What Is Haplotyping In Context Of Gwas?

Question

[kumar.vinod81]

I am not understanding the concept of haplotyping in GWAS. I think that we can only make haplotypes in case where we have dense SNPs throughout the genome which are completely in LD or we can make haplotype when we have very less number of SNPs which might be in LD or not. Or haplotyping denotes some other thing in case of GWAS? Thanks,

Answer 1

[Zev.Kronenberg]

A haplotype can be one base pair or span an entire chromosome. With population data you can phase the heterozygous SNPs/SNVs to tell you which base goes with which strand. With low density SNP arrays you can still identify stretches of mutations that are always found on the same strand / haplotype.

One consideration is resolution. Lets say you have two phased hets (A:G, T:C) 3 Mb apart. Just because you see A(pos 1) and T(pos 2) together all the time does not guarantee that they are on the same haplotype. There could be a lot of mutations in between that break up the haplotype. The denser the genotyping the better haplotype predictions.

Make sense?

EDIT:

Thanks for the suggestion.

Here is an Annual Review article on the medical importance of haplotypes:

http://www.annualreviews.org/doi/pdf/10.1146/annurev.med.56.082103.104540

[Khader Shameer]

I would add a link to haplotype wiki page, hapmap and one or two good review articles to complete this fantastic answer :) !

[Giovanni M Dall'Olio]

Another good review is Kingsmore et al 2008, Genome-wide association studies: progress and potential for drug discovery and development

[kumar.vinod81]

Its a good answer. You mean if two SNPs present close or too apart on same strand but their tendency to appear on the same strand in a population is high, then it make a haplotype.