Polygenic Score (PGS) ID: PGS000162

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

Score Construction
PGS Name cGRS_Thyroid
Development Method
Name Pruning and Thresholding (P+T)
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.
Variants
Original Genome Build NR
Number of Variants 6
Effect Weight Type Odds Ratio over expected risk
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
355,697 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004144
Europe PMC: 28195142
 290,551 individuals European NR
GWAS Catalog: GCST001382
Europe PMC: 222672
 27,758 individuals European NR
GWAS Catalog: GCST000335
Europe PMC: 19198613
 37,388 individuals European NR

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
PPM000493 PSS000282|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Thyroid cancer — — Odds Ratio (OR; high vs. average risk groups): 1.7 [1.29, 2.25] — —
PPM000482 PSS000282|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Thyroid cancer — — Mean realative risk: 1.09 [1.04, 1.15]
Wilcoxon test (case vs. control) p-value: 4e-05		 — —

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
PSS000282 Primary tumor samples from TCGA —
[
  • 387 cases
  • , 0 controls
]
 Mean = 49.0 years
Sd = 16.0 years		 European — TCGA —
PSS000282 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —