Changes between Initial Version and Version 3 of Ticket #1576


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Timestamp:
Mar 28, 2024, 11:54:05 AM (8 months ago)
Author:
Nicklas Nordborg
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  • Ticket #1576

    • Property Summary Calculate Polygenic Risc Scores (PRS) → Calculate Polygenic Risk Scores (PRS)

  • Ticket #1576 – Description

    initial v3  
    1 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/
     1With 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/
    22
    33The 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.