Exome sequencing for homozygous recessive disease

[Samarpana]

I am naive in the field of genomics. Please guide me through these questions.

If I have exome sequencing data of a family with a homozygous recessive disease, how should I analyze the data?Do we assume that the cases should be homozygous for a given genotype and controls as heterozygous?

Also, are there any tool/webpage that help us identify known SNPs associated to a particular disease? I want to check if the SNPs that I have obtained are previously known to be associated with my disease of interest?

[blancha]

For your second question, how about ClinVar?

https://www.ncbi.nlm.nih.gov/clinvar/

[dpryan]

Are you positive that they're homozygous and not compound heterozygous? The latter would be more likely unless they're consanguineous.

[Samarpana]

@ dpryan - There is a few incidents of consanguinity in the family but since I am looking at a complex disease (asthma), compound heterozygosity is also a possibility. Can you please tell me how can we decide which model fits best?

@blancha - Thank you for the suggestion. I would try it.. Thanks again

[dpryan]

There's no hard and fast rule that I'm aware of. In general, the greater the consanguinity the more likely the variant is homozygous.

[Samarpana]

okay.. Thanks a lot