Polygenic Score (PGS) ID: PGS001799

Predicted Trait
Reported Trait Thyroid cancer
Mapped Trait(s) thyroid carcinoma (EFO_0002892)
Released in PGS Catalog: Sept. 8, 2022
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Terms and Licenses
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Score Details

Score Construction
PGS Name 1kgeur_gbmi_ThC_pst_eff_a1_b0.5_phiauto
Development Method
Name PRS-CS-auto
Parameters effective sample size and other defualt parameters
Variants
Original Genome Build GRCh37
Number of Variants 885,482
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000262
Citation (link to publication) Wang Y et al. Cell Genom (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 82.7%
East Asian: 15.7%
African: 0.9%
Additional Diverse Ancestries: 0.7%
1,620,354 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 53 cases
  • , 14,794 controls
]
 African unspecified NR
—
[
  • 116 cases
  • , 11,005 controls
]
 Native American NR
—
[
  • 515 cases
  • , 254,102 controls
]
 East Asian 13 cohorts
  • BioMe
  • ,BioVU
  • ,CCPM
  • ,EB
  • ,FinnGen
  • ,GS:SFHS
  • ,HUNT
  • ,LifeLines
  • ,MGBB
  • ,MGI
  • ,QSKIN
  • ,UCLA
  • ,UKB
—
[
  • 6,015 cases
  • , 1,333,754 controls
]
 European 11 cohorts
  • BioMe
  • ,BioVU
  • ,CCPM
  • ,EB
  • ,FinnGen
  • ,HUNT
  • ,MGBB
  • ,MGI
  • ,QSKIN
  • ,UKB
  • ,deCODE

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
PPM009315 PSS007697|
European Ancestry|
7,128 individuals
 PGP000262 |
Wang Y et al. Cell Genom (2023)
 Reported Trait: Thyroid cancer — AUROC: 0.685 Nagelkerke's R2 (covariates regressed out): 0.01036 sex,age, 20PCs —

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
PSS007697 — —
[
  • 72 cases
  • , 7,055 controls
]
 — European — CanPath —