LD and complex diseases:
LD between a marker and the (unknown) genetic variant
contributing to the disease underlies the association approach (i.e., comparing allele frequencies
between cases and controls)
And remember one can select tag-SNPs…
a. Short stretch of DNA for 4 different people – 3 SNPs are present
b. Haplotypes made up of a combination of different alleles at 20 nearby SNPs
c. Genotyping just 3 “tag” SNPs can distinguish all 4 haplotypes
Haplotyping: Phase Problem
Observed: SNP1 G/T SNP2 A/CPossible Haplotypes: GA, TC or GC, TA
n SNPs 2n possible haplotypes
G AT C
SNP1 SNP2
Diploid