Predicted Trait | |
Reported Trait | Prostate cancer |
Mapped Trait(s) | prostate carcinoma (EFO_0001663) |
Score Construction | |
PGS Name | PRS_PC |
Variants | |
Original Genome Build | hg19 |
Number of Variants | 6,606,785 |
Development Method | |
Name | LDpred |
Parameters | ρ = 0.01; LD radius = 4000; LD reference panel = 2,690 Finnish individuals [autosomal variants only] |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000100 |
Citation (link to publication) | Mars N et al. Nat Med (2020) |
Study Identifiers | Sample Numbers | Sample Ancestry |
---|---|---|
GWAS Catalog: GCST006085 EuropePMC: 29892016 |
140,254 individuals | European |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|
National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. | — | 21,813 individuals, 47.3 % Male samples |
Mean (Age At Baseline) = 48.0 years | European (Finnish) |
— | FINRISK | Used to select optimal threshold of ρ for all subsequent analyses. FINRISK surveys from 1992, 1997, 2002 and 2007 |
PGS Performance Metric ID (PPM ID) |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|
PPM000890 | PSS000446 | PGP000100 Mars N et al. (2020) |
Reported Trait: Prostate cancer (incident and prevalent cases) | HR: 1.83 [1.78, 1.9] | — | — | genotyping array/batch, 10 ancestry PCs | — |
PPM000895 | PSS000447 | PGP000100 Mars N et al. (2020) |
Reported Trait: Incident prostate cancer | — | C-index: 0.857 | — | age, genotyping array/batch, 10 ancestry PCs | 10-year risk |
PPM000900 | PSS000447 | PGP000100 Mars N et al. (2020) |
Reported Trait: Incident prostate cancer | — | C-index: 0.866 | — | age, family history, history of benign prostate hyperplasia, genotyping array/batch, 10 ancestry PCs | 10-year risk |
PGS Sample Set ID (PSS ID) |
Phenotype Definitions and Methods | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|---|
PSS000446 | National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. | — | [ ,
100.0 % Male samples |
— | European (Finnish) |
— | FinnGen | — |
PSS000447 | National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. | — | [
|
— | European (Finnish) |
— | FinnGen | — |