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Can I ignore somatic mutations that are NOT located in the conserved genomic regions?

Hi all

I am often using annovar to annotate my somatic mutations and "the conserved genomic regions" filter in annovar is the one that I usually enjoy using to analyze my detected variants.

Until now, I filtered out mutations that are not located in converged genomic regions by annovar because I think that those filtered variants are not significantly meaningful for clinical issues. However, nowadays, I think that it is slightly dangerous procedures to ignore the mutations located in conserved regions. Even though they are not conserved regions,they are driver or significant mutations that are required to be further examined.

What do you think about my procedures which are ...

1) ignoring the mutations that are filtered out conserved genomic regions by annovar. (assumption: they never have any clinical or functional impacts so they don't need to be examined at the later step)

2) instead of ignoring them, put the filtered mutations as second groups just in case.

genome sequence
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updated by Ram Ram • written by mangfu100 mangfu100

1 answer

I would personally favor route (2). Variants in unconserved regions are much less likely to be relevant, but they shouldn't just be excluded at the outset. De-prioritizing them into a second class seems like the most reasonable route.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Thanks for your prompt reply.

As you said, I will put them into a second class. Can I ask you a question about annotation for mutation in detail?

When I analyze somatic mutations, I usually judge the mutations according to many annotation filters such as conserved genomic regions (previously mentioned), segmental_duplications and other many databases including cosmic. In my case, I don't use and believe any filter-based annotation which are SIFT or mutation_assessor annotated with score. This is because some cases have lower score but they are much likely to be relevant to the disease or dominant effects. Anyway I really appreciate it if you would give me advice for any useful annotation for mutations. :)

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updated by Ram Ram • written by mangfu100 mangfu100

I unfortunately can't give any advice on that part, you're asking about something that I rarely do at the moment. You might post another question and see if others have good suggestions there.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

Okay. That's also fine with me!

Thanks.

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updated by Ram Ram • written by mangfu100 mangfu100

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