Polygenic Score (PGS) ID: PGS001181

Predicted Trait
Reported Trait Other hypothyroidism (time-to-event)
Mapped Trait(s) hypothyroidism (EFO_0004705)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC643
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC643
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,739
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
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
—
[
  • 18,252 cases
  • , 251,452 controls
]
 European UKB — — — white British 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
PPM008594 PSS004555|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other hypothyroidism — AUROC: 0.70862 [0.67381, 0.74343] R²: 0.06703
Incremental AUROC (full-covars): 0.01118
PGS R2 (no covariates): 0.01121
PGS AUROC (no covariates): 0.58683 [0.5475, 0.62616]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008595 PSS004556|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other hypothyroidism — AUROC: 0.71469 [0.64687, 0.78251] R²: 0.07343
Incremental AUROC (full-covars): 0.03489
PGS R2 (no covariates): 0.01956
PGS AUROC (no covariates): 0.60912 [0.53836, 0.67988]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008596 PSS004557|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other hypothyroidism — AUROC: 0.76338 [0.75207, 0.77469] R²: 0.14671
Incremental AUROC (full-covars): 0.06656
PGS R2 (no covariates): 0.06971
PGS AUROC (no covariates): 0.68243 [0.66936, 0.69549]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008597 PSS004558|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other hypothyroidism — AUROC: 0.74011 [0.72045, 0.75977] R²: 0.1348
Incremental AUROC (full-covars): 0.03883
PGS R2 (no covariates): 0.04904
PGS AUROC (no covariates): 0.6475 [0.62543, 0.66957]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008598 PSS004559|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other hypothyroidism — AUROC: 0.76691 [0.7602, 0.77362] R²: 0.15134
Incremental AUROC (full-covars): 0.0729
PGS R2 (no covariates): 0.07419
PGS AUROC (no covariates): 0.68962 [0.68178, 0.69747]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004555 — —
[
  • 196 cases
  • , 6,301 controls
]
 — African unspecified — UKB —
PSS004556 — —
[
  • 61 cases
  • , 1,643 controls
]
 — East Asian — UKB —
PSS004557 — —
[
  • 1,684 cases
  • , 23,221 controls
]
 — European non-white British ancestry UKB —
PSS004558 — —
[
  • 653 cases
  • , 7,178 controls
]
 — South Asian — UKB —
PSS004559 — —
[
  • 4,577 cases
  • , 62,848 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)