Polygenic Score (PGS) ID: PGS000696

Predicted Trait
Reported Trait Testosterone [nmol/L]
Mapped Trait(s) testosterone measurement (EFO_0004908)
Released in PGS Catalog: Feb. 3, 2021
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Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Testosterone
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 8,223
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 45.5%
African: 18.2%
East Asian: 18.2%
South Asian: 18.2%
11 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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001424 PSS000757|
African Ancestry|
5,453 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Testosterone [nmol/L] — — R²: 0.89659
Spearman's ρ: 0.091		 Age, sex, PCs(1-40) —
PPM001459 PSS000758|
East Asian Ancestry|
1,008 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Testosterone [nmol/L] — — R²: 0.91376
Spearman's ρ: 0.115		 Age, sex, PCs(1-40) —
PPM001494 PSS000759|
European Ancestry|
21,344 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Testosterone [nmol/L] — — R²: 0.90433
Spearman's ρ: 0.169		 Age, sex, PCs(1-40) —
PPM001529 PSS000760|
South Asian Ancestry|
6,680 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Testosterone [nmol/L] — — R²: 0.89983
Spearman's ρ: 0.149		 Age, sex, PCs(1-40) —
PPM001564 PSS000761|
European Ancestry|
57,774 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Testosterone [nmol/L] — — R²: 0.9055
Spearman's ρ: 0.175		 Age, sex, PCs(1-40) —
PPM001572 PSS000831|
European Ancestry|
2,129 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Testosterone [nmol/L] — — Spearman's ρ: 0.104 Age, sex —
PPM007405 PSS007196|
African Ancestry|
5,534 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Testosterone — — R²: 0.80968 [0.80136, 0.81801]
Incremental R2 (full-covars): 0.00067
PGS R2 (no covariates): 0.00079 [-0.00058, 0.00215]		 age, sex, UKB array type, Genotype PCs —
PPM007406 PSS007197|
East Asian Ancestry|
1,506 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Testosterone — — R²: 0.865 [0.8531, 0.8769]
Incremental R2 (full-covars): 0.0008
PGS R2 (no covariates): 0.00346 [-0.00209, 0.00902]		 age, sex, UKB array type, Genotype PCs —
PPM007407 PSS007198|
European Ancestry|
21,549 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Testosterone — — R²: 0.8185 [0.81442, 0.82257]
Incremental R2 (full-covars): 0.00147
PGS R2 (no covariates): 0.00189 [0.00081, 0.00297]		 age, sex, UKB array type, Genotype PCs —
PPM007408 PSS007199|
South Asian Ancestry|
6,754 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Testosterone — — R²: 0.77833 [0.76967, 0.78698]
Incremental R2 (full-covars): 0.00157
PGS R2 (no covariates): 0.00425 [0.00137, 0.00712]		 age, sex, UKB array type, Genotype PCs —
PPM007409 PSS007200|
European Ancestry|
58,509 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Testosterone — — R²: 0.8074 [0.80479, 0.81001]
Incremental R2 (full-covars): 0.00156
PGS R2 (no covariates): 0.00319 [0.00234, 0.00404]		 age, sex, UKB array type, Genotype 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
PSS007196 — — 5,534 individuals — African unspecified — UKB —
PSS007197 — — 1,506 individuals — East Asian — UKB —
PSS007198 — — 21,549 individuals — European non-white British ancestry UKB —
PSS007199 — — 6,754 individuals — South Asian — UKB —
PSS007200 — — 58,509 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000757 — — 5,453 individuals — African unspecified — UKB —
PSS000758 — — 1,008 individuals — East Asian — UKB —
PSS000759 — — 21,344 individuals — European Non-British White UKB —
PSS000760 — — 6,680 individuals — South Asian — UKB —
PSS000761 — — 57,774 individuals — European
(British)		 — UKB —
PSS000831 — — 2,129 individuals — European Participants self-identifying as white MESA —