Opened 9 months ago

Last modified 7 months ago

#1576 closed task

Calculate Polygenic Risk Scores (PRS) — at Version 3

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.54
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

With ticket #1575 we get a lot of genotypes for the Oncoarray data. We would like to be able to calculate Polygenic Risk Scores from this data set. To begin with the PRS with 313 variants that is described here ​https://pubmed.ncbi.nlm.nih.gov/30554720/

The implementation idea is that it should be relatively easy to filter the imputed VCF so that only the data for the 313 variants remain. We could save this as a separate file and include the PRS weights in it. Then it would be relatively easy to calculate the final score and store it as an annotation. But we need to investigate how to handle variants with a lower INFO (quality) score.

Change History (3)

comment:1 by Nicklas Nordborg, 9 months ago

In 7609:

References #1576: Calculate Polygenic Risc Scores

Added an item list for Oncoarray items and a link on the front page.

comment:2 by Nicklas Nordborg, 8 months ago

Summary: Calculate Polygenic Risc Scores (PRS) → Calculate Polygenic Risk Scores (PRS)

comment:3 by Nicklas Nordborg, 8 months ago

Description: modified (diff)
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