Polygenic Score (PGS) ID: PGS003559

Predicted Trait
Reported Trait Testosterone (male only)
Mapped Trait(s) testosterone measurement (EFO_0004908)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name cont-decay-M_log_testosterone
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
161,936 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 161,936 individuals,
1.0 % Male samples
 European UKB — Mean = 57.1 years
Sd = 8.1 years		 — white British —

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
PPM017907 PSS010506|
South Asian Ancestry|
3,208 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017487 PSS010926|
European Ancestry|
8,753 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017571 PSS010842|
European Ancestry|
1,479 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017655 PSS010674|
European Ancestry|
2,755 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017739 PSS010590|
Greater Middle Eastern Ancestry|
648 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017823 PSS010254|
European Ancestry|
1,002 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017991 PSS010422|
East Asian Ancestry|
565 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018075 PSS010338|
African Ancestry|
842 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM018159 PSS010758|
African Ancestry|
1,669 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Testosterone (male only) — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —

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
PSS010590 — — 648 individuals,
100.0 % Male samples
 Mean = 51.8 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010338 — — 842 individuals,
100.0 % Male samples
 Mean = 52.8 years
Sd = 8.4 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010758 — — 1,669 individuals,
100.0 % Male samples
 Mean = 51.4 years
Sd = 8.2 years		 African unspecified Nigerian UKB —
PSS010506 — — 3,208 individuals,
100.0 % Male samples
 Mean = 53.6 years
Sd = 8.7 years		 South Asian Indian UKB —
PSS010926 — — 8,753 individuals,
100.0 % Male samples
 Mean = 57.1 years
Sd = 8.0 years		 European white British UKB —
PSS010254 — — 1,002 individuals,
100.0 % Male samples
 Mean = 58.4 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010674 — — 2,755 individuals,
100.0 % Male samples
 Mean = 54.8 years
Sd = 8.5 years		 European Italian UKB —
PSS010422 — — 565 individuals,
100.0 % Male samples
 Mean = 52.3 years
Sd = 8.2 years		 East Asian Chinese UKB —
PSS010842 — — 1,479 individuals,
100.0 % Male samples
 Mean = 54.2 years
Sd = 7.4 years		 European Polish UKB —