Polygenic Score (PGS) ID: PGS001865

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-PLR_600
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 1,712
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM009809 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): 0.0846 [0.0636, 0.1054] sex, age, birth date, deprivation index, 16 PCs
PPM009810 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): 0.1233 [0.0727, 0.1733] sex, age, birth date, deprivation index, 16 PCs
PPM009811 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): 0.0911 [0.0545, 0.1275] sex, age, birth date, deprivation index, 16 PCs
PPM009812 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): 0.0715 [-0.0039, 0.146] sex, age, birth date, deprivation index, 16 PCs
PPM009814 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): 0.0651 [-0.0173, 0.1467] sex, age, birth date, deprivation index, 16 PCs
PPM009815 PSS007787|
African Ancestry|
827 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Hyperplasia of prostate Partial Correlation (partial-r): 0.1134 [0.0448, 0.1809] sex, age, birth date, deprivation index, 16 PCs
PPM009816 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): 0.0524 [0.0046, 0.0999] sex, age, birth date, deprivation index, 16 PCs
PPM009813 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): 0.0339 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