The files below list the variants for
breast cancer PRS: BCAC
77; BCAC 313; BCAC 3820; BRIDGES 306; EGLH-CEN 301; EGLH-CEN 303
; 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
View file name BCAC_77_PRS.prs height 150
BCAC 313
View file name BCAC_313_PRS.prs height 150
BCAC 3820
View file name BCAC_3820_PRS.prs height 150
BRIDGES 306
View file name BRIDGES_306_PRS.prs height 150
EGLH-CEN 301
View file name EGLH-CEN_301_PRS.prs height 150
EGLH-CEN 303
View file name EGLH-CEN_303_PRS.prs height 150
PERSPECTIVE 295
View file name PERSPECTIVE_295_PRS.prs height 150
PRISMA 268
_289View file name PRISM _268_PRS.prs height 150
WISDOM 75
View file name WISDOM_75_PRS.prs height 150
WISDOM 128
View file name WISDOM_128_PRS.prs height 150
OCAC 36
| View file | ||||
|---|---|---|---|---|
|
OC-EGLH-CEN 34
| View file | ||||
|---|---|---|---|---|
|
Note: For use in BOADICEA, once the vcf file is uploaded, a raw PRS is calculated and standardised using the following
populationmean 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 | 0.441501 | |
| 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. | 439496 |
| EGLH-CEN 303 | Breast | -0.407 | 0.606 | 0.438497 | |
PERSPECTIVE 295 | Breast | -0.448 | 0.599 | 0.433492 | |
| PRISMA 289268 | Breast | 0.322 | 0.558 | 0.396451 | |
| 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.
