PGS Publication: PGP000163

Publication Information (EuropePMC)
Title A polygenic risk score to predict future adult short stature amongst children.
PubMed ID 33788949(Europe PMC)
doi 10.1210/clinem/dgab215
Publication Date March 31, 2021
Journal J Clin Endocrinol Metab
Author(s) Lu T, Forgetta V, Wu H, Perry JRB, Ong KK, Greenwood CMT, Timpson NJ, Manousaki D, Richards JB.
Released in PGS Catalog: April 7, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000758
(LASSO_Height)
 PGP000163 |
Lu T et al. J Clin Endocrinol Metab (2021)
 Adult standing height body height 33,938
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000758/ScoringFiles/PGS000758.txt.gz - Check Terms/Licenses

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) 		Evaluated Score 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 PGS000758
(LASSO_Height)
 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 PGS000758
(LASSO_Height)
 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 PGS000758
(LASSO_Height)
 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 PGS000758
(LASSO_Height)
 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 PGS000758
(LASSO_Height)
 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