Polygenic Score (PGS) ID: PGS000928

Predicted Trait
Reported Trait Other non-toxic goitre (time-to-event)
Mapped Trait(s) nontoxic goiter (MONDO_0001658)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC644
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_HC644
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 170
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
—
[
  • 2,463 cases
  • , 267,241 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
PPM007467 PSS004560|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other non-toxic goitre — AUROC: 0.72128 [0.66829, 0.77427] R²: 0.0605
Incremental AUROC (full-covars): 0.01397
PGS R2 (no covariates): 0.01481
PGS AUROC (no covariates): 0.60656 [0.54212, 0.67101]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007468 PSS004561|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other non-toxic goitre — AUROC: 0.6964 [0.60514, 0.78765] R²: 0.04766
Incremental AUROC (full-covars): 0.00791
PGS R2 (no covariates): 0.00213
PGS AUROC (no covariates): 0.559 [0.46259, 0.65542]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007469 PSS004562|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other non-toxic goitre — AUROC: 0.71135 [0.68228, 0.74042] R²: 0.0552
Incremental AUROC (full-covars): 0.0365
PGS R2 (no covariates): 0.01651
PGS AUROC (no covariates): 0.62112 [0.58564, 0.6566]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007470 PSS004563|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other non-toxic goitre — AUROC: 0.77727 [0.73439, 0.82016] R²: 0.09335
Incremental AUROC (full-covars): 0.02392
PGS R2 (no covariates): 0.01984
PGS AUROC (no covariates): 0.62519 [0.56312, 0.68726]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007471 PSS004564|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other non-toxic goitre — AUROC: 0.72495 [0.70529, 0.74461] R²: 0.05905
Incremental AUROC (full-covars): 0.03129
PGS R2 (no covariates): 0.01271
PGS AUROC (no covariates): 0.60048 [0.57499, 0.62598]		 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
PSS004560 — —
[
  • 84 cases
  • , 6,413 controls
]
 — African unspecified — UKB —
PSS004561 — —
[
  • 32 cases
  • , 1,672 controls
]
 — East Asian — UKB —
PSS004562 — —
[
  • 249 cases
  • , 24,656 controls
]
 — European non-white British ancestry UKB —
PSS004563 — —
[
  • 81 cases
  • , 7,750 controls
]
 — South Asian — UKB —
PSS004564 — —
[
  • 548 cases
  • , 66,877 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)