Polygenic Score (PGS) ID: PGS001229

Predicted Trait
Reported Trait Standing height
Mapped Trait(s) body height (EFO_0004339)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI50
Released in PGS Catalog: Oct. 21, 2021
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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_INI50
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 51,209
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%
269,136 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
— 269,136 individuals European UKB — — — white British ancestry —

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
PPM008659 PSS007396|
African Ancestry|
6,407 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Standing height — — R²: 0.50012 [0.48294, 0.5173]
Incremental R2 (full-covars): 0.02391
PGS R2 (no covariates): 0.03665 [0.02769, 0.04561]		 age, sex, UKB array type, Genotype PCs —
PPM008660 PSS007397|
East Asian Ancestry|
1,697 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Standing height — — R²: 0.60758 [0.5786, 0.63657]
Incremental R2 (full-covars): 0.06552
PGS R2 (no covariates): 0.09127 [0.06525, 0.11728]		 age, sex, UKB array type, Genotype PCs —
PPM008661 PSS007398|
European Ancestry|
24,826 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Standing height — — R²: 0.7018 [0.69559, 0.708]
Incremental R2 (full-covars): 0.16478
PGS R2 (no covariates): 0.1861 [0.17738, 0.19482]		 age, sex, UKB array type, Genotype PCs —
PPM008662 PSS007399|
South Asian Ancestry|
7,650 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Standing height — — R²: 0.66523 [0.65314, 0.67732]
Incremental R2 (full-covars): 0.08156
PGS R2 (no covariates): 0.08889 [0.07686, 0.10092]		 age, sex, UKB array type, Genotype PCs —
PPM008663 PSS007400|
European Ancestry|
67,298 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Standing height — — R²: 0.71726 [0.71364, 0.72087]
Incremental R2 (full-covars): 0.17893
PGS R2 (no covariates): 0.17757 [0.17234, 0.1828]		 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
PSS007396 — — 6,407 individuals — African unspecified — UKB —
PSS007397 — — 1,697 individuals — East Asian — UKB —
PSS007398 — — 24,826 individuals — European non-white British ancestry UKB —
PSS007399 — — 7,650 individuals — South Asian — UKB —
PSS007400 — — 67,298 individuals — European white British ancestry UKB Testing cohort (heldout set)