This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to conduct germline sharing WES analysis of three probands in a large family with the same tumour type.

I have a question regarding sharing. Is there a 'sharing of the same putitative genes across 3 probands' type of tutorial or pipeline you could point me to?

I essentially have exome data for a trio and 2 other probands in a large family who have all been affected by a certain rare cancer type. These are germline cancers as per pedigree information. I want to see if these probands share any variants or a specific gene region/gene. Ideally to uncover, for example, a truncated protein mutation in all 3 that may cause the disease.

I believe this is more of a downstream analysis question, once a pipeline such as GATK has been completed.

Any help would be greatly appreciated.

exomes germline variant analysis
• 1,240 views • link
written by Maverick77 • Maverick77

How are these "2 other probands" related to the trio?

I don't think their relatedness would be a factor in looking at shared variants unless you wish to track the variant inheritance, for which you will need sequences for almost all family members between the extra probands and the trio.

• 0 views • link
written by Ram Ram

Indeed, it doesn't really matter that they're related. It's basically looking at a trio and seeing what is different in the proband compared to the parents. And then comparing that specific difference to see if it can be found in the other 2 probands

• 0 views • link
written by Maverick77 • Maverick77

Those are two different steps. For the trio analysis, plinkseq denovo might be of use. For the latter, you might need to use some other plinkseq sub-tool or maybe bcftools.

• 0 views • link
written by Ram Ram

1 answer

Indeed, it doesn't really matter that they're related. It's basically looking at a trio and seeing what is different in the proband compared to the parents. And then comparing that specific difference to see if it can be found in the other 2 probands.

• 0 views • link
written by Maverick77 • Maverick77

Hi Maverick77 ,

This reply is better suited as a reply to my comment. Could you make the appropriate change please? That would involve the following steps:

  1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + click the link to open it in a new tab) and do a Select All -> Copy there).
  2. Click on Add Reply on my comment here: C: How to conduct germline sharing WES analysis of three probands in a large family
  3. Paste the copied text
  4. Click on the green Add Comment button
  5. Click on moderate back in your answer here: A: How to conduct germline sharing WES analysis of three probands in a large family
  6. Choose Delete Post
  7. Click on the blue Submit button.

Thank you!

P.S: Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate.

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this