Which Way Is Right? Roh Or Ibd
1
1
Entering edit mode
10.9 years ago
mlscmahe ▴ 100

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 • 3.5k views
ADD COMMENT
4
Entering edit mode
10.9 years ago
ff.cc.cc ★ 1.3k

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 COMMENT

Login before adding your answer.

Traffic: 1289 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6