Polygenic Score (PGS) ID: PGS002241

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: April 13, 2022
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Terms and Licenses
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Score Details

Score Construction
PGS Name ldpred_prostatecancer
Development Method
Name LDpred
Parameters p = 0.01, LD radius = 2000, LD reference panel: European ancestry in 1000 Genomes
Variants
Original Genome Build GRCh37
Number of Variants 6,497,734
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000271
Citation (link to publication) Mars N et al. Cell Genom (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
140,254 individuals (100%)
Score Development/Training
European: 100%
175,364 individuals (100%)
PGS Evaluation
European: 55.6%
African: 22.2%
East Asian: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006085
Europe PMC: 29892016
 140,254 individuals European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 5,283 cases
  • , 170,081 controls
]
 European
(Finnish)		 FinnGen — — — — —

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
PPM012739 PSS009520|
European Ancestry|
110,597 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.79 [1.68, 1.91] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012743 PSS009516|
East Asian Ancestry|
178,726 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.69 [1.64, 1.74] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012747 PSS009528|
European Ancestry|
69,422 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.8 [1.72, 1.88] — — birth year, 10 PCs (+/- dataset-specific technical covariates) —
PPM012751 PSS009536|
European Ancestry|
25,696 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.66 [1.57, 1.76] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012755 PSS009532|
African Ancestry|
1,535 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.19 [0.91, 1.55] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012759 PSS009544|
European Ancestry|
687,352 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.91 [1.86, 1.96] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012764 PSS009540|
African Ancestry|
15,236 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.35 [1.14, 1.61] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012769 PSS009548|
South Asian Ancestry|
15,256 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 2.21 [1.73, 2.81] — — age, 10 PCs (+/- dataset-specific technical covariates) —
PPM012735 PSS009524|
European Ancestry|
258,402 individuals
 PGP000271 |
Mars N et al. Cell Genom (2022)
 Reported Trait: Prostate cancer OR: 1.96 [1.91, 2.01] — — age, 10 PCs (+/- dataset-specific technical covariates) —

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
PSS009536 — —
[
  • 1,593 cases
  • , 24,103 controls
]
,
100.0 % Male samples
 — European — MGBB —
PSS009540 — —
[
  • 199 cases
  • , 7,419 controls
]
,
100.0 % Male samples
 — African unspecified — UKB —
PSS009540 — —
[
  • 199 cases
  • , 7,419 controls
]
,
100.0 % Male samples
 — African unspecified — UKB —
PSS009544 — —
[
  • 7,429 cases
  • , 336,247 controls
]
,
100.0 % Male samples
 — European British UKB —
PSS009544 — —
[
  • 7,429 cases
  • , 336,247 controls
]
,
100.0 % Male samples
 — European British UKB —
PSS009516 — —
[
  • 5,192 cases
  • , 173,534 controls
]
,
100.0 % Male samples
 — East Asian
(Japanese)		 — BBJ —
PSS009548 — —
[
  • 72 cases
  • , 7,556 controls
]
,
100.0 % Male samples
 — South Asian — UKB —
PSS009548 — —
[
  • 72 cases
  • , 7,556 controls
]
,
100.0 % Male samples
 — South Asian — UKB —
PSS009520 — —
[
  • 1,202 cases
  • , 109,395 controls
]
,
100.0 % Male samples
 — European
(Estonian)		 — EB —
PSS009524 — —
[
  • 8,709 cases
  • , 249,693 controls
]
,
100.0 % Male samples
 — European
(Finnish)		 — FinnGen —
PSS009528 — —
[
  • 2,224 cases
  • , 67,198 controls
]
,
100.0 % Male samples
 — European Norwegian HUNT —
PSS009532 — —
[
  • 80 cases
  • , 1,455 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean — MGBB —