I don’t see this question was asked already. Will there be a V4 screened for cancer?
It would be great to hear from the gnomAD team about next future plans on this topic.
For gnomAD v.4.0, this section might be relevant for you: gnomAD v4.0 | gnomAD browser
No. As Javier already linked, we explain this in the v4 release blog:
We have removed support for subsets from the gnomAD v4 exomes for two major reasons: given the large size of gnomAD v4 and the small size of any single cohort, we do not feel that the prevalence of any disease is high enough to warrant subsets. In addition, there is increased inclusion of biobank samples, and we do not have concise phenotype metadata for these and many other gnomAD samples, so we cannot ensure that samples in a non-disease subset do not have the specified disease.
Hi, thanks for the helpful discussion. I was wondering if there’s a recommended allele frequency threshold that can be used to filter out potential cancer-associated variants?
For instance, known somatic hotspot mutations like TP53 R175H and KRAS G12D appear in gnomAD with very low frequencies (e.g., 4.34e-6 and 3.72e-6, respectively). Would applying a filter to exclude variants below, say, 1e-4 or 1e-5 be a reasonable strategy to minimize the inclusion of such variants?
If possible, could you please share an AF cutoff you recommend based on your experience?
Thank you!