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
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Synonyms |
44 synonyms
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Mapped term(s) |
12 mapped terms
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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 | squamous cell carcinoma | 14 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000731/ScoringFiles/PGS000731.txt.gz |
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. Nat Commun (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. PLoS Genet (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. PLoS Genet (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. PLoS Genet (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. Am J Hum Genet (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. Am J Hum Genet (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. Am J Hum Genet (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. Am J Hum Genet (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. Am J Hum Genet (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. Am J Hum Genet (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. Am J Hum Genet (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. Am J Hum Genet (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. Am J Hum Genet (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 |
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 | — | [ ,
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 | — | [ ,
46.9 % Male samples |
Mean = 54.2 years Sd = 15.9 years |
European | — | MGI | — |
PSS000211 | PheCode 172 | — | [ ,
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) | — | [ ,
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 | — | [
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— | 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 | — | [
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— | European | — | MGI | — |