What variants are used in the PRS?

The files below list the BCAC 313 variants, the BRIDGES 306 variants, the EGLH-CEN 303 variants, the PERSPECTIVE 295 variants and the PRISMA 268 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

EGLH-CEN 303

PERSPECTIVE 295

PRISMA 268


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-0.4240.6110.441
BRIDGES 306Breast-0.4220.608

0.439

EGLH-CEN 303
Breast-0.4070.6060.438

PERSPECTIVE 295

Breast-0.4480.5990.433
PRISMA 268
Breast0.3220.5580.396