Opened 2 months ago
Last modified 2 weeks ago
#1576 closed task
Calculate Polygenic Risc Scores (PRS) — at Initial Version
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | Reggie v4.54 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
With ticket #1575 we get a lot of genotypes for the Oncoarray data. We would like to be able to calculate Polygenic Risc 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.
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