Question: Haplotype sharing of mutation carriers
gravatar for Lio04
8 months ago by
Lio040 wrote:

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!

snp wes ngs haplotype • 267 views
ADD COMMENTlink modified 8 months ago by Kevin Blighe41k • written 8 months ago by Lio040
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe41k
London, England
Kevin Blighe41k wrote:

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.


ADD COMMENTlink modified 8 months ago • written 8 months ago by Kevin Blighe41k
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