What variants are used in the PRS?
- Tim Carver
- Lorenzo Ficorella
- Alex Cunningham PhD (Unlicensed)
Owned by Tim Carver
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.
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.
| 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 |
References
- Incorporating alternative Polygenic Risk Scores into the BOADICEA breast cancer risk prediction model.
- T Tasa, et al., medRxiv. Precision Breast Cancer Screening with a Polygenic Risk Score.
