Polygenic Score (PGS) ID: PGS002016

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_185
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 450,963
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011002 PSS009275|
European Ancestry|
8,501 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.1489 [0.128, 0.1696] sex, age, birth date, deprivation index, 16 PCs —
PPM011003 PSS009049|
European Ancestry|
1,468 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.1605 [0.1099, 0.2103] sex, age, birth date, deprivation index, 16 PCs —
PPM011004 PSS008603|
European Ancestry|
2,749 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.0944 [0.057, 0.1314] sex, age, birth date, deprivation index, 16 PCs —
PPM011006 PSS008157|
South Asian Ancestry|
3,182 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.0875 [0.0528, 0.1219] sex, age, birth date, deprivation index, 16 PCs —
PPM011007 PSS007945|
East Asian Ancestry|
575 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.0813 [-0.0018, 0.1634] sex, age, birth date, deprivation index, 16 PCs —
PPM011008 PSS007727|
African Ancestry|
844 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.0792 [0.011, 0.1466] sex, age, birth date, deprivation index, 16 PCs —
PPM011009 PSS008829|
African Ancestry|
1,711 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.0467 sex, age, birth date, deprivation index, 16 PCs —
PPM011005 PSS008381|
Greater Middle Eastern Ancestry|
664 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Cancer of prostate — — Partial Correlation (partial-r): 0.1504 [0.0741, 0.225] sex, age, birth date, deprivation index, 16 PCs —

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
PSS009275 — — 8,501 individuals — European UK (+ Ireland) UKB —
PSS007945 — — 575 individuals — East Asian China (East Asia) UKB —
PSS008381 — — 664 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS007727 — — 844 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008829 — — 1,711 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009049 — — 1,468 individuals — European Poland (NE Europe) UKB —
PSS008603 — — 2,749 individuals — European Italy (South Europe) UKB —
PSS008157 — — 3,182 individuals — South Asian India (South Asia) UKB —