particular alleles of particular SNPS and phenotype of interest. eg. illumina chip.
- fine mapping use more snps from region of interest, zoom in on smaller genomic interval.
- identify base changes that appear only in those individuals.
how many people does AMD effect and waht is it?
10^7 americans
age related muscular degeration
decreasing degeneration of macula
what is the macula
high density of cone cells - colour receptors in the centre of the retina
how was affymetrix chip used for amd
tested 100,000 snps among 96 cases and 50 control
strong signal mapped to 1q31
further high res SNP genotyping identified the complement factor H gene individuals with variant form have higher risk of AMD
what does H gene do in AMD
oxidative damage to lipids in cell membrane creates reactive decomp of product malondialdehyde which forms adducts with cell proteins
complement factor H (CFH) bind to MDA with high affinity, blocking inflammatory reactions.
mutant fails to bind so cant prevent inflammation = AMD
what is the change in the H complement mutant leading to AMD
histidine substitued for tyrosine at residue 402
give an example of personalised treatment
HIV and abacavir
highly effective HIV treatment targetting reverse transcriptase
5-% patients exhibit potentially life threatening hypersensitive reaction associated with a variant in MHC (HLA-B5701)
individuals screened for this variant and abacavir avoided where possible.
