Polygenic Score (PGS) ID: PGS000760

Predicted Trait
Reported Trait Vitiligo
Mapped Trait(s) Vitiligo (EFO_0004208)
Released in PGS Catalog: June 11, 2021
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Score Details

Score Construction
PGS Name VIT
Development Method
Name GCTA-COJO forward selection highest PPA variants
Parameters p < 5e-8, +/-500kb window, 10K EUR UKB individuals as LD reference, MHC region removed
Variants
Original Genome Build hg19
Number of Variants 42
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000164
Citation (link to publication) Khan Z et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
40,258 individuals (100%)
Score Development/Training
European: 100%
408,959 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: GCST004785
Europe PMC: 27723757
 40,258 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
—
[
  • 25,072 cases
  • , 383,887 controls
]
 European UKB ICD9 244 and self-reported hypothyroidism — — — Source GWAS summary statistics without MHC https://my.locuszoom.org/gwas/552910/

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
PPM001935 PSS000970|
European Ancestry|
1,584 individuals
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Reported Trait: anti-PD-L1 induced hypothyroidism in cancer patients HR: 1.41 [1.22, 1.61] — meta-analysis p-value: 1.10e-06 5 genotype PCs —

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
PSS000970 — Median = 400.0 days 1,584 individuals — European — GNEHGI2020Q2 —