Polygenic Score (PGS) ID: PGS000738

Predicted Trait
Reported Trait Vitiligo
Mapped Trait(s) Vitiligo (EFO_0004208)
Released in PGS Catalog: Feb. 23, 2021
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Score Details

Score Construction
PGS Name CONFIRMED_PGS
Development Method
Name Genome-wide significant variants
Parameters P<5e-8
Variants
Original Genome Build hg19
Number of Variants 48
Number of Variant Interaction Terms 1
Effect Weight Type ln(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000145
Citation (link to publication) Roberts GHL et al. Am J Hum Genet (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
40,258 individuals (100%)
PGS Evaluation
European: 100%
5 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

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
PPM001761 PSS000907|
European Ancestry|
4,008 individuals
 PGP000145 |
Roberts GHL et al. Am J Hum Genet (2019)
 Reported Trait: Vitiligo — — Odds Ratio (OR, top 20% vs remaining 80% of score distribution): 4.87 [4.21, 5.64] — —
PPM001762 PSS000907|
European Ancestry|
4,008 individuals
 PGP000145 |
Roberts GHL et al. Am J Hum Genet (2019)
 Reported Trait: Vitiligo — — Odds Ratio (OR, top 10% vs remaining 90% of score distribution): 5.26 [4.42, 6.29] — —
PPM001763 PSS000907|
European Ancestry|
4,008 individuals
 PGP000145 |
Roberts GHL et al. Am J Hum Genet (2019)
 Reported Trait: Vitiligo — — Odds Ratio (OR, top 10% vs remaining 95% of score distribution): 6.2 [4.96, 7.79] — —
PPM001764 PSS000907|
European Ancestry|
4,008 individuals
 PGP000145 |
Roberts GHL et al. Am J Hum Genet (2019)
 Reported Trait: Vitiligo — — Odds Ratio (OR, top 1% vs remaining 99% of score distribution): 8.79 [5.85, 13.78] — —
PPM018437 PSS010969|
European Ancestry|
4,945 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Fitzpatrick scale β: 0.02234 — R²: 0.02897 — —
PPM018438 PSS010968|
European Ancestry|
4,702 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Red hair β: 0.69478 — pseudo R²: 0.03857 — —
PPM018435 PSS010977|
European Ancestry|
4,987 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Freckles β: -0.04382 — R²: 0.02103 — —
PPM018436 PSS010974|
European Ancestry|
4,979 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Phototype score β: 0.4039 — R²: 0.03252 — —

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
PSS010974 — —
[
  • 34 cases
  • , 4,945 controls
]
 — European — NR GCAT
PSS010977 — — 4,987 individuals — European — NR GCAT
PSS000907 Cases are individuals with vitiligo. Diagnoses of vitiligo in multiplex-affected subjects and reportedly unaffected family members were verified by manual review of all available phenotype information for each subject. —
[
  • 1,827 cases
  • , 2,181 controls
]
 — European — NR —
PSS010968 — —
[
  • 3,750 cases
  • , 952 controls
]
 — European — NR GCAT
PSS010969 — —
[
  • 243 cases
  • , 4,702 controls
]
 — European — NR GCAT