Polygenic Score (PGS) ID: PGS000965

Predicted Trait
Reported Trait Hypothyroidism/myxoedema
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC219
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC219
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 4,535
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 17,190 cases
  • , 252,514 controls
]
European white British ancestry 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
PPM007649 PSS004354|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Hypothyroidism/myxoedema AUROC: 0.70914 [0.67391, 0.74437] : 0.06732
Incremental AUROC (full-covars): 0.00847
PGS R2 (no covariates): 0.01005
PGS AUROC (no covariates): 0.58277 [0.54281, 0.62272]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007650 PSS004355|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Hypothyroidism/myxoedema AUROC: 0.68903 [0.61236, 0.7657] : 0.05952
Incremental AUROC (full-covars): 0.01842
PGS R2 (no covariates): 0.01318
PGS AUROC (no covariates): 0.58777 [0.50589, 0.66966]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007651 PSS004356|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Hypothyroidism/myxoedema AUROC: 0.76462 [0.75294, 0.7763] : 0.14559
Incremental AUROC (full-covars): 0.06544
PGS R2 (no covariates): 0.06844
PGS AUROC (no covariates): 0.68233 [0.66882, 0.69583]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007652 PSS004357|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Hypothyroidism/myxoedema AUROC: 0.74628 [0.72661, 0.76594] : 0.13858
Incremental AUROC (full-covars): 0.03694
PGS R2 (no covariates): 0.04737
PGS AUROC (no covariates): 0.64507 [0.62236, 0.66778]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007653 PSS004358|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Hypothyroidism/myxoedema AUROC: 0.76828 [0.76142, 0.77515] : 0.14978
Incremental AUROC (full-covars): 0.07249
PGS R2 (no covariates): 0.07271
PGS AUROC (no covariates): 0.68907 [0.68098, 0.69716]
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
PSS004354
[
  • 194 cases
  • , 6,303 controls
]
African unspecified UKB
PSS004355
[
  • 53 cases
  • , 1,651 controls
]
East Asian UKB
PSS004356
[
  • 1,582 cases
  • , 23,323 controls
]
European non-white British ancestry UKB
PSS004357
[
  • 624 cases
  • , 7,207 controls
]
South Asian UKB
PSS004358
[
  • 4,298 cases
  • , 63,127 controls
]
European white British ancestry UKB Testing cohort (heldout set)