PGS Publication: PGP000467

Publication Information (EuropePMC)
Title Skin Phototype and Disease: A Comprehensive Genetic Approach to Pigmentary Traits Pleiotropy Using PRS in the GCAT Cohort.
PubMed ID 36672889(Europe PMC)
doi 10.3390/genes14010149
Publication Date Jan. 5, 2023
Journal Genes (Basel)
Author(s) Farré X, Blay N, Cortés B, Carreras A, Iraola-Guzmán S, de Cid R.
Released in PGS Catalog: June 1, 2023

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

External PGS Evaluated By This Publication

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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)
VitiligoVitiligo48
G
-
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000738/ScoringFiles/PGS000738.txt.gz
PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Melanomas of skin (diagnosis or history)melanoma1,119,238
G
D
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000430/ScoringFiles/PGS000430.txt.gz
PGS001040
(GBE_cancer1060)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Non melanoma skin cancernon-melanoma skin carcinoma1,610
-
D
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001040/ScoringFiles/PGS001040.txt.gz
PGS001302
(GBE_HC25)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Cataractcataract1,214
-
D
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001302/ScoringFiles/PGS001302.txt.gz
PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Basal cell carcinomabasal cell carcinoma1,111,490
G
D
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000446/ScoringFiles/PGS000446.txt.gz
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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.

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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
PPM018435PGS000738
(CONFIRMED_PGS)
PSS010977|
European Ancestry|
4,987 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Frecklesβ: -0.04382: 0.02103
PPM018436PGS000738
(CONFIRMED_PGS)
PSS010974|
European Ancestry|
4,979 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Phototype scoreβ: 0.4039: 0.03252
PPM018437PGS000738
(CONFIRMED_PGS)
PSS010969|
European Ancestry|
4,945 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Fitzpatrick scaleβ: 0.02234: 0.02897
PPM018438PGS000738
(CONFIRMED_PGS)
PSS010968|
European Ancestry|
4,702 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Red hairβ: 0.69478pseudo R²: 0.03857
PPM018439PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010977|
European Ancestry|
4,987 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Skin colourβ: -0.02584: 0.01389
PPM018440PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010970|
European Ancestry|
4,984 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Frecklesβ: 0.07956: 0.02392
PPM018441PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010971|
European Ancestry|
4,985 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Ease suntanβ: -0.0466: 0.01554
PPM018442PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010976|
European Ancestry|
4,973 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Ease sunburnβ: 0.05703: 0.012
PPM018443PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010973|
European Ancestry|
4,933 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Sunscreen in exteriorβ: 0.03277: 0.03826
PPM018444PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010972|
European Ancestry|
4,933 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Phototype scoreβ: -0.9044: 0.03608
PPM018445PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010975|
European Ancestry|
4,985 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Fitzpatrick scaleβ: -0.04982: 0.03301
PPM018446PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010978|
European Ancestry|
4,918 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Red hairβ: 1.49896pseudo R²: 0.0406
PPM018447PGS000430
(PRSWEB_PHECODE172.1_UKBB-SAIGE-HRC-X172.1_PRS-CS_MGI_20200608)
PSS010979|
European Ancestry|
4,352 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Brown hairβ: 1.13169pseudo R²: 0.0684
PPM018448PGS001302
(GBE_HC25)
PSS010980|
European Ancestry|
4,797 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Eye colourβ: 0.11584: 0.01115
PPM018449PGS001302
(GBE_HC25)
PSS010980|
European Ancestry|
4,797 individuals
PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.
Reported Trait: Sunscreen in exteriorβ: -0.03314: 0.0383
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Evaluated Samples

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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
PSS010968
[
  • 3,750 cases
  • , 952 controls
]
EuropeanNRGCAT
PSS010969
[
  • 243 cases
  • , 4,702 controls
]
EuropeanNRGCAT
PSS0109704,984 individualsEuropeanNRGCAT
PSS0109714,985 individualsEuropeanNRGCAT
PSS0109724,933 individualsEuropeanNRGCAT
PSS0109734,933 individualsEuropeanNRGCAT
PSS010974
[
  • 34 cases
  • , 4,945 controls
]
EuropeanNRGCAT
PSS0109754,985 individualsEuropeanNRGCAT
PSS0109764,973 individualsEuropeanNRGCAT
PSS0109774,987 individualsEuropeanNRGCAT
PSS0109784,918 individualsEuropeanNRGCAT
PSS0109794,352 individualsEuropeanNRGCAT
PSS0109804,797 individualsEuropeanNRGCAT
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