Polygenic Score (PGS) ID: PGS000162

Predicted Trait
Reported Trait Thyroid cancer
Mapped Trait(s) thyroid carcinoma (EFO_0002892)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Thyroid
Original Genome Build NR
Number of Variants 6
Development Method
Name Pruning + Thresholding
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST004144
EuropePMC: 28195142
290,551 individuals European
GWAS Catalog: GCST001382
EuropePMC: 22267200
27,758 individuals European
GWAS Catalog: GCST000335
EuropePMC: 19198613
37,388 individuals European

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
PGS Sample Set ID
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000482 PSS000282 PGP000075
Shi Z et al. (2019)
Reported Trait: Thyroid cancer Mean realative risk: 1.09[1.04, 1.15]
Wilcoxon test (case vs. control) p-value: 3.64e-05
PPM000493 PSS000282 PGP000075
Shi Z et al. (2019)
Reported Trait: Thyroid cancer Odds Ratio (OR; high vs. average risk groups): 1.7[1.29, 2.25]

Evaluated Samples

PGS Sample Set ID
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000282 Primary tumor samples from TCGA
  • 387 cases
  • , 0 controls
Mean = 49.0 years
Sd = 16.0 years
European TCGA
  • 0 cases
  • , 13,427 controls
European eMERGE