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

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
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) melanoma 1,119,238
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 cancer non-melanoma skin carcinoma 1,610
-
 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)
 Cataract cataract 1,214
-
 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 carcinoma basal cell carcinoma 1,111,490
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000446/ScoringFiles/PGS000446.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
PPM018463 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease sunburn β: 0.08836 — R²: 0.01475 — —
PPM018465 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Fitzpatrick scale β: -0.0689 — R²: 0.03786 — —
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 — —
PPM018439 PGS000430
(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 colour β: -0.02584 — R²: 0.01389 — —
PPM018440 PGS000430
(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: Freckles β: 0.07956 — R²: 0.02392 — —
PPM018441 PGS000430
(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 suntan β: -0.0466 — R²: 0.01554 — —
PPM018442 PGS000430
(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 sunburn β: 0.05703 — R²: 0.012 — —
PPM018444 PGS000430
(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 score β: -0.9044 — R²: 0.03608 — —
PPM018445 PGS000430
(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 scale β: -0.04982 — R²: 0.03301 — —
PPM018446 PGS000430
(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 hair β: 1.49896 — pseudo R²: 0.0406 — —
PPM018447 PGS000430
(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 hair β: 1.13169 — pseudo R²: 0.0684 — —
PPM018448 PGS001302
(GBE_HC25)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Eye colour β: 0.11584 — R²: 0.01115 — —
PPM018449 PGS001302
(GBE_HC25)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Sunscreen in exterior β: -0.03314 — R²: 0.0383 — —
PPM018450 PGS001302
(GBE_HC25)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Phototype score β: 0.70812 — R²: 0.03441 — —
PPM018451 PGS001302
(GBE_HC25)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Fitzpatrick scale β: 0.04334 — R²: 0.03185 — —
PPM018452 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Skin colour β: -0.02375 — R²: 0.01374 — —
PPM018453 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Freckles β: 0.04205 — R²: 0.02091 — —
PPM018454 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease suntan β: -0.0266 — R²: 0.01362 — —
PPM018455 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease sunburn β: 0.04289 — R²: 0.01118 — —
PPM018456 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Phototype score β: -0.62656 — R²: 0.03377 — —
PPM018457 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Fitzpatrick scale β: -0.02673 — R²: 0.0294 — —
PPM018458 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Red hair β: 1.77173 — R²: 0.05421
pseudo R²: 0.05421		 — —
PPM018459 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Eye colour β: -0.11302 — R²: 0.0106 — —
PPM018460 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Skin colour β: -0.05462 — R²: 0.01757 — —
PPM018461 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Freckles β: 0.09955 — R²: 0.02643 — —
PPM018462 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Ease suntan β: -0.06804 — R²: 0.01892 — —
PPM018464 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Phototype score β: -1.51455 — R²: 0.04441 — —
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 — —
PPM018443 PGS000430
(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 exterior β: 0.03277 — R²: 0.03826 — —
PPM018466 PGS001040
(GBE_cancer1060)
 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Blond hair β: 1.14835 — pseudo R²: 0.01006 — —

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
PSS010971 — — 4,985 individuals — European — NR GCAT
PSS010972 — — 4,933 individuals — European — NR GCAT
PSS010973 — — 4,933 individuals — European — NR GCAT
PSS010974 — —
[
  • 34 cases
  • , 4,945 controls
]
 — European — NR GCAT
PSS010975 — — 4,985 individuals — European — NR GCAT
PSS010976 — — 4,973 individuals — European — NR GCAT
PSS010977 — — 4,987 individuals — European — NR GCAT
PSS010978 — — 4,918 individuals — European — NR GCAT
PSS010979 — — 4,352 individuals — European — NR GCAT
PSS010980 — — 4,797 individuals — European — NR GCAT
PSS010968 — —
[
  • 3,750 cases
  • , 952 controls
]
 — European — NR GCAT
PSS010969 — —
[
  • 243 cases
  • , 4,702 controls
]
 — European — NR GCAT
PSS010970 — — 4,984 individuals — European — NR GCAT