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 16 synonyms
  • SCC
  • carcinoma, squamous cell, malignant
  • epidermoid carcinoma
  • epidermoid cell cancer
  • malignant epidermoid cell neoplasm
  • malignant epidermoid cell tumor
  • malignant epidermoid cell tumour
  • malignant squamous cell neoplasm
  • malignant squamous cell tumor
  • malignant squamous cell tumour
  • squamous carcinoma
  • squamous cell cancer
  • squamous cell carcinoma
  • squamous cell carcinoma (morphologic abnormality)
  • squamous cell carcinoma NOS (morphologic abnormality)
  • squamous cell epithelioma
Mapped terms 10 mapped terms
  • DOID:1749
  • EFO:0000707
  • GARD:0001091
  • ICDO:8070/3
  • MEDGEN:2874
  • MESH:D002294
  • MONDO:0005096
  • NCIT:C2929
  • SCTID:402815007
  • UMLS:C0007137
Child trait(s) 2 child traits

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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 ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000120
(SCC10)
 PGP000055 |
Fritsche LG et al. PLoS Genet (2019)
 Squamous cell carcinoma squamous cell carcinoma 10
https://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
https://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
https://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
https://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
https://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
https://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
https://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
https://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
https://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
https://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
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000731/ScoringFiles/PGS000731.txt.gz - Check Terms/Licenses
PGS003390
(best_HNSC)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Head and neck squamous cell carcinoma head and neck squamous cell carcinoma 931,477
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003390/ScoringFiles/PGS003390.txt.gz
PGS003392
(best_LUSC)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Lung squamous cell carcinoma squamous cell lung carcinoma 90
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003392/ScoringFiles/PGS003392.txt.gz

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) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000343 PGS000120
(SCC10)
 PSS000207|
European Ancestry|
20,468 individuals
 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|
European Ancestry|
20,468 individuals
 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 —
PPM000346 PGS000120
(SCC10)
 PSS000211|
European Ancestry|
149,857 individuals
 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 —
PPM001145 PGS000460
(PRSWEB_PHECODE172.22_20001-1062_LASSOSUM_MGI_20200608)
 PSS000545|
European Ancestry|
8,473 individuals
 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
PPM001146 PGS000461
(PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_P_5e-08_MGI_20200608)
 PSS000545|
European Ancestry|
8,473 individuals
 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|
European Ancestry|
60,018 individuals
 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
PPM001148 PGS000463
(PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_MGI_20200608)
 PSS000545|
European Ancestry|
8,473 individuals
 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
PPM001149 PGS000464
(PRSWEB_PHECODE172.22_GWAS-Catalog-r2019-05-03-X172.22_PT_UKB_20200608)
 PSS000569|
European Ancestry|
60,018 individuals
 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|
European Ancestry|
8,473 individuals
 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
PPM001151 PGS000466
(PRSWEB_PHECODE172.22_cSCC-Chahal_P_5e-08_UKB_20200608)
 PSS000569|
European Ancestry|
60,018 individuals
 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
PPM001152 PGS000467
(PRSWEB_PHECODE172.22_cSCC-Chahal_PT_MGI_20200608)
 PSS000545|
European Ancestry|
8,473 individuals
 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|
European Ancestry|
60,018 individuals
 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
PPM001671 PGS000731
(PRS_SCC)
 PSS000873|
European Ancestry|
88,924 individuals
 PGP000138 |
Fontanillas P et al. Nat Commun (2021)
 Reported Trait: Squamous cell carcinoma OR: 1.44 [1.41, 1.48] AUROC: 0.605 — — —
PPM016265 PGS003390
(best_HNSC)
 PSS010079|
European Ancestry|
270,233 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: head and neck squamous cell carcinoma — AUROC: 0.672 R²: 0.00561 age, sex, top 20 genetic principal components —
PPM016267 PGS003392
(best_LUSC)
 PSS010082|
European Ancestry|
270,054 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: lung squamous cell carcinoma — AUROC: 0.778 R²: 0.00075 age, sex, top 20 genetic principal components —

Evaluated Samples

PGS Sample Set ID
(PSS) 		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 —
PSS010079 C01-06, C09, C10, C13, C14 —
[
  • 689 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer
PSS010082 C34, histology was one of the followings: Adenocarcinoma, intestinal type; Adenocarcinoma in tubulovillous adenoma; Adenocarcinoma in villous adenoma; Adenocarcinoma (NOS) —
[
  • 510 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer
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 —