Polygenic Score (PGS) ID: PGS001405

Predicted Trait
Reported Trait Height
Mapped Trait(s) body height (EFO_0004339)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI12144
Released in PGS Catalog: Nov. 25, 2021
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_INI12144
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,166
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
26,788 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
— 26,788 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM005231 PSS004802|
East Asian Ancestry|
133 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Height — — R²: 0.509 [0.47581, 0.5422]
Incremental R2 (full-covars): 0.00258
PGS R2 (no covariates): 0.00401 [-0.00197, 0.00998]		 age, sex, UKB array type, Genotype PCs —
PPM005230 PSS004801|
African Ancestry|
253 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Height — — R²: 0.58747 [0.5721, 0.60284]
Incremental R2 (full-covars): 0.01915
PGS R2 (no covariates): 0.00938 [0.00471, 0.01404]		 age, sex, UKB array type, Genotype PCs —
PPM005232 PSS004803|
European Ancestry|
2,131 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Height — — R²: 0.59354 [0.58576, 0.60132]
Incremental R2 (full-covars): 0.04611
PGS R2 (no covariates): 0.05219 [0.04681, 0.05757]		 age, sex, UKB array type, Genotype PCs —
PPM005233 PSS004804|
South Asian Ancestry|
414 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Height — — R²: 0.56418 [0.54969, 0.57868]
Incremental R2 (full-covars): 0.03739
PGS R2 (no covariates): 0.02079 [0.01454, 0.02704]		 age, sex, UKB array type, Genotype PCs —
PPM005234 PSS004805|
European Ancestry|
6,641 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Height — — R²: 0.59871 [0.59403, 0.6034]
Incremental R2 (full-covars): 0.05016
PGS R2 (no covariates): 0.05141 [0.04816, 0.05466]		 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
PSS004801 — — 253 individuals — African unspecified — UKB —
PSS004802 — — 133 individuals — East Asian — UKB —
PSS004803 — — 2,131 individuals — European non-white British ancestry UKB —
PSS004804 — — 414 individuals — South Asian — UKB —
PSS004805 — — 6,641 individuals — European white British ancestry UKB Testing cohort (heldout set)