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
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 population mean and standard deviation parameters. These calculations are done internally.
PRS | Disease | mean (mu) | standard deviation (sigma) | alpha |
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BCAC 313 | Breast | -0.424 | 0.611 | 0.441 |
BCAC 3820 | Breast | -0.445 | 0.460 | 0.454 |
BRIDGES 306 | Breast | -0.422 | 0.608 | 0.439 |
EGLH-CEN 303
| Breast | -0.407 | 0.606 | 0.438 |
PERSPECTIVE 295 | Breast | -0.448 | 0.599 | 0.433 |
PRISMA 268
| Breast | 0.322 | 0.558 | 0.396 |
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OC-EGLH-CEN 34 | Ovarian | -0.092 | 0.309 | 0.219 |
OCAC 36 | Ovarian | -0.259 | 0.315 | 0.223 |