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(Variants and weights)

Polygenic Score (PGS) ID: PGS000049

Predicted Trait

Reported Trait: Prostate Cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): prostate carcinoma

Score Details

Name: PRS103_PrCa

Original Genome Build: GRCh37
Number of Variants: 103

PGS Development Method: Known susceptibility loci (genome-wide significant SNPs)
PGS Development Details/Relevant Parameters: Sum of log(ORs)

Citation: Lecarpentier J et al. J Clin Oncol (2017) | PGS Catalog Publication ID: PGP000034

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002606
PubMed: 25217961
67,543 individuals European
GWAS Catalog: GCST002606
PubMed: 25217961
2,080 individuals Hispanic or Latin American
GWAS Catalog: GCST002606
PubMed: 25217961
6,954 individuals East Asian
GWAS Catalog: GCST002606
PubMed: 25217961
10,463 individuals Sub-Saharan African, African American or Afro-Caribbean

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.
PGS Performance Metric (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000123 PSS000075 Lecarpentier J et al. (2017) Reported Trait: Prostate cancer in male carriers of BRCA1/2 mutations OR: 1.56 [1.35 - 1.81] AUROC: 0.62 [0.58 - 0.66] 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2
PPM000124 PSS000077 Lecarpentier J et al. (2017) Reported Trait: Low prostate cancer aggressiveness (Gleason score < 7) OR: 1.44 [1.1 - 1.87] 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2
PPM000125 PSS000076 Lecarpentier J et al. (2017) Reported Trait: High prostate cancer aggressiveness (Gleason score ≥ 7) OR: 1.67 [1.37 - 2.04] 3 PCs of ancestry, age at breast or prostate cancer for patient-cases and age at interview for controls, mutation status of BRCA1 or BRCA2

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000075 Breast and prostate cancer cases were defined on the basis of age at diagnosis, whichever occurred first. If breast and prostate cancer occurred at the same time, individuals were treated as patients with breast cancer. 1,525 individuals
[ 212 cases, 1,313 controls]
1.00 %% Male samples
European Self-reported European ancestry BFBOCC, BRICOH, BCFR, CONSIT, CBCS, Chicago, CIMBA, DKFZ, HEBON, EMBRACE, FCCC, G-FaST, GEMO, GC-HBOC, HCSC, HUNBOCS, HVH, HEBCS, ICO, IOVHBOCS, IPOBCS, MUV, MSKCC, NCI, OCGN, OUH, PBCS, CNIO, MAYO, OSU, DEMOKRITOS, ILUH, KCONFAB, SWE-BRCA, UPENN, UPITT, VFCTG
PSS000076 3,325 individuals
[ 2,012 cases, 1,313 controls]
1.00 %% Male samples
European Self-reported European ancestry BFBOCC, BRICOH, BCFR, CONSIT, CBCS, Chicago, CIMBA, DKFZ, HEBON, EMBRACE, FCCC, G-FaST, GEMO, GC-HBOC, HCSC, HUNBOCS, HVH, HEBCS, ICO, IOVHBOCS, IPOBCS, MUV, MSKCC, NCI, OCGN, OUH, PBCS, CNIO, MAYO, OSU, DEMOKRITOS, ILUH, KCONFAB, SWE-BRCA, UPENN, UPITT, VFCTG
PSS000077 1,366 individuals
[ 53 cases, 1,313 controls]
1.00 %% Male samples
European Self-reported European ancestry BFBOCC, BRICOH, BCFR, CONSIT, CBCS, Chicago, CIMBA, DKFZ, HEBON, EMBRACE, FCCC, G-FaST, GEMO, GC-HBOC, HCSC, HUNBOCS, HVH, HEBCS, ICO, IOVHBOCS, IPOBCS, MUV, MSKCC, NCI, OCGN, OUH, PBCS, CNIO, MAYO, OSU, DEMOKRITOS, ILUH, KCONFAB, SWE-BRCA, UPENN, UPITT, VFCTG