What variants are used in the PRS?

The files below list the variants for

  • breast cancer PRS: BCAC 313; BCAC 3820BRIDGES 306; EGLH-CEN 303; PERSPECTIVE 295PRISMA 268; WISDOM 75; WISDOM 128.

  • ovarian cancer PRS: OCAC 36OC-EGLH-CEN 34.

In the header 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



BCAC 3820


BRIDGES 306


EGLH-CEN 303



PERSPECTIVE 295


PRISMA 268


WISDOM 75


WISDOM 128




OCAC 36



OC-EGLH-CEN 34


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

PRSDiseasemean (mu)standard deviation (sigma)alpha
BCAC 313Breast-0.4240.6110.441
BCAC 3820Breast-0.4450.4600.454
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
WISDOM 75Breast-1.0570.5670.315
WISDOM 128Breast-0.1800.4640.402





OC-EGLH-CEN 34Ovarian-0.0920.3090.219
OCAC 36Ovarian-0.2590.3150.223