creating chr17 haplotypes h1 and h2 from exome / gwas data

Question

[Floris Brenk]

Hi all,

I have exome data and gwas data of about 100 individuals. I want check which individual has which chr17 MAPT inversion haplotype (h1 or h2). So I found a paper from 2010 listing 21 inversion markers. In the snp dataset that I have 3 of those markers are present. So my question is: Are 3 of those markers enough to conclude which haplotype is present in which individual?

[rkbunton]

Not an answer I'm afraid, but a follow up question- I too want to know whether it is possible to tell H1/H2 MAPT haplotype from exome data and was wondering if you ever came to a conclusion for this question?

Thanks!

Answer 1

[Floris Brenk]

Yes, you can take almost any SNP from the haplotype. See for example this figure where the association is stable for a long region http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2787725/figure/F3/

Useful papers for further reading:

http://www.ncbi.nlm.nih.gov/pubmed/22751100

http://www.ncbi.nlm.nih.gov/pubmed/22751096