Polygenic Score (PGS) ID: PGS000321

Predicted Trait
Reported Trait Serum testosterone levels
Mapped Trait(s) testosterone measurement (EFO_0004908)
Released in PGS Catalog: Sept. 4, 2020
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Score Details

Score Construction
PGS Name snpnet_Testosterone_combined
Development Method
Name snpnet
Parameters Lasso-penalized regression (BASIL) of LD-pruned variants (plink '--indep 50 5 2') outside MHC region (chr6:25477797-36448354); MAF > 1%
Variants
Original Genome Build GRCh37
Number of Variants 7,319
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000097
Citation (link to publication) Flynn E et al. Eur J Hum Genet (2020)
Ancestry Distribution
Score Development/Training
European: 100%
229,120 individuals (100%)
PGS Evaluation
European: 100%
2 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
200,477 individuals,
50.34 % Male samples
 European UKB Blood testosterone levels (UKB field 30850). Individuals taking the following testosterone-related drugs (methyltestosterone, finasteride, dutasteride, testosterone, mesterolone, and cyproterone) were excluded. — — — Training
28,643 individuals,
50.95 % Male samples
 European UKB Blood testosterone levels (UKB field 30850). Individuals taking the following testosterone-related drugs (methyltestosterone, finasteride, dutasteride, testosterone, mesterolone, and cyproterone) were excluded. — — — Validation (used to select the optimal lambda value for sparsity)

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
PPM000865 PSS000421|
European Ancestry|
28,640 individuals
 PGP000097 |
Flynn E et al. Eur J Hum Genet (2020)
 Reported Trait: Serum testosterone levels in females — — R²: 0.13 age, sex, PCs 1-40, blood draw time, fasting time, sample dilution factor, batch, genotyping array —
PPM000862 PSS000422|
European Ancestry|
28,601 individuals
 PGP000097 |
Flynn E et al. Eur J Hum Genet (2020)
 Reported Trait: Serum testosterone levels in males — — R²: 0.21 age, sex, PCs 1-40, blood draw time, fasting time, sample dilution factor, batch, genotyping array —

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
PSS000421 Blood testosterone levels (UKB field 30850). Individuals taking the following testosterone-related drugs (methyltestosterone, finasteride, dutasteride, testosterone, mesterolone, and cyproterone) were excluded. — 28,640 individuals,
0.0 % Male samples
 — European — UKB —
PSS000422 Blood testosterone levels (UKB field 30850). Individuals taking the following testosterone-related drugs (methyltestosterone, finasteride, dutasteride, testosterone, mesterolone, and cyproterone) were excluded. — 28,601 individuals,
100.0 % Male samples
 — European — UKB —