What’s the Answer? Open Thread (GWAS genotyping)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

Question of the Week:

How much of the genome is captured by a GWAS?

Two great answers to this questions, a quote from the first one. Click the above link for more.

Human genome encodes 1 SNP/100-300bp; ~3GB sequence ~10million SNPs. It is impossible to analyze such a large number of data due to several limiting factors. To deal with this issue we can use Linkage Disequilibrium (LD) mapping (See section on D’, recombination rate), HaplotypeHaplotype blocks and Haplotype Tag SNPs (tagSNPs). (Read about HapMap project here). Instead of genotyping all the 10M SNPs we can genotype tagSNPs in a haplotype block. This is a representative SNP in a given region of genome with high LD. This will enable to find genetic variation without genotyping all the 10M SNPs. Previous studies indicated that genotyping chips with .5M-1M SNPs will be sufficient for a good GWAS.