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