Trait: basal cell carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004193
Description The most frequently seen skin cancer. It arises from basal cells of the epidermis and pilosebaceous units. Clinically it is divided into the following types: nodular, ulcerative, superficial, multicentric, erythematous, and sclerosing or morphea-like. More than 95% of these carcinomas occur in patients over 40. They develop on hair-bearing skin, most commonly on sun-exposed areas. Approximately 85% are found on the head and neck and the remaining 15% on the trunk and extremities. Basal cell carcinoma usually grows in a slow and indolent fashion. However, if untreated, the tumor may invade the subcutaneous fat, skeletal muscle and bone. Distant metastases are rare. Excision, curettage and irradiation cure most basal cell carcinomas. [NCIT: P378]
Trait category
Cancer
Synonyms 15 synonyms
  • basal cell carcinoma of skin
  • BCC
  • skin basal cell carcinoma
  • malignant basal cell neoplasm
  • basal cell skin carcinoma
  • basal cell neoplasm
  • basal cell epithelioma
  • epithelioma basal cell
  • Rodent ulcer
  • Skin Basal Cell Carcinoma
  • basal cell cancer
  • basal cell carcinoma of the skin
  • carcinoma, basal cell
  • basal cell carcinoma
  • skin basal cell cancer
Mapped term(s) 18 mapped terms
  • HP:0002671
  • NCIT:C2921
  • UMLS:C0206710
  • KEGG:05217
  • SNOMEDCT:1338007
  • MSH:D002280
  • ONCOTREE:BCC
  • UMLS:C0007117
  • OMIM:614740
  • COHD:4112752
  • UMLS:C0751676
  • MONDO:0005341
  • CSP:2000-2719
  • ICDO:8090/3
  • OMIM:605462
  • DOID:2513
  • SCTID:254701007
  • NCIt:C2921

Associated Polygenic Score(s)

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

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
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

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description 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