how to adjust ascertainment bias (GWAS study)

Question

[famstats]

Hi,

I'm working in a family-based cohort and my goal is to do a GWAS. The problem is: the families were selected because of the measures of one individual (proband).

I can adjust the bias created by relatedness using the kinship matrix, but how can I adjust the bias generated by the proband? of course, all of them have high levels of the disease I'm studying and this generates false positives.

I have to condition the likelihood of each family by the value of the proband, but I don't know how to do that (I'm working with R). Do you know any software useful for this problem?

[Fabio Marroni]

Out of curiosity: why do you want to use association instead of linkage or transmission-disequilibrium test?

This said, you might search the literature for "family-based association test", there are several tools around.

I remember using FBAT

[famstats]

Thanks for the answer.

I ended up doing it in SOLAR-ECLIPSE (which uses Measured Genotype Approach and adjust for ascertainment) instead of trying to do all by myself.

I know Linkage Analysis is more suitable for my dataset but GWAS also provides you information and allows you to do other stuff like meta-analysis, gene-based tests or LD-hub.