Haplotype sharing of mutation carriers

Question

[Lio04]

Hi everyone,

I have a question regarding the construction of haplotypes. We have WES data of (unrelated) patients available. In our gene of interest, we found 4 different loss-of-function mutations that are shared by at least 2 patients. So we want to know if the patients who share the same LOF mutation are sharing the same haplotype or not. What is the best way to check this? Is it possible to do this in a reliable way by checking SNPs (from the WES data) spanning my gene of interest? I am not yet experienced with this matter, but I found some information about how WES data is not suited to construct haplotypes and an additional SNP panel has to be done. But since I guess I only need information from a specific region it is reliable to do this?

Thank you for your suggestions!

Answer 1

[Kevin Blighe]

WES data is fine for conducting haplotyping if your region of interest has high SNP density. You should consider using the program HaploView (Broad Institute). I usually get my NGS data into PLINK format and then export to HaploView format, which I then use for linkage disequilibrium analysis, 'tagging' analysis, and haplotyping.

Kevin