What variants are used in the PRS?

The files below list the BCAC 313 variants, the BRIDGES 306 variants and the PERSPECTIVE 295 variants used in the breast cancer PRS and the OCAC 36 variants used in the ovarian cancer PRS. The first line in each file is the square root of the proportion of the overall polygenic variance explained by the PRS (alpha). The rest of the file consists of data records containing the following comma separated fields:

  • name - the name of the variant

  • chromosome - the chromosome on which the variant resides

  • position -  Build 37 (hg19), with 1-based variant positions

  • reference_allele - the reference allele for the variant

  • effect_allele - the effect allele for the variant

  • log_odds_ratio - the log odds ratio for the variant

  • effect_allele_frequency - the allele frequency for the variant



BCAC 313

 


BRIDGES 306


PERSPECTIVE 295


OCAC 36

Note: For use in BOADICEA, once the vcf file is uploaded, a raw PRS is calculated and standardised using the following population mean and standard deviation parameters. These calculations are done internally.

PRSDiseasemean (mu)standard deviation (sigma)alpha
BCAC 313Breast-0.42403410.60314720.444
BRIDGES 306Breast-0.42197830.59893190.442
PERSPECTIVE 295Breast-0.44846630.59133090.440