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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] Include columns for SNVs showing LoH / CNV in new TGA CNV PDF #1366

Open mathiasbio opened 7 months ago

mathiasbio commented 7 months ago

Description

Clinicians need to be able to detect LoH and CNV in TGA cases. Currently a CNV report is produced which contains diagrams and tables for CNVs and LoH, CNVs are also in the SV VCF file and both are uploaded to Scout. However they may not be good enough, or intuitive enough to understand, and either the way the results are displayed -- or the results themselves may need improvement.

Before Christmas Lucia and Aleksandra Krstic requested the new LoH analysis before v13 was released. I ran the current validation branch for their case and shared the results manually.

They were unable to solve their question solely with the CNV report produced and asked for SNV frequencies overlapping the LoH of interest (at TP53) and I then prepared a small excel sheet with this info. They then requested if we could add info like this in the CNV report.

Related ticket here: https://clinical-scilifelab.supportsystem.com/scp/tickets.php?id=64549

Intuitively I find it hard to see how we could include the info they want in a PDF report, which is already quite dense! And probably what is needed is a meeting with the customers to better understand their needs, and then create a more viable solution in some different format.

Suggested approach

Instead of merely implementing their request we should set up a meeting with the customers to better understand their needs.

Criteria

Dialogue with customers and going over results.

Origin

No response

Anything else?

No response

mathiasbio commented 7 months ago

This could perhaps be solved by this: https://github.com/Clinical-Genomics/BALSAMIC/issues/1385