Polygenic Score (PGS) ID: PGS001043

Predicted Trait
Reported Trait Hyperthyroidism, thyrotoxicosis
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC55
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_HC55
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 69
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
—
[
  • 3,195 cases
  • , 266,509 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
PPM007973 PSS004526|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hyperthyroidism/thyrotoxicosis — AUROC: 0.73999 [0.69812, 0.78186] R²: 0.07663
Incremental AUROC (full-covars): -0.00598
PGS R2 (no covariates): 0.00164
PGS AUROC (no covariates): 0.53513 [0.48316, 0.5871]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007974 PSS004527|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hyperthyroidism/thyrotoxicosis — AUROC: 0.62359 [0.53601, 0.71117] R²: 0.03132
Incremental AUROC (full-covars): 0.0205
PGS R2 (no covariates): 0.01311
PGS AUROC (no covariates): 0.58858 [0.50442, 0.67274]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007975 PSS004528|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hyperthyroidism/thyrotoxicosis — AUROC: 0.69729 [0.66674, 0.72784] R²: 0.04646
Incremental AUROC (full-covars): 0.03676
PGS R2 (no covariates): 0.01638
PGS AUROC (no covariates): 0.61845 [0.58525, 0.65166]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007976 PSS004529|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hyperthyroidism/thyrotoxicosis — AUROC: 0.68797 [0.63675, 0.7392] R²: 0.04145
Incremental AUROC (full-covars): 0.04372
PGS R2 (no covariates): 0.01807
PGS AUROC (no covariates): 0.60983 [0.54762, 0.67204]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007977 PSS004530|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hyperthyroidism/thyrotoxicosis — AUROC: 0.71366 [0.6965, 0.73082] R²: 0.0566
Incremental AUROC (full-covars): 0.04641
PGS R2 (no covariates): 0.02158
PGS AUROC (no covariates): 0.6323 [0.61251, 0.6521]		 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
PSS004526 — —
[
  • 116 cases
  • , 6,381 controls
]
 — African unspecified — UKB —
PSS004527 — —
[
  • 44 cases
  • , 1,660 controls
]
 — East Asian — UKB —
PSS004528 — —
[
  • 286 cases
  • , 24,619 controls
]
 — European non-white British ancestry UKB —
PSS004529 — —
[
  • 92 cases
  • , 7,739 controls
]
 — South Asian — UKB —
PSS004530 — —
[
  • 805 cases
  • , 66,620 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)