Polygenic Score (PGS) ID: PGS001289

Predicted Trait
Reported Trait Thyroid cancer
Mapped Trait(s) thyroid carcinoma (EFO_0002892)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/cancer1065
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_cancer1065
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 11
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
—
[
  • 466 cases
  • , 269,238 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
PPM008943 PSS007656|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Thyroid cancer — AUROC: 0.72837 [0.59989, 0.85685] R²: 0.0395
Incremental AUROC (full-covars): 0.01385
PGS R2 (no covariates): 0.0141
PGS AUROC (no covariates): 0.6101 [0.46446, 0.75575]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008944 PSS007657|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Thyroid cancer — AUROC: 0.83233 [0.67782, 0.98683] R²: 0.16699
Incremental AUROC (full-covars): -0.00184
PGS R2 (no covariates): 0.01024
PGS AUROC (no covariates): 0.54057 [0.24283, 0.83831]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008945 PSS007658|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Thyroid cancer — AUROC: 0.71465 [0.65621, 0.77309] R²: 0.04643
Incremental AUROC (full-covars): 0.00897
PGS R2 (no covariates): 0.00455
PGS AUROC (no covariates): 0.55967 [0.48236, 0.63699]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008946 PSS007659|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Thyroid cancer — AUROC: 0.71171 [0.57425, 0.84917] R²: 0.04277
Incremental AUROC (full-covars): 0.00229
PGS R2 (no covariates): 0.00022
PGS AUROC (no covariates): 0.51375 [0.35907, 0.66843]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008947 PSS007660|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Thyroid cancer — AUROC: 0.63744 [0.5901, 0.68478] R²: 0.016
Incremental AUROC (full-covars): 0.03389
PGS R2 (no covariates): 0.01236
PGS AUROC (no covariates): 0.61843 [0.56413, 0.67273]		 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
PSS007656 — —
[
  • 15 cases
  • , 6,482 controls
]
 — African unspecified — UKB —
PSS007657 — —
[
  • 8 cases
  • , 1,696 controls
]
 — East Asian — UKB —
PSS007658 — —
[
  • 57 cases
  • , 24,848 controls
]
 — European non-white British ancestry UKB —
PSS007659 — —
[
  • 13 cases
  • , 7,818 controls
]
 — South Asian — UKB —
PSS007660 — —
[
  • 104 cases
  • , 67,321 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)