Polygenic Score (PGS) ID: PGS002653

Predicted Trait
Reported Trait Hypothyroidism
Mapped Trait(s) hypothyroidism (EFO_0004705)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name disease_HYPOTHYROIDISM_SELF_REP.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 197,450
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
337,488 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 337,488 individuals European UKB

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
PPM014369 PSS009787|
African Ancestry|
6,503 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Hypothyroidism — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0046 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014418 PSS009788|
East Asian Ancestry|
922 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Hypothyroidism — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0129 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014467 PSS009789|
European Ancestry|
43,505 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Hypothyroidism — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0262 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014516 PSS009790|
South Asian Ancestry|
8,098 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Hypothyroidism — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0183 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_HYPOTHYROIDISM_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
PSS009788 — — 922 individuals — East Asian — UKB —
PSS009789 — — 43,505 individuals — European Non-British European UKB —
PSS009790 — — 8,098 individuals — South Asian — UKB —
PSS009787 — — 6,503 individuals — African unspecified — UKB —