Polygenic Score (PGS) ID: PGS003896

Predicted Trait
Reported Trait Sitting height
Mapped Trait(s) sitting height measurement (EFO_0011011)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI20015
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI20015
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 44,543
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
324,362 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
— 324,362 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
PPM018799 PSS011147|
European Ancestry|
67,606 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Sitting height — — R²: 0.56702 [0.56211, 0.57193]
PGS R2 (no covariates): 0.13337 [0.12861, 0.13814]
Incremental R2 (full-covars): 0.13166		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018800 PSS011102|
European Ancestry|
2,883 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Sitting height — — R²: 0.56319 [0.53933, 0.58705]
PGS R2 (no covariates): 0.14822 [0.12435, 0.17208]
Incremental R2 (full-covars): 0.12786		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018801 PSS011114|
South Asian Ancestry|
1,448 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Sitting height — — R²: 0.47658 [0.43993, 0.51322]
PGS R2 (no covariates): 0.06813 [0.04346, 0.09279]
Incremental R2 (full-covars): 0.05017		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018802 PSS011159|
African Ancestry|
1,191 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Sitting height — — R²: 0.36181 [0.31873, 0.40489]
PGS R2 (no covariates): 0.01877 [0.00368, 0.03386]
Incremental R2 (full-covars): 0.00631		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018803 PSS011172|
Multi-ancestry (excluding European)|
7,967 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Sitting height — — R²: 0.56286 [0.5485, 0.57722]
PGS R2 (no covariates): 0.1462 [0.1319, 0.16049]
Incremental R2 (full-covars): 0.10616		 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
PSS011172 — — 7,967 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011114 — — 1,448 individuals — South Asian — UKB —
PSS011147 — — 67,606 individuals — European
(white British ancestry)		 — UKB —
PSS011159 — — 1,191 individuals — African unspecified — UKB —
PSS011102 — — 2,883 individuals — European
(non-white British ancestry)		 — UKB —