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
  • Carcinoma, Epidermoid
  • Carcinoma, Planocellular
  • Carcinoma, Squamous
  • Carcinoma, Squamous Cell
  • Carcinomas, Epidermoid
  • Carcinomas, Planocellular
  • Carcinomas, Squamous
  • Carcinomas, Squamous Cell
  • Epidermoid Carcinoma
  • Epidermoid Carcinomas
  • Epidermoid Cell Cancer
  • Epidermoid carcinoma, NOS
  • Malignant Epidermoid Cell Neoplasm
  • Malignant Epidermoid Cell Tumor
  • Malignant Squamous Cell Neoplasm
  • Malignant Squamous Cell Tumor
  • Planocellular Carcinoma
  • Planocellular Carcinomas
  • SCC - Squamous cell carcinoma
  • Squamous Carcinomas
  • Squamous Cell Cancer
  • Squamous Cell Carcinomas
  • Squamous cell carcinoma (disorder)
  • Squamous cell carcinoma (morphologic abnormality)
  • Squamous cell carcinoma, NOS
  • Squamous cell carcinoma, no ICD-O subtype
  • Squamous cell carcinoma, no ICD-O subtype (morphologic abnormality)
  • Squamous cell epithelioma
  • [M]Squamous cell carcinoma NOS
  • [M]Squamous cell carcinoma NOS (morphologic abnormality)
  • carcinoma, squamous cell, malignant
  • epidermoid carcinoma
  • epidermoid cell cancer
  • malignant epidermoid cell neoplasm
  • malignant epidermoid cell tumor
  • malignant squamous cell neoplasm
  • malignant squamous cell tumor
  • skin squamous cell carcinoma
  • squamous carcinoma
  • squamous cell cancer
  • squamous cell carcinoma
  • squamous cell carcinoma (morphologic abnormality)
  • squamous cell carcinoma NOS (morphologic abnormality)
  • squamous cell epithelioma
Mapped term(s) 12 mapped terms
  • DOID:1749
  • GARD:0001091
  • ICDO:8070/3
  • MESH:D002294
  • MONDO:0005096
  • MSH:D002294
  • NCIT:C2929
  • NCIt:C2929
  • SCTID:402815007
  • SNOMEDCT:28899001
  • SNOMEDCT:402815007
  • UMLS:C0007137
Child trait(s) Ovarian Squamous Cell Carcinoma

Associated Polygenic Score(s)

Note: This table shows all PGS for "squamous cell carcinoma" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000120 SCC10 PGP000055 Fritsche LG et al. PLoS Genet (2019) Squamous cell carcinoma squamous cell carcinoma 10 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000120/ScoringFiles/PGS000120.txt.gz
PGS000460 PRSWEB_PHECODE172.22_20001-1062_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 4,279,140 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000460/ScoringFiles/PGS000460.txt.gz
PGS000461 PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 13 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000461/ScoringFiles/PGS000461.txt.gz
PGS000462 PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 13 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000462/ScoringFiles/PGS000462.txt.gz
PGS000463 PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 7 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000463/ScoringFiles/PGS000463.txt.gz
PGS000464 PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 14 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000464/ScoringFiles/PGS000464.txt.gz
PGS000465 PRSWEB_PHECODE172.22_cSCC-Chahal_P_5e-08_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 10 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000465/ScoringFiles/PGS000465.txt.gz
PGS000466 PRSWEB_PHECODE172.22_cSCC-Chahal_P_5e-08_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 10 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000466/ScoringFiles/PGS000466.txt.gz
PGS000467 PRSWEB_PHECODE172.22_cSCC-Chahal_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 6 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000467/ScoringFiles/PGS000467.txt.gz
PGS000468 PRSWEB_PHECODE172.22_cSCC-Chahal_PT_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Squamous cell carcinoma squamous cell carcinoma 9 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000468/ScoringFiles/PGS000468.txt.gz
PGS000731 PRS_SCC PGP000138 Fontanillas P et al. Nat Commun (2021) Squamous cell carcinoma Ovarian Squamous Cell Carcinoma 14 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000731/ScoringFiles/PGS000731.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
PPM001671 PGS000731 (PRS_SCC) PSS000873 PGP000138 Fontanillas P et al. (2021) Reported Trait: Squamous cell carcinoma OR: 1.44 [1.41, 1.48] AUROC: 0.605 — — —
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 —
PPM001145 PGS000460 (PRSWEB_PHECODE172.22_20001-1062_LASSOSUM_MGI_20200608) PSS000545 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.096 [1.025, 1.172]
β: 0.0917 (0.0344)		 AUROC: 0.523 [0.503, 0.543] Nagelkerke's Pseudo-R²: 0.00155
Brier score: 0.0996
Odds Ratio (OR, top 1% vs. Rest): 1.56 [0.892, 2.74]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_20001-1062_LASSOSUM_MGI_20200608
PPM001148 PGS000463 (PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_MGI_20200608) PSS000545 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.448 [1.356, 1.546]
β: 0.37 (0.0335)		 AUROC: 0.593 [0.573, 0.613] Nagelkerke's Pseudo-R²: 0.0268
Brier score: 0.0977
Odds Ratio (OR, top 1% vs. Rest): 3.74 [2.46, 5.68]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_MGI_20200608
PPM001151 PGS000466 (PRSWEB_PHECODE172.22_cSCC-Chahal_P_5e-08_UKB_20200608) PSS000569 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma β: 0.283 (0.0138)
OR: 1.327 [1.292, 1.364]		 AUROC: 0.57 [0.562, 0.578] Nagelkerke's Pseudo-R²: 0.0146
Brier score: 0.082
Odds Ratio (OR, top 1% vs. Rest): 1.75 [1.4, 2.18]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_cSCC-Chahal_P_5e-08_UKB_20200608
PPM001146 PGS000461 (PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_MGI_20200608) PSS000545 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.491 [1.395, 1.593]
β: 0.4 (0.0338)		 AUROC: 0.599 [0.579, 0.618] Nagelkerke's Pseudo-R²: 0.0304
Brier score: 0.0974
Odds Ratio (OR, top 1% vs. Rest): 3.51 [2.29, 5.39]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_MGI_20200608
PPM001147 PGS000462 (PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_UKB_20200608) PSS000569 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.324 [1.288, 1.361]
β: 0.28 (0.014)		 AUROC: 0.573 [0.564, 0.58] Nagelkerke's Pseudo-R²: 0.0141
Brier score: 0.082
Odds Ratio (OR, top 1% vs. Rest): 2.13 [1.74, 2.61]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_UKB_20200608
PPM001149 PGS000464 (PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_UKB_20200608) PSS000569 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.332 [1.296, 1.369]
β: 0.287 (0.014)		 AUROC: 0.575 [0.567, 0.582] Nagelkerke's Pseudo-R²: 0.0147
Brier score: 0.082
Odds Ratio (OR, top 1% vs. Rest): 2.19 [1.79, 2.67]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_UKB_20200608
PPM001150 PGS000465 (PRSWEB_PHECODE172.22_cSCC-Chahal_P_5e-08_MGI_20200608) PSS000545 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.457 [1.365, 1.554]
β: 0.376 (0.033)		 AUROC: 0.589 [0.57, 0.61] Nagelkerke's Pseudo-R²: 0.0282
Brier score: 0.0976
Odds Ratio (OR, top 1% vs. Rest): 4.54 [3.07, 6.71]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_cSCC-Chahal_P_5e-08_MGI_20200608
PPM001152 PGS000467 (PRSWEB_PHECODE172.22_cSCC-Chahal_PT_MGI_20200608) PSS000545 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.43 [1.341, 1.525]
β: 0.358 (0.0328)		 AUROC: 0.583 [0.564, 0.603] Nagelkerke's Pseudo-R²: 0.0261
Brier score: 0.0978
Odds Ratio (OR, top 1% vs. Rest): 3.75 [2.49, 5.64]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_cSCC-Chahal_PT_MGI_20200608
PPM001153 PGS000468 (PRSWEB_PHECODE172.22_cSCC-Chahal_PT_UKB_20200608) PSS000569 PGP000118 Fritsche LG et al. (2020) Reported Trait: Squamous cell carcinoma OR: 1.334 [1.299, 1.371]
β: 0.288 (0.0138)		 AUROC: 0.571 [0.563, 0.579] Nagelkerke's Pseudo-R²: 0.0151
Brier score: 0.0819
Odds Ratio (OR, top 1% vs. Rest): 1.93 [1.56, 2.39]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE172.22_cSCC-Chahal_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 —
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 —
PSS000873 Squamous 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) —
[
  • 7,914 cases
  • , 81,010 controls
]
,
38.9 % Male samples
 European — 23andMe —
PSS000569 PheCode:172.22; 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 —
PSS000545 PheCode:172.22; ICD9CM:173.02, 173.12, 173.22, 173.32, 173.42, 173.52, 173.62, 173.72, 173.82, 173.92; ICD10CM:C44.02, C44.121, C44.122, C44.129, C44.221, C44.222, C44.229, C44.320, C44.321, C44.329, C44.42, C44.520, C44.521, C44.529, C44.621, C44.622, C44.629, C44.721, C44.722, C44.729, C44.82, C44.92 —
[
  • 982 cases
  • , 7,491 controls
]
 — European — MGI —