Question: Which Way Is Right? Roh Or Ibd
1
gravatar for mlscmahe
5.4 years ago by
mlscmahe80
Kuwait
mlscmahe80 wrote:

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?

gwas • 2.2k views
ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by mlscmahe80
4
gravatar for ff.cc.cc
5.4 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

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.

ADD COMMENTlink written 5.4 years ago by ff.cc.cc1.3k
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