Question: 1000 Genomes exomes as controls
1
gravatar for knishimura
4.6 years ago by
knishimura10
United States
knishimura10 wrote:

I'm analyzing a small case-only exome sequencing study and am hoping to use publicly-available controls for statistical comparison with SKAT or the C-alpha test.  People have suggested that I use the 1000 Genomes exomes.  Does anyone know of any studies that have been published that use 1000G exomes as controls?  I would like to review the methods that people have used.

Thanks!

 

forum • 1.4k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 4.6 years ago by knishimura10

tell us you searched something, what did you find ?

ADD REPLYlink written 4.6 years ago by Pierre Lindenbaum127k

I am also working on an exome sequencing study with 122 affected samples and no controls. Could you please let me know how you eventually performed the rare variant association analysis?

 

ADD REPLYlink written 4.1 years ago by mkaushal110

I have now the very same problem. Did you find any valuable resource? I'm reading the original paper by Neale trying to implement c-alpha test based on allele counts found in ExAC data. In principle you won't need individual genotypes, only allele counts. Unfortunately the methodology described has some quirks (apparently data in figure 2A don't match table 1)

ADD REPLYlink written 3.4 years ago by Dawe270
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