Polygenic Score (PGS) ID: PGS001042

Predicted Trait
Reported Trait Thyrotoxicosis [hyperthyroidism] (time-to-event)
Mapped Trait(s) Thyrotoxicosis (EFO_0009190)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC645
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_HC645
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 226
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
—
[
  • 3,770 cases
  • , 265,934 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
PPM007968 PSS004565|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE thyrotoxicosis [hyperthyroidism] — AUROC: 0.74292 [0.70274, 0.7831] R²: 0.0808
Incremental AUROC (full-covars): -0.001
PGS R2 (no covariates): 0.00441
PGS AUROC (no covariates): 0.55406 [0.50519, 0.60292]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007969 PSS004566|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE thyrotoxicosis [hyperthyroidism] — AUROC: 0.64568 [0.56662, 0.72474] R²: 0.04341
Incremental AUROC (full-covars): 0.0279
PGS R2 (no covariates): 0.02341
PGS AUROC (no covariates): 0.6179 [0.53755, 0.69825]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007970 PSS004567|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE thyrotoxicosis [hyperthyroidism] — AUROC: 0.69253 [0.66505, 0.72] R²: 0.0468
Incremental AUROC (full-covars): 0.03643
PGS R2 (no covariates): 0.01594
PGS AUROC (no covariates): 0.61209 [0.58178, 0.6424]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007971 PSS004568|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE thyrotoxicosis [hyperthyroidism] — AUROC: 0.68899 [0.63846, 0.73951] R²: 0.04589
Incremental AUROC (full-covars): 0.03955
PGS R2 (no covariates): 0.01668
PGS AUROC (no covariates): 0.60594 [0.54869, 0.66319]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007972 PSS004569|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE thyrotoxicosis [hyperthyroidism] — AUROC: 0.71296 [0.69708, 0.72884] R²: 0.05914
Incremental AUROC (full-covars): 0.04673
PGS R2 (no covariates): 0.02359
PGS AUROC (no covariates): 0.63392 [0.61562, 0.65223]		 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
PSS004565 — —
[
  • 127 cases
  • , 6,370 controls
]
 — African unspecified — UKB —
PSS004566 — —
[
  • 51 cases
  • , 1,653 controls
]
 — East Asian — UKB —
PSS004567 — —
[
  • 334 cases
  • , 24,571 controls
]
 — European non-white British ancestry UKB —
PSS004568 — —
[
  • 107 cases
  • , 7,724 controls
]
 — South Asian — UKB —
PSS004569 — —
[
  • 935 cases
  • , 66,490 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)