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Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
https://balsamic.readthedocs.io/
MIT License
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[Assessment] Do we need additional callers for ITD? #1399

Open mathiasbio opened 9 months ago

mathiasbio commented 9 months ago

Description

In conjunction with developing a PR for changing filters and settings for variants called with Manta, I reached out to one of our customers to ask if they were aware of any WGS cases with known FLT3-ITD which I could use to assess the effects of my filtering.

This lead to them bringing up a WGS case wherein they had observed FLT3-ITD in a TGA analysis of the same sample called by VarDict, but which was missing from the WGS case, despite a VAF of 90%. Case can be seen here too: https://docs.google.com/spreadsheets/d/1NdHbUH6zfEGK3EL7BVJBdcydTwdzcAXGhanypQPoKTM/edit#gid=0

This variant was called by TNscope but was filtered out, and wasn't called by either of the SV-callers. It seems that perhaps we should look into adding specific callers for ITD if there are any better equipped to detect these types of variants. It seems at least to be an active field of research to develop such callers: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05173-8

Added ticket for from email-conversation: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=66550

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mathiasbio commented 1 week ago

In new update of balsamic v16.0.0 we saw that the SNV callers have a reduced ability of detecting the FLT3 ITD variants. The SV callers are still detecting them, but it would be good to look into some dedicated callers for this variant.