Trait: prostate carcinoma

Information

Experimental Factor Ontology ID: EFO_0001663

EFO Trait Description: A carcinoma that arises from epithelial cells of the prostate gland. [MONDO: DesignPattern]

Associated PGS

PGS 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 Evaluated Score 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
PPM000061 PGS000030 (PrCa) PSS000041 Schumacher FR et al. (2018) Reported Trait: Prostate cancer OR: 1.86 [1.83 - 1.89] Top 7 Genetic PCs, country Samples were also part of the variant association
PPM000104 PGS000044 (PrCa66) PSS000068 Pashayan N et al. (2015) Reported Trait: Elevated serum prostate-specific antigen (PSA) levels OR (per 1-point increase in PRS): 1.23 [1.1 - 1.37] cancer stage, Gleason score
PPM000105 PGS000044 (PrCa66) PSS000069 Pashayan N et al. (2015) Ext. Reported Trait: aggressive prostate cancer (Gleason score ⩾7) OR (above vs. below 50th percentile of PRS): 1.56 [1.15 - 2.1]
PPM000123 PGS000049 (PRS103_PrCa) 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 PGS000049 (PRS103_PrCa) 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 PGS000049 (PRS103_PrCa) 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
PSS000041 For each cohort core data on disease status, age at diagnosis (age at observation or questionnaire for controls), family history of PrCa, and clinical factors for cases (for example, PSA at diagnosis and Gleason score) was extracted 74,849 individuals
[ 46,939 cases, 27,910 controls]
European APCB, CPS, CONOR, COSM, CPCS, ESTHER, ERSPC, EPIC, FHCRC, Gene-PARE, PROFILE, HZ, HPFS, IPO-Porto, IMPACT, Leuven, LAAPC, MDACCS, MCCS, MOFFITT_PC, MCC-Spain, MEC, PROCAP, PRAGGA, PHS, Poland, SWOG-PCPT, PCMUS, PROGReSS_PrCa, ProtecT, ProMPT, PLCO, RAPPER, QLD, SFPCS, SWOG-SELECT, SNP_Prostate_Ghent, SPAG, STHM2, SEARCH, TAMPERE, UKGPCS, TOR These samples (OncoArray) were also used in the GWAS meta-analysis
PSS000068 Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml. 8,796 individuals
[ 2,148 cases, 6,648 controls]
100.00 %% Male samples
European ProtecT
PSS000068 Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml. 5,059 individuals
[ 4,099 cases, 960 controls]
100.00 %% Male samples
European SEARCH
PSS000068 Prostate cancer was classified as localized disease with tumor-node-metastasis stage T2 and below and advanced disease (regional-distant) was classified as localized disease with tumor-node-metastasis stage T3 and above (low aggressive tumor, Gleason score <7; intermediate to highly aggressive tumor, Gleason score ≥7). Elevated serum prostate-specific antigen (PSA) levels were defined as ≥4 ng/ml. 3,157 individuals
[ 3,157 cases, 0 controls]
100.00 %% Male samples
European UKGPCS
PSS000069 Prostate cancer was classified as localised disease with tumour-node-metastasis (TNM) stage T1-2 N0 M0; and advanced disease (regional-distant) with stage T3 and above or any T N1 M1; as non-aggressive tumour, Gleason score <7, and aggressive tumour, Gleason score ⩾7. 4,967 individuals
[ 1,089 cases, 3,878 controls]
100.00 %% Male samples
European
(Finnish)
ERSPC
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