Question: small case-control exome sequencing study
gravatar for User6891
4.4 years ago by
User6891240 wrote:

Hi everyone,

I have exome data of 25 unrelated patients and 40 unrelated control samples. I'm looking for rare variants associated with the disease. 

I've checked some obvious things: one variant present in cases not in controls. One gene enriched for rare variants in cases compared to controls.

However, now I want to do some statistical testing to find association of a variant/gene with the disease. Since this is just a small-scale study I don't think I can work with methods used in GWAS. Can someone point me to some papers/methods/ideas that could be of interest for my specific situation?

Thanks in advance

exome • 2.4k views
ADD COMMENTlink modified 4.4 years ago by Katie D'Aco990 • written 4.4 years ago by User6891240
gravatar for Katie D'Aco
4.4 years ago by
Katie D'Aco990
Katie D'Aco990 wrote:

As Sam pointed out, SKAT is a good place to start but unless there is a very strong signal from one gene/variant it's unlikely that you will get a statistically significant association from 25 cases.  This paper from Lander & co has some calculations to estimate minimum sample size needed in these types of studies to get good results, and even under the best conditions there generally needs to be hundreds of cases.  But it's worth a shot and even if nothing comes up with a low enough p-value the top hits still might be of interest.

If you haven't already, try answering questions such as: "what rare variants show up in at least two cases, but no controls" "what genes contain novel variants in at least two cases, but no controls"

Have you done any filtering by types of variants (eg, removing all synonymous variants from your analysis, or only looking at stop loss/gain variants)?

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by Katie D'Aco990
gravatar for Sam
4.4 years ago by
Sam2.2k wrote:

My suggestion will be trying to look into SKAT (, our lab is trying to use that for the association test on exome sequencing. You might also try to perform annotation or prioritization using plinkSeq ( or kggSeq (

If you are interested, you can always read into their paper

ADD COMMENTlink written 4.4 years ago by Sam2.2k
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