The files below list the BCAC 313 variants, the BRIDGES 306 variants and the PERSPECTIVE 295 variants used in the breast cancer PRS and the OCAC 36. 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
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BRIDGES 306
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PERSPECTIVE 295
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OCAC 36
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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 population mean and standard deviation parameters. These calculations are done internally.
| PRS | Disease | mean (mu) | standard deviation (sigma) | alpha |
|---|---|---|---|---|
| BCAC 313 | Breast | -0.4240341 | 0.6031472 | 0.444 |
| BRIDGES 306 | Breast | -0.4219783 | 0.5989319 | 0.442 |
| PERSPECTIVE 295 | Breast | -0.4484663 | 0.5913309 | 0.440 |
