Polygenic Score (PGS) ID: PGS002076

Predicted Trait
Reported Trait Hyperplasia of prostate
Mapped Trait(s) benign prostatic hyperplasia (EFO_0000284)
Additional Trait Information genitourinary
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_600
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 627,341
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
PPM011469 PSS009340|
European Ancestry|
8,710 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0856 [0.0647, 0.1065] sex, age, birth date, deprivation index, 16 PCs —
PPM011470 PSS009114|
European Ancestry|
1,493 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1369 [0.0864, 0.1866] sex, age, birth date, deprivation index, 16 PCs —
PPM011471 PSS008668|
European Ancestry|
2,859 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1059 [0.0694, 0.1421] sex, age, birth date, deprivation index, 16 PCs —
PPM011472 PSS008442|
Greater Middle Eastern Ancestry|
696 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0928 [0.0175, 0.1669] sex, age, birth date, deprivation index, 16 PCs —
PPM011473 PSS008222|
South Asian Ancestry|
3,344 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0415 [0.0075, 0.0754] sex, age, birth date, deprivation index, 16 PCs —
PPM011474 PSS008003|
East Asian Ancestry|
586 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.071 [-0.0114, 0.1525] sex, age, birth date, deprivation index, 16 PCs —
PPM011475 PSS007787|
African Ancestry|
827 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.1389 [0.0706, 0.2059] sex, age, birth date, deprivation index, 16 PCs —
PPM011476 PSS008891|
African Ancestry|
1,703 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Hyperplasia of prostate — — Partial Correlation (partial-r): 0.0775 [0.0299, 0.1248] 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
PSS007787 — — 827 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008668 — — 2,859 individuals — European Italy (South Europe) UKB —
PSS008891 — — 1,703 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009114 — — 1,493 individuals — European Poland (NE Europe) UKB —
PSS008442 — — 696 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009340 — — 8,710 individuals — European UK (+ Ireland) UKB —
PSS008222 — — 3,344 individuals — South Asian India (South Asia) UKB —
PSS008003 — — 586 individuals — East Asian China (East Asia) UKB —