Which Way Is Right? Roh Or Ibd

Question

[mlscmahe]

Dear friends,

I am working on a GWAS data. While finding association for height phenotype, I find a gene BBS (bardet beidl syndrome, a autosomal recessive disorder which effects height) gene getting associated with height trait. The population on which I am working on has high rate of consanguineous marriages. I would like to check whether this marriage pattern is something to do with this gene or not by ROH or IBD analysis. However, I am in a bit of confusion whether to do ROH or IBD as it is a autosomal recessive disorder.

I will be greatful if somebody suggest me which analysis is right in this context?

Answer 1

[ff.cc.cc]

I suggest you to first perform relatedness analysis, estimating the IBD coefficients and then plotting results into a dendrogram or MDS form.

First check HW equilibrium and heterozygosity, then compute IBD with:

i) with plink check the --genome command

or

ii) with R I suggest the SNPRelate package (fast and well documented)

Runs of homozygosity are strictly concerned with the marriage pattern of your population, but I would use it to investigate the hypothesis of consanguineity in a second step.