Trait: non-melanoma skin carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009260
Description Any skin carcinoma that is not melanoma, with the most common types being basal cell carcinoma and squamous cell carcinoma
Trait category
Cancer
Synonyms 3 synonyms
  • non-melanoma skin cancer
  • nonmelanoma skin cancer
  • nonmelanoma skin carcinoma
Mapped term MedDRA:10007116
Child trait(s) 2 child traits

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
Note: This table shows all PGS for "non-melanoma skin carcinoma" and any child terms of this trait in the EFO hierarchy by default.
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)
PGS000119
(BCC32)
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Basal cell carcinoma basal cell carcinoma 32
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000119/ScoringFiles/PGS000119.txt.gz
PGS000445
(PRSWEB_PHECODE172.21_20001-1061_P_5e-08_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 19
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000445/ScoringFiles/PGS000445.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
PGS000447
(PRSWEB_PHECODE172.21_20001-1061_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 72
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000447/ScoringFiles/PGS000447.txt.gz
PGS000448
(PRSWEB_PHECODE172.21_20001-1061_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 183
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000448/ScoringFiles/PGS000448.txt.gz
PGS000449
(PRSWEB_PHECODE172.21_20001-1073_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 1,073,162
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000449/ScoringFiles/PGS000449.txt.gz
PGS000450
(PRSWEB_PHECODE172.21_20001-1073_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 8
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000450/ScoringFiles/PGS000450.txt.gz
PGS000451
(PRSWEB_PHECODE172.21_20001-1073_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 2,231
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000451/ScoringFiles/PGS000451.txt.gz
PGS000452
(PRSWEB_PHECODE172.21_BCC-Chahal_P_5e-08_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 28
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000452/ScoringFiles/PGS000452.txt.gz
PGS000453
(PRSWEB_PHECODE172.21_BCC-Chahal_P_5e-08_UKB_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 28
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000453/ScoringFiles/PGS000453.txt.gz
PGS000454
(PRSWEB_PHECODE172.21_BCC-Chahal_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 27
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000454/ScoringFiles/PGS000454.txt.gz
PGS000455
(PRSWEB_PHECODE172.21_BCC-Chahal_PT_UKB_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 28
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000455/ScoringFiles/PGS000455.txt.gz
PGS000456
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_P_5e-08_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 30
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000456/ScoringFiles/PGS000456.txt.gz
PGS000457
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_P_5e-08_UKB_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 30
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000457/ScoringFiles/PGS000457.txt.gz
PGS000458
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 23
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000458/ScoringFiles/PGS000458.txt.gz
PGS000459
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_UKB_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Basal cell carcinoma basal cell carcinoma 24
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000459/ScoringFiles/PGS000459.txt.gz
PGS000730
(PRS_BCC)
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Basal cell carcinoma basal cell carcinoma 47
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000730/ScoringFiles/PGS000730.txt.gz - Check Terms/Licenses
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
PGS003416
(MTAGPRS)
 PGP000429 |
Seviiri M et al. Nat Commun (2022)
 Basal cell carcinoma (MTAG) basal cell carcinoma 462
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003416/ScoringFiles/PGS003416.txt.gz
PGS003417
(UKBPRS)
 PGP000429 |
Seviiri M et al. Nat Commun (2022)
 Basal cell carcinoma basal cell carcinoma 273
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003417/ScoringFiles/PGS003417.txt.gz
PGS004592
(PRS_KC)
 PGP000571 |
Liyanage UE et al. J Eur Acad Dermatol Venereol (2022)
 Keratinocyte cancer keratinocyte carcinoma 78
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004592/ScoringFiles/PGS004592.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
PPM000344 PGS000119
(BCC32)
 PSS000207|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.32 [1.27, 1.36] AUROC: 0.58 [0.56, 0.58] — age, sex, batch, PC1-4 —
PPM000341 PGS000119
(BCC32)
 PSS000209|
European Ancestry|
20,468 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Basal cell carcinoma OR: 1.65 [1.56, 1.75] AUROC: 0.64 [0.62, 0.66] — age, sex, batch, PC1-4 —
PPM000347 PGS000119
(BCC32)
 PSS000211|
European Ancestry|
149,857 individuals
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Reported Trait: Skin cancer OR: 1.4 [1.42, 1.48] — — age, sex, genotyping array, first 4 genotype PCs —
PPM001130 PGS000445
(PRSWEB_PHECODE172.21_20001-1061_P_5e-08_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.334 [1.264, 1.409]
β: 0.289 (0.0278)		 AUROC: 0.571 [0.555, 0.587] Nagelkerke's Pseudo-R²: 0.0184
Brier score: 0.108
Odds Ratio (OR, top 1% vs. Rest): 2.54 [1.72, 3.74]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1061_P_5e-08_MGI_20200608
PPM001131 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.291 [1.221, 1.366]
β: 0.256 (0.0286)		 AUROC: 0.575 [0.559, 0.591] Nagelkerke's Pseudo-R²: 0.0139
Brier score: 0.109
Odds Ratio (OR, top 1% vs. Rest): 1.42 [0.871, 2.33]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608
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		 — —
PPM001132 PGS000447
(PRSWEB_PHECODE172.21_20001-1061_PT_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.398 [1.322, 1.477]
β: 0.335 (0.0282)		 AUROC: 0.591 [0.575, 0.607] Nagelkerke's Pseudo-R²: 0.0237
Brier score: 0.108
Odds Ratio (OR, top 1% vs. Rest): 2.5 [1.68, 3.71]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1061_PT_MGI_20200608
PPM001133 PGS000448
(PRSWEB_PHECODE172.21_20001-1061_LASSOSUM_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.411 [1.335, 1.491]
β: 0.344 (0.0282)		 AUROC: 0.587 [0.57, 0.604] Nagelkerke's Pseudo-R²: 0.0254
Brier score: 0.108
Odds Ratio (OR, top 1% vs. Rest): 2.93 [2.03, 4.25]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1061_LASSOSUM_MGI_20200608
PPM001134 PGS000449
(PRSWEB_PHECODE172.21_20001-1073_PRS-CS_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.093 [1.034, 1.155]
β: 0.0888 (0.0282)		 AUROC: 0.525 [0.509, 0.54] Nagelkerke's Pseudo-R²: 0.00141
Brier score: 0.109
Odds Ratio (OR, top 1% vs. Rest): 1.65 [1.04, 2.61]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1073_PRS-CS_MGI_20200608
PPM001135 PGS000450
(PRSWEB_PHECODE172.21_20001-1073_PT_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.079 [1.022, 1.139]
β: 0.0759 (0.0278)		 AUROC: 0.504 [0.489, 0.52] Nagelkerke's Pseudo-R²: 0.00145
Brier score: 0.109
Odds Ratio (OR, top 1% vs. Rest): 1.42 [0.882, 2.3]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1073_PT_MGI_20200608
PPM001136 PGS000451
(PRSWEB_PHECODE172.21_20001-1073_LASSOSUM_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.144 [1.084, 1.208]
β: 0.135 (0.0278)		 AUROC: 0.521 [0.506, 0.536] Nagelkerke's Pseudo-R²: 0.00396
Brier score: 0.109
Odds Ratio (OR, top 1% vs. Rest): 2.44 [1.65, 3.62]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_20001-1073_LASSOSUM_MGI_20200608
PPM001137 PGS000452
(PRSWEB_PHECODE172.21_BCC-Chahal_P_5e-08_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.663 [1.57, 1.761]
β: 0.508 (0.0293)		 AUROC: 0.632 [0.616, 0.647] Nagelkerke's Pseudo-R²: 0.0487
Brier score: 0.106
Odds Ratio (OR, top 1% vs. Rest): 3.61 [2.53, 5.15]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_BCC-Chahal_P_5e-08_MGI_20200608
PPM001138 PGS000453
(PRSWEB_PHECODE172.21_BCC-Chahal_P_5e-08_UKB_20200608)
 PSS000568|
European Ancestry|
60,018 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.511 [1.47, 1.554]
β: 0.413 (0.0142)		 AUROC: 0.611 [0.604, 0.619] Nagelkerke's Pseudo-R²: 0.0301
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 2.8 [2.33, 3.36]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_BCC-Chahal_P_5e-08_UKB_20200608
PPM001139 PGS000454
(PRSWEB_PHECODE172.21_BCC-Chahal_PT_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.661 [1.568, 1.759]
β: 0.507 (0.0293)		 AUROC: 0.632 [0.616, 0.647] Nagelkerke's Pseudo-R²: 0.0489
Brier score: 0.106
Odds Ratio (OR, top 1% vs. Rest): 3.79 [2.68, 5.35]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_BCC-Chahal_PT_MGI_20200608
PPM001140 PGS000455
(PRSWEB_PHECODE172.21_BCC-Chahal_PT_UKB_20200608)
 PSS000568|
European Ancestry|
60,018 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.511 [1.47, 1.554]
β: 0.413 (0.0142)		 AUROC: 0.611 [0.604, 0.619] Nagelkerke's Pseudo-R²: 0.0301
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 2.8 [2.33, 3.36]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_BCC-Chahal_PT_UKB_20200608
PPM001141 PGS000456
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_P_5e-08_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.633 [1.541, 1.729]
β: 0.49 (0.0293)		 AUROC: 0.63 [0.615, 0.646] Nagelkerke's Pseudo-R²: 0.0456
Brier score: 0.106
Odds Ratio (OR, top 1% vs. Rest): 3.95 [2.79, 5.58]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_P_5e-08_MGI_20200608
PPM001142 PGS000457
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_P_5e-08_UKB_20200608)
 PSS000568|
European Ancestry|
60,018 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.535 [1.493, 1.579]
β: 0.429 (0.0144)		 AUROC: 0.617 [0.609, 0.625] Nagelkerke's Pseudo-R²: 0.0322
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 3.11 [2.6, 3.71]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_P_5e-08_UKB_20200608
PPM001143 PGS000458
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_MGI_20200608)
 PSS000544|
European Ancestry|
11,322 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.634 [1.542, 1.732]
β: 0.491 (0.0296)		 AUROC: 0.628 [0.612, 0.644] Nagelkerke's Pseudo-R²: 0.0457
Brier score: 0.106
Odds Ratio (OR, top 1% vs. Rest): 4.03 [2.86, 5.69]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_MGI_20200608
PPM001144 PGS000459
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_UKB_20200608)
 PSS000568|
European Ancestry|
60,018 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Basal cell carcinoma OR: 1.528 [1.485, 1.572]
β: 0.424 (0.0144)		 AUROC: 0.615 [0.608, 0.623] Nagelkerke's Pseudo-R²: 0.0314
Brier score: 0.0813
Odds Ratio (OR, top 1% vs. Rest): 3.05 [2.55, 3.64]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_UKB_20200608
PPM001670 PGS000730
(PRS_BCC)
 PSS000871|
European Ancestry|
88,924 individuals
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Reported Trait: Basal cell carcinoma OR: 1.57 [1.55, 1.6] AUROC: 0.624 — — —
PPM007958 PGS001040
(GBE_cancer1060)
 PSS007651|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-melanoma skin cancer — AUROC: 0.80478 [0.72556, 0.884] R²: 0.07029
Incremental AUROC (full-covars): -0.00066
PGS R2 (no covariates): 0.00133
PGS AUROC (no covariates): 0.54127 [0.39017, 0.69237]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007959 PGS001040
(GBE_cancer1060)
 PSS007652|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-melanoma skin cancer — AUROC: 0.86455 [0.80574, 0.92335] R²: 0.12918
Incremental AUROC (full-covars): -0.00442
PGS R2 (no covariates): 0.00152
PGS AUROC (no covariates): 0.4523 [0.1694, 0.73519]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007960 PGS001040
(GBE_cancer1060)
 PSS007653|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-melanoma skin cancer — AUROC: 0.73342 [0.72065, 0.74619] R²: 0.10751
Incremental AUROC (full-covars): 0.0378
PGS R2 (no covariates): 0.05185
PGS AUROC (no covariates): 0.66327 [0.64889, 0.67765]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007961 PGS001040
(GBE_cancer1060)
 PSS007654|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-melanoma skin cancer — AUROC: 0.76366 [0.66832, 0.85901] R²: 0.06447
Incremental AUROC (full-covars): -0.00934
PGS R2 (no covariates): 0.00078
PGS AUROC (no covariates): 0.47181 [0.35611, 0.58752]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007962 PGS001040
(GBE_cancer1060)
 PSS007655|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Non-melanoma skin cancer — AUROC: 0.70656 [0.69863, 0.7145] R²: 0.08615
Incremental AUROC (full-covars): 0.04717
PGS R2 (no covariates): 0.03949
PGS AUROC (no covariates): 0.64209 [0.6334, 0.65078]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
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 — —
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 — —
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 — —
PPM017069 PGS003416
(MTAGPRS)
 PSS010113|
European Ancestry|
18,933 individuals
 PGP000429 |
Seviiri M et al. Nat Commun (2022)
 Reported Trait: Keratinocyte cancers OR: 1.66 [1.55, 1.79] — — age, sex, 10 ancesty PCs —
PPM017070 PGS003417
(UKBPRS)
 PSS010113|
European Ancestry|
18,933 individuals
 PGP000429 |
Seviiri M et al. Nat Commun (2022)
 Reported Trait: Keratinocyte cancers OR: 1.56 [1.45, 1.67] — — age, sex, 10 ancesty PCs —
PPM020722 PGS004592
(PRS_KC)
 PSS011383|
European Ancestry|
998 individuals
 PGP000571 |
Liyanage UE et al. J Eur Acad Dermatol Venereol (2022)
 Reported Trait: Keratinocyte cancer OR: 1.51 [1.3, 1.76] AUROC: 0.74 R²: 0.231 Age, sex, self-reported skin tanning ability, clinical grade of neck elastosis, genotyping batch, first 2 PCs —
PPM020723 PGS004592
(PRS_KC)
 PSS011383|
European Ancestry|
998 individuals
 PGP000571 |
Liyanage UE et al. J Eur Acad Dermatol Venereol (2022)
 Reported Trait: Keratinocyte cancer — — Odds ratio (OR, top PRS quintile vs bottom PRS quintile): 3.45 [2.18, 5.5] Age, sex, self-reported skin tanning ability, clinical grade of neck elastosis, genotyping batch, first 2 PCs —

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
PSS000207 PheCode 172 —
[
  • 3,002 cases
  • , 17,466 controls
]
,
46.9 % Male samples
 Mean = 54.2 years
Sd = 15.9 years		 European — MGI —
PSS000209 Basal cell carcinoma: ICD9-173.01,173.11,173.21,173.31,173.41,173.51,173.61,173.71,173.81,173.91 —
[
  • 884 cases
  • , 19,584 controls
]
,
46.9 % Male samples
 Mean = 54.2 years
Sd = 15.9 years		 European — MGI —
PSS000211 PheCode 172 —
[
  • 13,624 cases
  • , 136,233 controls
]
,
45.9 % Male samples
 Mean = 57.7 years
Sd = 8.1 years		 European White British Subset UKB —
PSS007651 — —
[
  • 11 cases
  • , 6,486 controls
]
 — African unspecified — UKB —
PSS010980 — — 4,797 individuals — European — NR GCAT
PSS000871 Basal cell carcinoma cases were determined by a baseline survey containing 34 questions regarding personal history of skin cancer(including skin cancer type, age at diagnosis, body location, prescribed treatments and information regarding cancer recurrence) —
[
  • 16,184 cases
  • , 72,740 controls
]
,
38.9 % Male samples
 European — 23andMe —
PSS007652 — —
[
  • 6 cases
  • , 1,698 controls
]
 — East Asian — UKB —
PSS007653 — —
[
  • 1,442 cases
  • , 23,463 controls
]
 — European non-white British ancestry UKB —
PSS007654 — —
[
  • 18 cases
  • , 7,813 controls
]
 — South Asian — UKB —
PSS000568 PheCode:172.21; ICD9:173, 173.0, 173.1, 173.2, 173.3, 173.4, 173.5, 173.6, 173.7, 173.8, 173.9; ICD10:C44.0, C44.1, C44.2, C44.3, C44.4, C44.5, C44.6, C44.7, C44.8, C44.9 —
[
  • 5,450 cases
  • , 54,568 controls
]
 — European — UKB —
PSS007655 — —
[
  • 4,141 cases
  • , 63,284 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS011383 — —
[
  • 432 cases
  • , 566 controls
]
,
44.0 % Male samples
 — European — NSCS —
PSS000544 PheCode:172.21; ICD9CM:173.01, 173.11, 173.21, 173.31, 173.41, 173.51, 173.61, 173.71, 173.81, 173.91; ICD10CM:C44.01, C44.111, C44.112, C44.119, C44.211, C44.212, C44.219, C44.310, C44.311, C44.319, C44.41, C44.510, C44.511, C44.519, C44.611, C44.612, C44.619, C44.711, C44.712, C44.719, C44.81, C44.91 —
[
  • 1,481 cases
  • , 9,841 controls
]
 — European — MGI —
PSS010113 — — 18,933 individuals — European — CLSA —