Polygenic Score (PGS) ID: PGS003895

Predicted Trait
Reported Trait Standing height
Mapped Trait(s) body height (EFO_0004339)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI50
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI50
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 62,419
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000502
Citation (link to publication) Tanigawa Y et al. AJHG (2023)
Ancestry Distribution
Score Development/Training
Multi-ancestry (including European): 100%
  • European
  • South Asian
  • African
  • Additional Diverse Ancestries
324,364 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
Multi-ancestry (excluding European): 20%
  • East Asian
  • Additional Diverse Ancestries
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
— 324,364 individuals European, South Asian, African unspecified, Other admixed ancestry UKB — — — European, South Asian, African unspecified, Other admixed 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
PPM018794 PSS011146|
European Ancestry|
67,603 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Standing height — — R²: 0.71901 [0.71542, 0.7226]
PGS R2 (no covariates): 0.1804 [0.17516, 0.18565]
Incremental R2 (full-covars): 0.17961		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018795 PSS011103|
European Ancestry|
2,885 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Standing height — — R²: 0.72848 [0.71161, 0.74534]
PGS R2 (no covariates): 0.21016 [0.18381, 0.23651]
Incremental R2 (full-covars): 0.18808		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018796 PSS011114|
South Asian Ancestry|
1,448 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Standing height — — R²: 0.66918 [0.64174, 0.69663]
PGS R2 (no covariates): 0.08326 [0.05643, 0.11009]
Incremental R2 (full-covars): 0.08875		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018797 PSS011159|
African Ancestry|
1,191 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Standing height — — R²: 0.50307 [0.46351, 0.54262]
PGS R2 (no covariates): 0.02787 [0.00966, 0.04609]
Incremental R2 (full-covars): 0.01372		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018798 PSS011173|
Multi-ancestry (excluding European)|
7,968 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Standing height — — R²: 0.69915 [0.68814, 0.71017]
PGS R2 (no covariates): 0.151 [0.13655, 0.16545]
Incremental R2 (full-covars): 0.14737		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —

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
PSS011173 — — 7,968 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011114 — — 1,448 individuals — South Asian — UKB —
PSS011146 — — 67,603 individuals — European
(white British ancestry)		 — UKB —
PSS011159 — — 1,191 individuals — African unspecified — UKB —
PSS011103 — — 2,885 individuals — European
(non-white British ancestry)		 — UKB —