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What variants are used in the PRS?

What variants are used in the PRS?

The files below list the variants for

  • breast cancer PRS: BCAC 77; BCAC 313; BCAC 3820; BRIDGES 306; EGLH-CEN 301; EGLH-CEN 303; MAINZ 309; PERSPECTIVE 295; PRISMA 268; WISDOM 75; WISDOM 128.

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

  • prostate cancer PRS: Nyberg 268.

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

 

 

Nyberg 268

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.

PRS

Disease

mean (mu)

standard deviation (sigma)

alpha

PRS

Disease

mean (mu)

standard deviation (sigma)

alpha

BCAC 77

Breast

-0.892

0.449

0.396

BCAC 313

Breast

-0.424

0.611

0.501

BCAC 3820

Breast

-0.445

0.460

0.516

BRIDGES 306

Breast

-0.422

0.608

0.498

EGLH-CEN 301

Breast

-0.378

0.604

0.496

EGLH-CEN 303

Breast

-0.407

0.606

0.497

MAINZ 309

Breast

-0.351

0.607

0.499

PERSPECTIVE 295

Breast

-0.448

0.599

0.492

PRISMA 268

Breast

0.322

0.558

0.451

WISDOM 75

Breast

-1.057

0.567

0.360

WISDOM 128

Breast

-0.180

0.464

0.452

 

 

 

 

 

OC-EGLH-CEN 34

Ovarian

-0.092

0.309

0.219

OCAC 36

Ovarian

-0.259

0.315

0.223

Nyberg 268

Prostate

23.954

0.860

0.523

References

  1. N Mavaddat, et al., Cancer Epidemiol Biomarkers Prev. Incorporating alternative Polygenic Risk Scores into the BOADICEA breast cancer risk prediction model. doi: https://doi.org/10.1101/2022.07.08.22276452

  2. T Tasa, et al., medRxiv. Precision Breast Cancer Screening with a Polygenic Risk Score. https://doi.org/10.1101/2020.08.17.20176263