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. |
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 |
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 |
---|---|---|---|---|---|---|---|---|---|
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 | — | — |
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 | — | — |
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 | — | — |
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 | — | — |
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 | — | — | [
| — | European | — | NR | GCAT |
PSS010969 | — | — | [
| — | European | — | NR | GCAT |
PSS010970 | — | — | 4,984 individuals | — | European | — | NR | GCAT |
PSS010971 | — | — | 4,985 individuals | — | European | — | NR | GCAT |
PSS010972 | — | — | 4,933 individuals | — | European | — | NR | GCAT |
PSS010973 | — | — | 4,933 individuals | — | European | — | NR | GCAT |
PSS010974 | — | — | [
| — | 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 |