GWAS from case/control + family based WGS data -how to effectively use together

Question

[datanerd]

HI all,

We have a GWAS from case/control run on exomechip.

We also have 8 families (not necessarily trios) with affected and unaffected members whole genome sequenced. This is a common disease more prevalent in this ethnic group.

I am hoping to use this familial study as a filter for the exomechip variants before replicating in other in dependent. Iam currently thinking of ways to use this filter - however aim a little concerned that the disease does not have 100% penetrance but sometimes skips a generation and shows up in the next.

Any suggestion how to effectively use the filter or any paper?

Thanks so much!! Mamta

[natasha.sernova]

Dear Mamta,

See these papers, I hope, they may be helpful:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085641/

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0138-2

http://www.nature.com/ncomms/2015/150116/ncomms6965/full/ncomms6965.html

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211559/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377835/

[datanerd]

Thanks. I will look into them.