Trait: prostate carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001663
Description A carcinoma that arises from epithelial cells of the prostate gland. [MONDO: DesignPattern]
Trait category
Cancer
Synonyms 7 synonyms
  • Carcinoma of Prostate
  • prostate gland carcinoma
  • carcinoma of the prostate
  • carcinoma of prostate gland
  • Carcinoma of the Prostate
  • prostate carcinoma
  • carcinoma of prostate
Mapped term(s) 9 mapped terms
  • DOID:10286
  • MONDO:0005159
  • NCIT:C4863
  • OMIM:176807
  • UMLS:C0600139
  • NCIt:C4863
  • ICD10:C61
  • SNOMEDCT:254900004
  • KEGG:05215

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000030 PrCa PGP000019 Schumacher FR et al. Nat Genet (2018) Prostate cancer prostate carcinoma 147 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000030/ScoringFiles/PGS000030.txt.gz
PGS000044 PrCa66 PGP000031 Pashayan N et al. Br J Cancer (2015) Prostate cancer prostate carcinoma 66 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000044/ScoringFiles/PGS000044.txt.gz
PGS000049 PRS103_PrCa PGP000034 Lecarpentier J et al. J Clin Oncol (2017) Prostate Cancer prostate carcinoma 103 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000049/ScoringFiles/PGS000049.txt.gz
PGS000067 PCa_PHS PGP000047 Seibert TM et al. BMJ (2018) Prostate cancer prostate carcinoma 54 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000067/ScoringFiles/PGS000067.txt.gz
PGS000084 CC_Prostate PGP000050 Graff RE et al. bioRxiv (2020) Pre Prostate cancer prostate carcinoma 161 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000084/ScoringFiles/PGS000084.txt.gz
PGS000160 cGRS_Prostate PGP000075 Shi Z et al. Cancer Med (2019) Prostate cancer prostate carcinoma 79 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000160/ScoringFiles/PGS000160.txt.gz
PGS000333 PRS_PC PGP000100 Mars N et al. Nat Med (2020) Prostate cancer prostate carcinoma 6,606,785 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000333/ScoringFiles/PGS000333.txt.gz

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 ID
(PPM ID)
Evaluated Score 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
PPM000061 PGS000030 (PrCa) PSS000041 PGP000019
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
PPM000204 PGS000084 (CC_Prostate) PSS000123 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Prostate cancer OR: 1.44[1.41, 1.47] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, 10 PCs. Results from meta-analysis of GERA and UKB
PPM000183 PGS000067 (PCa_PHS) PSS000105 PGP000047
Seibert TM et al. (2018)
Reported Trait: aggressive prostate cancer (age at onset) z-test (p-value) < 1e-16
PPM000105 PGS000044 (PrCa66) PSS000069 PGP000032
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]
PPM000182 PGS000067 (PCa_PHS) PSS000105 PGP000047
Seibert TM et al. (2018)
Reported Trait: aggressive prostate cancer HR (Hazard ratio; top 2% vs. average risk): 2.9[2.4, 3.4]
PPM000184 PGS000067 (PCa_PHS) PSS000106 PGP000047
Seibert TM et al. (2018)
Reported Trait: any prostate cancer HR (Hazard ratio; top 2% vs. average risk): 2.5[2.2, 2.8]
PPM000185 PGS000067 (PCa_PHS) PSS000106 PGP000047
Seibert TM et al. (2018)
Reported Trait: any prostate cancer (age at onset) z-test (p-value) < 1e-16
PPM000187 PGS000067 (PCa_PHS) PSS000107 PGP000047
Seibert TM et al. (2018)
Reported Trait: very aggressive prostate cancer (age at onset) z-test (p-value) < 1e-11
PPM000393 PGS000067 (PCa_PHS) PSS000221 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
Reported Trait: Age of aggressive prostate cancer onset Hazard Ratio (HR; top 20% vs. rest): 2.4[2.3, 2.6] Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000392 PGS000067 (PCa_PHS) PSS000222 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
Reported Trait: Age of aggressive prostate cancer onset Hazard Ratio (HR; top 20% vs. rest): 5.2[4.8, 5.6] Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000391 PGS000067 (PCa_PHS) PSS000223 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
Reported Trait: Age of aggressive prostate cancer onset Hazard Ratio (HR; top 20% vs. rest): 5.6[5.2, 6.0] Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000390 PGS000067 (PCa_PHS) PSS000220 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
Reported Trait: Age of aggressive prostate cancer onset Hazard Ratio (HR; top 20% vs. rest): 5.9[5.5, 6.3] Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000394 PGS000067 (PCa_PHS) PSS000224 PGP000058
Huynh-Le M et al. (2019)
Ext. Pre
Reported Trait: Age of prostate cancer death Hazard Ratio (HR; top 20% vs. rest): 5.7[4.6, 7.0] Association between PHS and age-at-onset p-value < 10e-16. Only SNPs directly genotyped on the OncoArray genotyping array were considered. 46 of the score's 54 SNPs were used: 24 directly genotyped, and 22 with acceptable proxies (r2>0.94).
PPM000104 PGS000044 (PrCa66) PSS000068 PGP000031
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
PPM000123 PGS000049 (PRS103_PrCa) PSS000075 PGP000034
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 PGP000034
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 PGP000034
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
PPM000895 PGS000333 (PRS_PC) 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 PGS000333 (PRS_PC) 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
PPM000890 PGS000333 (PRS_PC) 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
PPM000186 PGS000067 (PCa_PHS) PSS000107 PGP000047
Seibert TM et al. (2018)
Reported Trait: very aggressive prostate cancer HR (Hazard ratio; top 2% vs. average risk): 3.0[2.2, 4.0]
PPM000491 PGS000160 (cGRS_Prostate) PSS000280 PGP000075
Shi Z et al. (2019)
Reported Trait: Prostate cancer Odds Ratio (OR; high vs. average risk groups): 1.73[1.38, 2.17]
PPM000480 PGS000160 (cGRS_Prostate) PSS000280 PGP000075
Shi Z et al. (2019)
Reported Trait: Prostate cancer Mean realative risk: 1.3[1.21, 1.38]
Wilcoxon test (case vs. control) p-value: 2.07e-18

Evaluated Samples

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
PSS000076
[
  • 2,012 cases
  • , 1,313 controls
]
,
100.0 % Male samples
European Self-reported European ancestry 37 cohorts
  • BCFR
  • ,BFBOCC
  • ,BRICOH
  • ,CBCS
  • ,CIMBA
  • ,CNIO
  • ,CONSIT
  • ,Chicago
  • ,DEMOKRITOS
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,ILUH
  • ,IOVHBOCS
  • ,IPOBCS
  • ,KCONFAB
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSU
  • ,OUH
  • ,PBCS
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG
PSS000077
[
  • 53 cases
  • , 1,313 controls
]
,
100.0 % Male samples
European Self-reported European ancestry 37 cohorts
  • BCFR
  • ,BFBOCC
  • ,BRICOH
  • ,CBCS
  • ,CIMBA
  • ,CNIO
  • ,CONSIT
  • ,Chicago
  • ,DEMOKRITOS
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,ILUH
  • ,IOVHBOCS
  • ,IPOBCS
  • ,KCONFAB
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSU
  • ,OUH
  • ,PBCS
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG
PSS000123 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28010
[
  • 10,810 cases
  • , 190,706 controls
]
,
100.0 % Male samples
European GERA, UKB
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
[
  • 46,939 cases
  • , 27,910 controls
]
,
100.0 % Male samples
European 43 cohorts
  • APCB
  • ,CONOR
  • ,COSM
  • ,CPCS
  • ,CPS
  • ,EPIC
  • ,ERSPC
  • ,ESTHER
  • ,FHCRC
  • ,Gene-PARE
  • ,HPFS
  • ,HZ
  • ,IMPACT
  • ,IPO-Porto
  • ,LAAPC
  • ,Leuven
  • ,MCC-Spain
  • ,MCCS
  • ,MDACCS
  • ,MEC
  • ,MOFFITT_PC
  • ,PCMUS
  • ,PHS
  • ,PLCO
  • ,PRAGGA
  • ,PROCAP
  • ,PROFILE
  • ,PROGReSS_PrCa
  • ,Poland
  • ,ProMPT
  • ,ProtecT
  • ,QLD
  • ,RAPPER
  • ,SEARCH
  • ,SFPCS
  • ,SNP_Prostate_Ghent
  • ,SPAG
  • ,STHM2
  • ,SWOG-PCPT
  • ,SWOG-SELECT
  • ,TAMPERE
  • ,TOR
  • ,UKGPCS
These samples (OncoArray) were also used in the GWAS meta-analysis
PSS000220 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases
[
  • 26,419 cases
  • , 30,575 controls
]
,
100.0 % Male samples
Other Combined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified) OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000221 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases
[
  • 1,424 cases
  • , 3,013 controls
]
,
100.0 % Male samples
African unspecified Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000222 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases
[
  • 716 cases
  • , 1,185 controls
]
,
100.0 % Male samples
Asian unspecified Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000223 Age of onset of aggressive prostate cancer, defined by Gleason score ≥7, PSA ≥10 ng/mL, T3-T4 stage, nodal metastases, or distant metastases
[
  • 24,279 cases
  • , 26,377 controls
]
,
100.0 % Male samples
European Subset of OncoArray_APC_onset samples. Determined from genetic PCs via FastPop OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000224 Age at death due to prostate cancer.
[
  • 3,983 cases
  • , 30,575 controls
]
,
100.0 % Male samples
Mean = 70.0 years
Iqr = [63.0, 76.0] years
Other Combined analysis of multiple ancestries, including: European, East Asian, African American, Hawaiian, Hispanic American, South Asian, Black African, Black Caribbean, and Other (not specified) OncoArray_Prostate List of Cohorts available from dbGaP: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001391.v1.p1
PSS000280 Primary tumor samples from TCGA
[
  • 421 cases
  • , 0 controls
]
,
100.0 % Male samples
Mean = 62.0 years
Sd = 7.0 years
European TCGA
PSS000280
[
  • 0 cases
  • , 6,407 controls
]
,
100.0 % Male samples
European eMERGE
PSS000105 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. 4,828 individuals,
100.0 % Male samples
Mean = 59.0 years
Iqr = [55.0, 63.0] years
European ProtecT
PSS000105 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of aggressive prostate cancer (defined as any of Gleason score ≥7, stage T3-T4, PSA concentration ≥10 ng/mL, nodal metastasis, or distant metastasis)
[
  • 628 cases
]
,
100.0 % Male samples
Mean = 64.3 years
Iqr = [60.2, 67.5] years
European ProtecT
PSS000106 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. 4,828 individuals,
100.0 % Male samples
Mean = 59.0 years
Iqr = [55.0, 63.0] years
European ProtecT
PSS000106 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of prostate cancer.
[
  • 1,583 cases
]
,
100.0 % Male samples
Mean = 63.4 years
Iqr = [59.0, 67.5] years
European ProtecT
PSS000107 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. 4,828 individuals,
100.0 % Male samples
Mean = 59.0 years
Iqr = [55.0, 63.0] years
European ProtecT
PSS000107 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of very aggressive prostate cancer (defined as any of Gleason score ≥8, stage T3-4, positive nodes, or distant metastases)
[
  • 220 cases
]
,
100.0 % 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.
[
  • 2,148 cases
  • , 6,648 controls
]
,
100.0 % Male samples
Range = [50.0, 69.0] years 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.
[
  • 4,099 cases
  • , 960 controls
]
,
100.0 % Male samples
Range = [50.0, 69.0] years 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 cases
  • , 0 controls
]
,
100.0 % Male samples
Range = [50.0, 60.0] years 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. Median = 13.0 years
[
  • 1,089 cases
  • , 3,878 controls
]
,
100.0 % Male samples
Range = [55.0, 71.0] years European
(Finnish)
ERSPC
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.
[
  • 3,617 cases
  • , 55,509 controls
]
,
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.
[
  • 1,172 cases
  • , 47,679 controls
]
European
(Finnish)
FinnGen
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.
[
  • 212 cases
  • , 1,313 controls
]
,
100.0 % Male samples
European Self-reported European ancestry 37 cohorts
  • BCFR
  • ,BFBOCC
  • ,BRICOH
  • ,CBCS
  • ,CIMBA
  • ,CNIO
  • ,CONSIT
  • ,Chicago
  • ,DEMOKRITOS
  • ,DKFZ
  • ,EMBRACE
  • ,FCCC
  • ,G-FaST
  • ,GC-HBOC
  • ,GEMO
  • ,HCSC
  • ,HEBCS
  • ,HEBON
  • ,HUNBOCS
  • ,HVH
  • ,ICO
  • ,ILUH
  • ,IOVHBOCS
  • ,IPOBCS
  • ,KCONFAB
  • ,MAYO
  • ,MSKCC
  • ,MUV
  • ,NCI
  • ,OCGN
  • ,OSU
  • ,OUH
  • ,PBCS
  • ,SWE-BRCA
  • ,UPENN
  • ,UPITT
  • ,VFCTG