Polygenic Score (PGS) ID: PGS002668

Predicted Trait
Reported Trait Thyroid (self-reported conditions)
Mapped Trait(s) thyroid disease (EFO_1000627)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name disease_THYROID_ANY_SELF_REP.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 189,808
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
PPM014384 PSS009847|
African Ancestry|
6,503 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Thyroid — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0034 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_THYROID_ANY_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014433 PSS009848|
East Asian Ancestry|
922 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Thyroid — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0034 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_THYROID_ANY_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014482 PSS009849|
European Ancestry|
43,505 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Thyroid — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0254 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_THYROID_ANY_SELF_REP.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014531 PSS009850|
South Asian Ancestry|
8,098 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Thyroid — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0186 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_THYROID_ANY_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
PSS009847 — — 6,503 individuals — African unspecified — UKB —
PSS009848 — — 922 individuals — East Asian — UKB —
PSS009849 — — 43,505 individuals — European Non-British European UKB —
PSS009850 — — 8,098 individuals — South Asian — UKB —