Polygenic Score (PGS) ID: PGS000632

Predicted Trait
Reported Trait Thyroid cancer
Mapped Trait(s) thyroid carcinoma (EFO_0002892)
Additional Trait Information PheCode 193
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=3.16e-10
Variants
Original Genome Build GRCh37
Number of Variants 8
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
357,784 individuals (100%)
Score Development/Training
European: 100%
4,481 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: GCST000335
Europe PMC: 19198613
 37,388 individuals European NR
GWAS Catalog: GCST001382
Europe PMC: 22267200
 27,758 individuals European NR
GWAS Catalog: GCST002102
Europe PMC: 23894154
 1,187 individuals European NR
GWAS Catalog: GCST002873
Europe PMC: 25855579
 900 individuals European NR
GWAS Catalog: GCST004144
Europe PMC: 28195142
 290,551 individuals European NR
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
Europe PMC: 32991828
[
  • 409 cases
  • , 4,072 controls
]
 European MGI PheCode:193; ICD9CM:193, V10.87; ICD10CM:C73 — — — —

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
PPM001317 PSS000558|
European Ancestry|
4,270 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Thyroid cancer OR: 1.568 [1.412, 1.74]
β: 0.45 (0.0532)		 AUROC: 0.618 [0.587, 0.647] Nagelkerke's Pseudo-R²: 0.0365
Brier score: 0.0812
Odds Ratio (OR, top 1% vs. Rest): 5.14 [2.94, 8.99]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE193_GWAS-Catalog-r2019-05-03-X193_PT_MGI_20200608

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
PSS000558 PheCode:193; ICD9CM:193, V10.87; ICD10CM:C73 —
[
  • 389 cases
  • , 3,881 controls
]
 — European — MGI —