Trait: Vitiligo

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004208
Description Generalized well circumscribed patches of leukoderma that are generally distributed over symmetric body locations and is due to autoimmune destruction of melanocytes. [NCIT: P378]
Trait category
Immune system disorder
Synonym vitiligo
Mapped terms 16 mapped terms
  • DOID:12306
  • ICD10:L80
  • ICD10CM:L80
  • ICD9:709.01
  • MEDGEN:22677
  • MESH:D014820
  • MONDO:0008661
  • MeSH:D014820
  • MedDRA:10047642
  • NCIT:C26915
  • NCIt:C26915
  • OMIM:193200
  • Orphanet:247871
  • SNOMEDCT:56727007
  • UMLS:C0042900
  • icd11.foundation:1894744640

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000738
(CONFIRMED_PGS)
 PGP000145 |
Roberts GHL et al. Am J Hum Genet (2019)
 Vitiligo Vitiligo 48
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000738/ScoringFiles/PGS000738.txt.gz
PGS000760
(VIT)
 PGP000164 |
Khan Z et al. Nat Commun (2021)
 Vitiligo Vitiligo 42
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000760/ScoringFiles/PGS000760.txt.gz
PGS001536
(GBE_HC1188)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Vitiligo (time-to-event) Vitiligo 77
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001536/ScoringFiles/PGS001536.txt.gz

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) 		Evaluated Score 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 PGS000738
(CONFIRMED_PGS)
 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 PGS000738
(CONFIRMED_PGS)
 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 PGS000738
(CONFIRMED_PGS)
 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 PGS000738
(CONFIRMED_PGS)
 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 PGS000738
(CONFIRMED_PGS)
 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 PGS000738
(CONFIRMED_PGS)
 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 PGS000738
(CONFIRMED_PGS)
 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 PGS000738
(CONFIRMED_PGS)
 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 — —
PPM001935 PGS000760
(VIT)
 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 —
PPM005215 PGS001536
(GBE_HC1188)
 PSS004173|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.63509 [0.52563, 0.74454] R²: 0.01654
Incremental AUROC (full-covars): -0.00281
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.51169 [0.39527, 0.62811]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005216 PGS001536
(GBE_HC1188)
 PSS004174|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.82774 [0.75298, 0.90249] R²: 0.08055
Incremental AUROC (full-covars): 0.01924
PGS R2 (no covariates): 0.00431
PGS AUROC (no covariates): 0.57823 [0.37976, 0.7767]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005217 PGS001536
(GBE_HC1188)
 PSS004175|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.6991 [0.61917, 0.77902] R²: 0.03993
Incremental AUROC (full-covars): 0.01341
PGS R2 (no covariates): 0.00254
PGS AUROC (no covariates): 0.55625 [0.47549, 0.63701]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005218 PGS001536
(GBE_HC1188)
 PSS004176|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.64566 [0.58746, 0.70386] R²: 0.02575
Incremental AUROC (full-covars): 0.0309
PGS R2 (no covariates): 0.01048
PGS AUROC (no covariates): 0.60302 [0.5391, 0.66694]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005219 PGS001536
(GBE_HC1188)
 PSS004177|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE vitiligo — AUROC: 0.63449 [0.58754, 0.68144] R²: 0.01686
Incremental AUROC (full-covars): 0.08163
PGS R2 (no covariates): 0.01621
PGS AUROC (no covariates): 0.64193 [0.59907, 0.68478]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS000970 — Median = 400.0 days 1,584 individuals — European — GNEHGI2020Q2 —
PSS004173 — —
[
  • 17 cases
  • , 6,480 controls
]
 — African unspecified — UKB —
PSS004174 — —
[
  • 6 cases
  • , 1,698 controls
]
 — East Asian — UKB —
PSS004175 — —
[
  • 45 cases
  • , 24,860 controls
]
 — European non-white British ancestry UKB —
PSS004176 — —
[
  • 71 cases
  • , 7,760 controls
]
 — South Asian — UKB —
PSS004177 — —
[
  • 131 cases
  • , 67,294 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
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