Trait: squamous cell carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000707
Description A carcinoma arising from squamous epithelial cells. Morphologically, it is characterized by the proliferation of atypical, often pleomorphic squamous cells. Squamous cell carcinomas are graded by the degree of cellular differentiation as well, moderately, or poorly differentiated. Well differentiated carcinomas are usually associated with keratin production and the presence of intercellular bridges between adjacent cells. Representative examples are lung squamous cell carcinoma, skin squamous cell carcinoma, and cervical squamous cell carcinoma. [NCIT: C2929]
Trait category
Cancer
Synonyms 44 synonyms
  • Malignant Squamous Cell Neoplasm
  • squamous cell epithelioma
  • Planocellular Carcinoma
  • Carcinoma, Planocellular
  • malignant epidermoid cell neoplasm
  • malignant squamous cell neoplasm
  • [M]Squamous cell carcinoma NOS
  • Squamous cell carcinoma, no ICD-O subtype (morphologic abnormality)
  • Carcinomas, Squamous
  • squamous cell carcinoma (morphologic abnormality)
  • Malignant Squamous Cell Tumor
  • Squamous cell carcinoma, NOS
  • Squamous Cell Cancer
  • Malignant Epidermoid Cell Neoplasm
  • malignant squamous cell tumor
  • Carcinomas, Planocellular
  • malignant epidermoid cell tumor
  • Carcinoma, Epidermoid
  • Planocellular Carcinomas
  • squamous cell cancer
  • Epidermoid carcinoma, NOS
  • Epidermoid Cell Cancer
  • Epidermoid Carcinomas
  • Squamous cell epithelioma
  • squamous cell carcinoma NOS (morphologic abnormality)
  • Squamous cell carcinoma (morphologic abnormality)
  • Carcinomas, Epidermoid
  • epidermoid carcinoma
  • Carcinoma, Squamous Cell
  • Squamous Carcinomas
  • Squamous cell carcinoma, no ICD-O subtype
  • Malignant Epidermoid Cell Tumor
  • skin squamous cell carcinoma
  • SCC - Squamous cell carcinoma
  • Squamous cell carcinoma (disorder)
  • Squamous Cell Carcinomas
  • [M]Squamous cell carcinoma NOS (morphologic abnormality)
  • Epidermoid Carcinoma
  • carcinoma, squamous cell, malignant
  • squamous carcinoma
  • epidermoid cell cancer
  • Carcinomas, Squamous Cell
  • Carcinoma, Squamous
  • squamous cell carcinoma
Mapped term(s) 12 mapped terms
  • MESH:D002294
  • UMLS:C0007137
  • SNOMEDCT:402815007
  • GARD:0001091
  • NCIt:C2929
  • SNOMEDCT:28899001
  • ICDO:8070/3
  • MONDO:0005096
  • DOID:1749
  • NCIT:C2929
  • MSH:D002294
  • SCTID:402815007

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Number of Variants PGS Scoring File (FTP Link)
PGS000120 SCC10 PGP000055
Fritsche LG et al. PLoS Genet (2019) 		Squamous cell carcinoma 10 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000120/ScoringFiles/PGS000120.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
PPM000346 PGS000120 (SCC10) PSS000211 PGP000055
Fritsche LG et al. (2019) 		Reported Trait: Skin cancer OR: 1.3[1.3, 1.34] — — age, sex, genotyping array, first 4 genotype PCs —
PPM000343 PGS000120 (SCC10) PSS000207 PGP000055
Fritsche LG et al. (2019) 		Reported Trait: Skin cancer OR: 1.34[1.3, 1.38] AUROC: 0.58[0.57, 0.6] — age, sex, batch, PC1-4 —
PPM000340 PGS000120 (SCC10) PSS000208 PGP000055
Fritsche LG et al. (2019) 		Reported Trait: Squamous cell carcinoma OR: 1.4[1.31, 1.5] AUROC: 0.59[0.56, 0.61] — 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 —
PSS000208 Squamous cell carcinoma: ICD9-173.02,173.12,173.22,173.32,173.42,173.52,173.62,173.72,173.82,173.92 —
[
  • 563 cases
  • , 19,905 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 —