What variants are used in the PRS?

The files below list the variants for

  • breast cancer PRS: BCAC 77; BCAC 313; BCAC 3820BRIDGES 306; EGLH-CEN 301; EGLH-CEN 303; MAINZ 309; 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 77


BCAC 313


BCAC 3820


BRIDGES 306


EGLH-CEN 301


EGLH-CEN 303


MAINZ 309


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 77
Breast-0.8920.4490.396
BCAC 313Breast-0.4240.6110.501
BCAC 3820Breast-0.4450.4600.516
BRIDGES 306Breast-0.4220.608

0.498

EGLH-CEN 301Breast-0.3780.6040.496
EGLH-CEN 303
Breast-0.4070.6060.497
MAINZ 309Breast-0.3510.6070.499

PERSPECTIVE 295

Breast-0.4480.5990.492
PRISMA 268
Breast0.3220.5580.451
WISDOM 75Breast-1.0570.5670.360
WISDOM 128Breast-0.1800.4640.452





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

References

  1. N Mavaddat, et al., Cancer Epidemiol Biomarkers Prev. Incorporating alternative Polygenic Risk Scores into the BOADICEA breast cancer risk prediction model.
  2. T Tasa, et al., medRxiv. Precision Breast Cancer Screening with a Polygenic Risk Score.