SNP statistical association

Question

[ginlucks]

Hi all

I have to do an exome sequencing in a high prevalence family, then I would study most interesting variants founded in this family in sporadic patients and healthy donors.

I would know what kind of statistical analysis I have to perform to associate SNPs to the pathology.

Is t-test be enough?

[Sean Davis]

Sounds like you have a linkage study (in the high-prevalence family) and an association study with the sporadic patients and healthy donors. A t-test would not be applicable in this situation. Since it sounds like this might be a kind of new topic for you, perhaps you could find a collaborator to work with you to get started?

[ginlucks]

Statistical significance of deleterious variant distribution in the families will be determined by linkage analysis (LOD score > 3.0 ). Then, an association study to compare the proportion of variants in patients versus healthy donors, will be performed by Fisher exact test and odds ratios (ORs).

My collaborator (mentor) told me he doesn't know and since I need to write a statistical analysis for a fellowship application that I would try to win he told me that I have to think about that by myself, so no, I can't find a collaborator to work with..

Thanks in advance for any help