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 categories
Cancer
Digestive system disorder
Synonyms 28 synonyms
  • cancer of oral cavity
  • malignant mouth neoplasm
  • malignant mouth tumor
  • malignant mouth tumour
  • malignant neoplasm of anterior portion of floor of mouth
  • malignant neoplasm of floor of mouth
  • malignant neoplasm of lateral floor of mouth
  • malignant neoplasm of lateral portion of floor of mouth
  • malignant neoplasm of mouth
  • malignant neoplasm of oral cavity
  • malignant neoplasm of the mouth
  • malignant oral cavity neoplasm
  • malignant oral cavity tumor
  • malignant oral cavity tumour
  • malignant tumor of anterior floor of mouth
  • malignant tumor of lateral floor of mouth
  • malignant tumor of mouth
  • malignant tumor of oral cavity
  • malignant tumor of the floor of the mouth
  • malignant tumor of the mouth
  • malignant tumour of anterior floor of mouth
  • malignant tumour of lateral floor of mouth
  • malignant tumour of mouth
  • malignant tumour of oral cavity
  • malignant tumour of the floor of the mouth
  • malignant tumour of the mouth
  • mouth cancer
  • oral cavity cancer
Mapped terms 28 mapped terms
  • COHD:25189
  • DOID:8618
  • EFO:0005570
  • ICD10:C04
  • ICD10:C04.0
  • ICD10:C04.1
  • ICD10:C04.9
  • ICD9:144
  • ICD9:144.0
  • ICD9:144.1
  • ICD9:144.9
  • ICD9:145.8
  • ICD9:145.9
  • ICD9:149.8
  • MEDGEN:56298
  • MONDO:0005515
  • MedDRA:10025923
  • MedDRA:10025930
  • MedDRA:10025931
  • MedDRA:10025932
  • MedDRA:10025933
  • MedDRA:10025934
  • MedDRA:10025935
  • MedDRA:10025936
  • NCIT:C9314
  • SCTID:363385007
  • SCTID:363505006
  • UMLS:C0153381

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
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)
PGS000081
(CC_Oral)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Oral cavity and pharyngeal cancers oral cavity cancer,
pharynx cancer		 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000081/ScoringFiles/PGS000081.txt.gz
PGS000357
(PRSWEB_PHECODE145_C3-LIP-ORAL-PHARYNX_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Oral cavity cancer oral cavity cancer 45
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000357/ScoringFiles/PGS000357.txt.gz
PGS000358
(PRSWEB_PHECODE145_UKBB-SAIGE-HRC-X145_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Oral cavity cancer oral cavity cancer 1,119,238
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000358/ScoringFiles/PGS000358.txt.gz
PGS000792
(CC_Oral_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Oral cavity and pharyngeal cancers oral cavity cancer,
pharynx cancer		 14
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000792/ScoringFiles/PGS000792.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
PPM000201 PGS000081
(CC_Oral)
 PSS000120|
European Ancestry|
411,577 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 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
PPM002047 PGS000081
(CC_Oral)
 PSS001020|
European Ancestry|
391,479 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.11 [1.01, 1.21] AUROC: 0.702
C-index: 0.686 (0.015)		 — Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017173 PGS000081
(CC_Oral)
 PSS010150|
European Ancestry|
415 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Oral cavity and pharyngeal cancers HR: 1.03 [0.94, 1.14] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —
PPM001042 PGS000357
(PRSWEB_PHECODE145_C3-LIP-ORAL-PHARYNX_PT_MGI_20200608)
 PSS000535|
European Ancestry|
6,328 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of mouth OR: 1.111 [1.021, 1.208]
β: 0.105 (0.0427)		 AUROC: 0.519 [0.498, 0.542] Nagelkerke's Pseudo-R²: 0.0021
Brier score: 0.0829
Odds Ratio (OR, top 1% vs. Rest): 1.26 [0.585, 2.73]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE145_C3-LIP-ORAL-PHARYNX_PT_MGI_20200608
PPM001043 PGS000358
(PRSWEB_PHECODE145_UKBB-SAIGE-HRC-X145_PRS-CS_MGI_20200608)
 PSS000535|
European Ancestry|
6,328 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of mouth OR: 1.116 [1.024, 1.216]
β: 0.11 (0.0438)		 AUROC: 0.528 [0.502, 0.552] Nagelkerke's Pseudo-R²: 0.00207
Brier score: 0.0829
Odds Ratio (OR, top 1% vs. Rest): 1.63 [0.812, 3.26]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE145_UKBB-SAIGE-HRC-X145_PRS-CS_MGI_20200608
PPM002063 PGS000792
(CC_Oral_IV)
 PSS001020|
European Ancestry|
391,479 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.12 [1.02, 1.23] AUROC: 0.702
C-index: 0.687 (0.015)		 R²: 0.356 Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
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 —
PSS001020 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 481 cases
  • , 390,998 controls
]
 — European — UKB —
PSS010150 — —
[
  • 26 cases
  • , 389 controls
]
 — European — UKB —
PSS000535 PheCode:145; ICD9CM:140.0, 140.1, 140.3, 140.4, 140.5, 140.6, 140.8, 140.9, 141.0, 141.1, 141.2, 141.3, 141.4, 141.5, 141.6, 141.8, 141.9, 142.0, 142.1, 142.2, 142.8, 142.9, 143.0, 143.1, 143.8, 143.9, 144.0, 144.1, 144.8, 144.9, 145.0, 145.1, 145.2, 145.3, 145.4, 145.5, 145.6, 145.8, 145.9, 230.0, V10.01; ICD10CM:C00, C00.0, C00.1, C00.2, C00.3, C00.4, C00.5, C00.6, C00.8, C00.9, C01, C02, C02.0, C02.1, C02.2, C02.3, C02.4, C02.8, C02.9, C03, C03.0, C03.1, C03.9, C04, C04.0, C04.1, C04.8, C04.9, C05, C05.0, C05.1, C05.2, C05.8, C05.9, C06, C06.0, C06.1, C06.2, C06.8, C06.80, C06.89, C06.9, C07, C08, C08.0, C08.1, C08.9, D00.0, D00.00, D00.01, D00.02, D00.03, D00.04, D00.05, D00.06, D00.07, D00.08 —
[
  • 578 cases
  • , 5,750 controls
]
 — European — MGI —