Trait: squamous cell lung carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000708
Description A carcinoma arising from squamous bronchial epithelial cells. It may be keratinizing or non-keratinizing. Keratinizing squamous cell carcinoma is characterized by the presence of keratinization, pearl formation, and/or intercellular bridges. Non-keratinizing squamous cell carcinoma is characterized by the absence of keratinization, pearl formation, and intercellular bridges. Cigarette smoking and arsenic exposure are strongly associated with squamous cell lung carcinoma. [NCIT: C3493]
Trait category
Cancer
Synonyms 8 synonyms
  • epidermoid cell carcinoma of lung
  • epidermoid cell carcinoma of the lung
  • epidermoid cell lung carcinoma
  • lung squamous cell carcinoma
  • squamous cell carcinoma of lung
  • squamous cell carcinoma of the lung
  • squamous cell lung cancer
  • squamous cell lung carcinoma
Mapped terms 9 mapped terms
  • DOID:3907
  • EFO:0000708
  • ICD9:162.9
  • MEDGEN:56202
  • MONDO:0005097
  • NCIT:C3493
  • ONCOTREE:LUSC
  • SCTID:254634000
  • UMLS:C0149782

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Additional Diverse Ancestries
Not Reported
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)
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
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
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