The files below list the variants for
breast cancer PRS: BCAC 77; BCAC 313; BCAC 3820; BRIDGES 306; 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 250150
BCAC 313
| View file | ||||
|---|---|---|---|---|
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BCAC 3820
| View file | ||||
|---|---|---|---|---|
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BRIDGES 306
| View file | ||||
|---|---|---|---|---|
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EGLH-CEN 303
| View file | ||||
|---|---|---|---|---|
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PERSPECTIVE 295
View file name PERSPECTIVE_295_PRS.prs height 150
PRISMA 268
| View file | ||||
|---|---|---|---|---|
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WISDOM 75
| View file | ||||
|---|---|---|---|---|
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WISDOM 128
| View file | ||||
|---|---|---|---|---|
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OCAC 36
| View file | ||||
|---|---|---|---|---|
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OC-EGLH-CEN 34
| View file | ||||
|---|---|---|---|---|
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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 |
|---|---|---|---|---|
| ANTEBC 28032 | Breast | -0.339 | 0.423 | 0.437 |
| BCAC 77 | Breast | -0.892 | 0.449 | 0.350 |
| 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 |
| WISDOM 75 | Breast | -1.057 | 0.567 | 0.315 |
| WISDOM 128 | Breast | -0.180 | 0.464 | 0.402 |
| 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.
