Polygenic Score (PGS) ID: PGS000348

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Dec. 8, 2020
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Terms and Licenses
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). © 2020 Ambry Genetics.

Score Details

Score Construction
PGS Name PRS_PrCa
Variants
Original Genome Build GRCh37
Number of Variants 72
Development Method
Name GWAS-significant variants
Parameters Risk was normalized to population average (see Methods 2.3). Includes proxy variants
PGS Source
PGS Catalog Publication (PGP) ID PGP000113
Citation (link to publication) Black MH et al. Prostate (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 88.9%
African: 4.9%
East Asian: 3.9%
Hispanic or Latin American: 2.2%
257,853 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002606
Europe PMC: 25217961
67,543 individuals European
GWAS Catalog: GCST002606
Europe PMC: 25217961
2,080 individuals Hispanic or Latin American
GWAS Catalog: GCST002606
Europe PMC: 25217961
6,954 individuals East Asian
GWAS Catalog: GCST002606
Europe PMC: 25217961
10,463 individuals Sub-Saharan African, African American or Afro-Caribbean
Europe PMC: 19767752
[
  • 1,906 cases
  • , 1,934 controls
]
European
GWAS Catalog: GCST000488
Europe PMC: 19767753
3,748 individuals European
GWAS Catalog: GCST000152
Europe PMC: 18264097
3,748 individuals European
GWAS Catalog: GCST001942
Europe PMC: 23535732
22,548 individuals European
GWAS Catalog: GCST000489
Europe PMC: 19767754
37,350 individuals European
GWAS Catalog: GCST000019
Europe PMC: 17401366
4,517 individuals European
GWAS Catalog: GCST000153
Europe PMC: 18264098
23,226 individuals European
GWAS Catalog: GCST002944
Europe PMC: 26034056
3,226 individuals East Asian
GWAS Catalog: GCST002944
Europe PMC: 26034056
2,251 individuals African American or Afro-Caribbean
GWAS Catalog: GCST002944
Europe PMC: 26034056
3,629 individuals Hispanic or Latin American
GWAS Catalog: GCST002944
Europe PMC: 26034056
37,272 individuals European
GWAS Catalog: GCST001148
Europe PMC: 21743467
13,560 individuals European
GWAS Catalog: GCST001147
Europe PMC: 21743057
7,240 individuals European
GWAS Catalog: GCST000154
Europe PMC: 18264096
2,329 individuals European
GWAS Catalog: GCST000017
Europe PMC: 17401363
2,329 individuals European

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)
PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000987 PSS000502|
European Ancestry|
1,039 individuals
PGP000113 |
Black MH et al. Prostate (2020)
Reported Trait: Prostate cancer in men with a family history of prostate cancer OR: 1.9 [1.53, 2.4] Age
PPM000986 PSS000501|
European Ancestry|
3,891 individuals
PGP000113 |
Black MH et al. Prostate (2020)
Reported Trait: Prostate cancer AUROC: 0.64 Age
PPM000985 PSS000501|
European Ancestry|
3,891 individuals
PGP000113 |
Black MH et al. Prostate (2020)
Reported Trait: Prostate cancer OR: 1.72 [1.59, 1.88] AUROC: 0.64 [0.62, 0.66]
PPM000988 PSS000503|
European Ancestry|
2,305 individuals
PGP000113 |
Black MH et al. Prostate (2020)
Reported Trait: Prostate cancer in men with no family history of prostate cancer OR: 1.65 [1.49, 1.84] Age

Evaluated Samples

PGS Sample Set ID
(PSS)
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
PSS000501 Cases: Male, self-reported European ancestry, greater or equal to 18 years of age at prostate cancer diagnosis. JHH cases were patients undergoing radical prostatectomy for the treatment of clinically localized PrCa in 2002 to 2015 and were included if disease was organ‐confined and Gleason score ≤6 or ≥8, as determined upon pathological evaluation of the prostatectomy specimen. Only the high‐ and low‐grade PrCa JHH cases were included because they were previously curated to assess the association of RPVs in cancer susceptibility genes with PrCa. JHH controls were included if they self repored with European American ancestry, had a normal digital rectal examination, PSA level less than 4.0 ng/mL and were older than 55 years. AG cases and controls were men referred for multigene panel testing in 2017 to 2019. Among AG cases, 104 patients had Gleason ≥8, and 59 patients had Gleason ≤6, and 230 patients had no pathology information. AG controls were unaffected with prostate cancer at the time of testing. NSGI controls had a minimum of 1 year clincal history available in the EHR and were exlucded if any ICD9/10 diagnosis of cancer was present at any time in the EHR. Men who tested positive for RPVs in any prostate cancer susceptibility gene were exlcuded from further analysis.
[
  • 1,972 cases
  • , 1,919 controls
]
,
100.0 % Male samples
European AG, JHH, NSGHI
PSS000502 Cases: Male, self-reported European ancestry, greater or equal to 18 years of age at prostate cancer diagnosis. JHH cases were patients undergoing radical prostatectomy for the treatment of clinically localized PrCa in 2002 to 2015 and were included if disease was organ‐confined and Gleason score ≤6 or ≥8, as determined upon pathological evaluation of the prostatectomy specimen. Only the high‐ and low‐grade PrCa JHH cases were included because they were previously curated to assess the association of RPVs in cancer susceptibility genes with PrCa. JHH controls were included if they self repored with European American ancestry, had a normal digital rectal examination, PSA level less than 4.0 ng/mL and were older than 55 years. AG cases and controls were men referred for multigene panel testing in 2017 to 2019. Among AG cases, 104 patients had Gleason ≥8, and 59 patients had Gleason ≤6, and 230 patients had no pathology information. AG controls were unaffected with prostate cancer at the time of testing.
[
  • 744 cases
  • , 295 controls
]
,
100.0 % Male samples
European AG, JHH
PSS000503 Cases: Male, self-reported European ancestry, greater or equal to 18 years of age at prostate cancer diagnosis. JHH cases were patients undergoing radical prostatectomy for the treatment of clinically localized PrCa in 2002 to 2015 and were included if disease was organ‐confined and Gleason score ≤6 or ≥8, as determined upon pathological evaluation of the prostatectomy specimen. Only the high‐ and low‐grade PrCa JHH cases were included because they were previously curated to assess the association of RPVs in cancer susceptibility genes with PrCa. JHH controls were included if they self repored with European American ancestry, had a normal digital rectal examination, PSA level less than 4.0 ng/mL and were older than 55 years. AG cases and controls were men referred for multigene panel testing in 2017 to 2019. Among AG cases, 104 patients had Gleason ≥8, and 59 patients had Gleason ≤6, and 230 patients had no pathology information. AG controls were unaffected with prostate cancer at the time of testing.
[
  • 1,133 cases
  • , 1,172 controls
]
,
100.0 % Male samples
European AG, JHH