Mixed design analysis with GenABEL

Questions about GenABEL (aka *ABEL) suite of packages
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Joined: Fri Nov 01, 2013 5:52 pm

Mixed design analysis with GenABEL

Postby genabelforum » Fri Nov 01, 2013 6:00 pm

Dear All,

I'm working on a GWAS study using samples that come from a set of villages with a certain degree of consanguinity/relatedness. Children (probands and sibs) are phenotyped, and we have samples from probands, their siblings, and, in some cases, parents. The questions that I have boil down to:

1) How useful it is to genotype parents in case when there is only one parent (or even two parents)? It would've been useful for reconstructing pedigree(s) but then again approaches like GRAMMAR-GC utilize genomic kinship data… In case when the parents are NOT phenotyped (e.g., like in the FBAT approach with nuclear families), can they be incorporated in the analysis? The examples I found (including the Amin et al.'s wonderful paper in PLoS One on GRAMMAR) mostly (only?) deal with situations when both phenotypes and genotypes are available for samples of potentially related individuals.

2) How suitable is this approach for the analysis of datasets that combine data from a) nuclear families with both parents genotyped but not phenotyped, b) trios of sib+sib+just one genotyped but not phenotyped parent, c) sib pairs, d) half-sib pairs, e) singletons?

I understand that this might be crossing into the territory beyond that of technical questions about GenABEL, but any and all advice would be much appreciated (especially concerning the use of GRAMMAR-GC).

Thank very much for your time!

Best regards,


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