Trait: basal cell carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004193
Description A carcinoma involving the basal cells. [NCIT: C156767]
Trait category
Cancer
Synonyms 6 synonyms
  • Skin Basal Cell Carcinoma
  • basal cell cancer
  • basal cell carcinoma
  • carcinoma, basal cell
  • epithelioma, basal cell
  • malignant basal cell neoplasm
Mapped term(s) 9 mapped terms
  • DOID:2513
  • MESH:D002280
  • MSH:D002280
  • NCIT:C156767
  • NCIT:C7586
  • NCIt:C2921
  • OMIM:605462
  • OMIM:614740
  • SNOMEDCT:1338007

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000119 BCC32 PGP000055 Fritsche LG et al. PLoS Genet (2019) Basal cell carcinoma basal cell carcinoma 32 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://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 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000730/ScoringFiles/PGS000730.txt.gz - Check Terms/Licenses

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001670 PGS000730
(PRS_BCC)
PSS000871 PGP000138 Fontanillas P et al. (2021) Reported Trait: Basal cell carcinoma OR: 1.57 [1.55, 1.6] AUROC: 0.624
PPM000347 PGS000119
(BCC32)
PSS000211 PGP000055 Fritsche LG et al. (2019) Reported Trait: Skin cancer OR: 1.4 [1.42, 1.48] age, sex, genotyping array, first 4 genotype PCs
PPM000344 PGS000119
(BCC32)
PSS000207 PGP000055 Fritsche LG et al. (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 PGP000055 Fritsche LG et al. (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
PPM001130 PGS000445
(PRSWEB_PHECODE172.21_20001-1061_P_5e-08_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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
PPM001132 PGS000447
(PRSWEB_PHECODE172.21_20001-1061_PT_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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
PPM001135 PGS000450
(PRSWEB_PHECODE172.21_20001-1073_PT_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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
PPM001138 PGS000453
(PRSWEB_PHECODE172.21_BCC-Chahal_P_5e-08_UKB_20200608)
PSS000568 PGP000118 Fritsche LG et al. (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
PPM001142 PGS000457
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_P_5e-08_UKB_20200608)
PSS000568 PGP000118 Fritsche LG et al. (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
PPM001131 PGS000446
(PRSWEB_PHECODE172.21_20001-1061_PRS-CS_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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
PPM001133 PGS000448
(PRSWEB_PHECODE172.21_20001-1061_LASSOSUM_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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 PGP000118 Fritsche LG et al. (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
PPM001136 PGS000451
(PRSWEB_PHECODE172.21_20001-1073_LASSOSUM_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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 PGP000118 Fritsche LG et al. (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
PPM001139 PGS000454
(PRSWEB_PHECODE172.21_BCC-Chahal_PT_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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 PGP000118 Fritsche LG et al. (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 PGP000118 Fritsche LG et al. (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
PPM001143 PGS000458
(PRSWEB_PHECODE172.21_GWAS-Catalog-r2019-05-03-X172.21_PT_MGI_20200608)
PSS000544 PGP000118 Fritsche LG et al. (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 PGP000118 Fritsche LG et al. (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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
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
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
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