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5 years, 11 months ago
Is there a vcf file on the GRCh38 assembly with common cancer mutations I can download somewhere? Maybe from one of the big international cancer genomics consortia?
By common, I mean whichever mutations have been found recurrent in different types of cancer.
Jun 15, 2017 at 11:56
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Your question doesn't give enough information for a specific answer but this should do for a start.
Get the VCF file describing all variants in Clinvar from NCBI:
Extract any variants whose VCF line contains the word "cancer":
zgrep -iE '^#|CLNDBN=[^;]*cancer' clinvar.vcf.gz > cancer.vcf
Now, you should probably filter that further based on variant frequency, type of cancer, etc etc but that should be a good start.
Jun 15, 2017 at 12:55
terdon ♦ terdon
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If you are looking for cancer mutations, the primary resource is COSMIC and they provide GRCh38 VCFs. The download page is here:
It'll be up to you how you define "common", but the VCF includes a lot of information you can use.
Jun 18, 2017 at 17:04
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The trouble with looking for cancer-associated variants is that it can be difficult to tease out spurious effects (e.g. ethnicity) from causative variants. If you're interested in what
genes are implicated in most types of cancer, the annotations for the NanoString panels are quite good:
The "Support documents" section of those pages has a link to an Excel file with gene lists and probe sequences. While these lists don't give information about variants that disrupt function, I'm struggling a bit to think through why it would be useful in advance to know that, unless the aim is to induce cancer through CRISPR or something like that.
Jun 15, 2017 at 13:22
gringer ♦ gringer
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