Polygenic Score (PGS) ID: PGS000694

Predicted Trait
Reported Trait SHBG [nmol/L]
Mapped Trait(s) sex hormone-binding globulin measurement (EFO_0004696)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.SHBG
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 19,328
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
PPM001422 PSS000744|
African Ancestry|
5,523 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: SHBG [nmol/L] — — R²: 0.22708
Spearman's ρ: 0.235		 Age, sex, PCs(1-40) —
PPM001457 PSS000745|
East Asian Ancestry|
979 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: SHBG [nmol/L] — — R²: 0.31846
Spearman's ρ: 0.311		 Age, sex, PCs(1-40) —
PPM001492 PSS000746|
European Ancestry|
21,313 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: SHBG [nmol/L] — — R²: 0.35511
Spearman's ρ: 0.384		 Age, sex, PCs(1-40) —
PPM001527 PSS000747|
South Asian Ancestry|
6,638 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: SHBG [nmol/L] — — R²: 0.28079
Spearman's ρ: 0.326		 Age, sex, PCs(1-40) —
PPM001562 PSS000748|
European Ancestry|
57,677 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: SHBG [nmol/L] — — R²: 0.34576
Spearman's ρ: 0.414		 Age, sex, PCs(1-40) —
PPM001571 PSS000830|
European Ancestry|
2,129 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: SHBG [nmol/L] — — Spearman's ρ: 0.19 Age, sex —
PPM007395 PSS007186|
African Ancestry|
5,606 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: SHBG — — R²: 0.15136 [0.13531, 0.16741]
Incremental R2 (full-covars): 0.00248
PGS R2 (no covariates): 0.04048 [0.0311, 0.04987]		 age, sex, UKB array type, Genotype PCs —
PPM007396 PSS007187|
East Asian Ancestry|
1,463 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: SHBG — — R²: 0.21699 [0.18242, 0.25155]
Incremental R2 (full-covars): 0.00252
PGS R2 (no covariates): 0.04369 [0.02475, 0.06264]		 age, sex, UKB array type, Genotype PCs —
PPM007397 PSS007188|
European Ancestry|
21,531 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: SHBG — — R²: 0.18855 [0.1798, 0.1973]
Incremental R2 (full-covars): 0.00395
PGS R2 (no covariates): 0.09661 [0.08964, 0.10359]		 age, sex, UKB array type, Genotype PCs —
PPM007398 PSS007189|
South Asian Ancestry|
6,736 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: SHBG — — R²: 0.13468 [0.12062, 0.14874]
Incremental R2 (full-covars): 0.004
PGS R2 (no covariates): 0.07268 [0.06161, 0.08375]		 age, sex, UKB array type, Genotype PCs —
PPM007399 PSS007190|
European Ancestry|
58,525 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: SHBG — — R²: 0.16541 [0.16028, 0.17053]
Incremental R2 (full-covars): 0.0045
PGS R2 (no covariates): 0.11086 [0.10639, 0.11533]		 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
PSS000744 — — 5,523 individuals — African unspecified — UKB —
PSS000745 — — 979 individuals — East Asian — UKB —
PSS000746 — — 21,313 individuals — European Non-British White UKB —
PSS000747 — — 6,638 individuals — South Asian — UKB —
PSS000748 — — 57,677 individuals — European
(British)		 — UKB —
PSS007187 — — 1,463 individuals — East Asian — UKB —
PSS007186 — — 5,606 individuals — African unspecified — UKB —
PSS000830 — — 2,129 individuals — European Participants self-identifying as white MESA —
PSS007188 — — 21,531 individuals — European non-white British ancestry UKB —
PSS007189 — — 6,736 individuals — South Asian — UKB —
PSS007190 — — 58,525 individuals — European white British ancestry UKB Testing cohort (heldout set)