Polygenic Score (PGS) ID: PGS000758

Predicted Trait
Reported Trait Adult standing height
Mapped Trait(s) body height (EFO_0004339)
Released in PGS Catalog: April 7, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)

Score Details

Score Construction
PGS Name LASSO_Height
Development Method
Name LASSO performed on P+T candidate SNPs
Parameters R^2 < 0.2, p < 5e-2, optimal λ = 1.34e-3
Variants
Original Genome Build hg19
Number of Variants 33,938
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000163
Citation (link to publication) Lu T et al. J Clin Endocrinol Metab (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
607,346 individuals (100%)
Score Development/Training
European: 100%
6,639 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002647
Europe PMC: 25282103
 253,288 individuals European 30 cohorts
  • ACTG
  • ,AEGS1
  • ,ASCOT
  • ,B-PROOF
  • ,BLSA
  • ,BioMe
  • ,DESIR
  • ,DNBC
  • ,EGCUT
  • ,ERF
  • ,FHS
  • ,HERITAGE
  • ,HYPERGENES
  • ,HealthABC
  • ,InCHIANTI
  • ,LLS
  • ,LOLIPOP
  • ,LifeLines
  • ,NELSON
  • ,PHASE
  • ,PLCO
  • ,PREVEND
  • ,PROCARDIS
  • ,PROSPER
  • ,QFS
  • ,QIMR
  • ,RISC
  • ,SHIP
  • ,TRAILS
  • ,TwinGene
Europe PMC: 33788949
 354,058 individuals,
46.0 % Male samples
 European UKB
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
— 6,639 individuals,
45.2 % Male samples
 European UKB — — — — Model selection dataset

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
PPM001931 PSS000967|
European Ancestry|
941 individuals
 PGP000163 |
Lu T et al. J Clin Endocrinol Metab (2021)
 Reported Trait: Short stature in adulthood — AUROC: 0.843 [0.796, 0.89] Area under the precision-recall curve (AUPRC): 0.284 [0.102, 0.5] Sex 33,783 SNPs were utilised from the 33,938 SNP score.
PPM001932 PSS000967|
European Ancestry|
941 individuals
 PGP000163 |
Lu T et al. J Clin Endocrinol Metab (2021)
 Reported Trait: Short stature in adulthood (females) OR: 0.62 [0.5, 0.75] AUROC: 0.861 [0.814, 0.907] Area under the precision-recall curve (AUPRC): 0.373 [0.087, 0.651] — 33,783 SNPs were utilised from the 33,938 SNP score.
PPM001930 PSS000967|
European Ancestry|
941 individuals
 PGP000163 |
Lu T et al. J Clin Endocrinol Metab (2021)
 Reported Trait: Standing height in adulthood — — R²: 0.71 [0.679, 0.741] Sex 33,783 SNPs were utilised from the 33,938 SNP score.
PPM001933 PSS000967|
European Ancestry|
941 individuals
 PGP000163 |
Lu T et al. J Clin Endocrinol Metab (2021)
 Reported Trait: Short stature in adulthood (males) OR: 0.7 [0.57, 0.83] AUROC: 0.82 [0.731, 0.909] Area under the precision-recall curve (AUPRC): 0.181 [0.044, 0.518] — 33,783 SNPs were utilised from the 33,938 SNP score.
PPM001929 PSS000969|
European Ancestry|
81,902 individuals
 PGP000163 |
Lu T et al. J Clin Endocrinol Metab (2021)
 Reported Trait: Standing height in adulthood — — R²: 0.711 [0.708, 0.714] Age, sex, recruitment center, genotyping array, PCs(1-20) —

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
PSS000967 — —
[
  • 21 cases
  • , 920 controls
]
,
42.5 % Male samples
 — European — ALSPAC —
PSS000969 — — 81,902 individuals,
45.9 % Male samples
 — European — UKB This dataset is independent of UKB source/training and model selection datasets