Trait: oral cavity cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005570
Description A primary or metastatic malignant neoplasm involving the oral cavity. The majority are squamous cell carcinomas. [NCIT: C9314]
Trait category
Cancer
Digestive system disorder
Synonyms 17 synonyms
  • malignant neoplasm of oral cavity
  • malignant tumor of anterior floor of mouth
  • malignant neoplasm of mouth
  • malignant tumor of oral cavity
  • malignant oral cavity tumor
  • malignant tumor of lateral floor of mouth
  • malignant neoplasm of floor of mouth
  • malignant tumor of the Floor of the Mouth
  • malignant tumor of the mouth
  • malignant mouth tumor
  • oral cavity cancer
  • Malignant Oral Cavity Neoplasm
  • malignant tumor of mouth
  • malignant oral cavity neoplasm
  • malignant neoplasm of the mouth
  • malignant mouth neoplasm
  • cancer of oral cavity
Mapped term(s) 17 mapped terms
  • ICD9:145.8
  • ICD9:144.9
  • ICD10:C04.9
  • ICD10:C04
  • ICD9:145.9
  • ICD9:149.8
  • NCIT:C9314
  • MONDO:0005515
  • NCIt:C9314
  • SCTID:363505006
  • COHD:25189
  • ICD10:C04.1
  • ICD9:144.1
  • ICD10:C04.0
  • ICD9:144
  • ICD9:144.0
  • DOID:8618

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000081 CC_Oral PGP000050 Graff RE et al. bioRxiv (2020) Pre Oral cavity and pharyngeal cancers carcinoma of pharynx
oral cavity cancer
14 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000081/ScoringFiles/PGS000081.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
PPM000201 PGS000081 (CC_Oral) PSS000120 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Oral cavity and pharyngeal cancers OR: 1.08[1.02, 1.14] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

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
PSS000120 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 20010, 20020, 20030, 20040, 20050, 20060, 20070, 20080, 20090, and 20100
[
  • 1,223 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB