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]Show more
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
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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 cancersoral cavity cancer,
pharynx cancer
14
G
-
E
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 canceroral cavity cancer45
G
D
E
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 canceroral cavity cancer1,119,238
G
D
E
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 cancersoral cavity cancer,
pharynx cancer
14
G
-
E
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000792/ScoringFiles/PGS000792.txt.gz
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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.

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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
PPM000201PGS000081
(CC_Oral)
PSS000120|
European Ancestry|
411,577 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
Reported Trait: Oral cavity and pharyngeal cancersOR: 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
PPM001042PGS000357
(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 mouthOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE145_C3-LIP-ORAL-PHARYNX_PT_MGI_20200608
PPM001043PGS000358
(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 mouthOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE145_UKBB-SAIGE-HRC-X145_PRS-CS_MGI_20200608
PPM002047PGS000081
(CC_Oral)
PSS001020|
European Ancestry|
391,479 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.
Reported Trait: Incident oral cavity and pharyngeal cancerHR: 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, year... s of smoking, smoing status (never vs. former vs. current)Show moreC-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002063PGS000792
(CC_Oral_IV)
PSS001020|
European Ancestry|
391,479 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
Reported Trait: Incident oral cavity and pharyngeal cancerHR: 1.12 [1.02, 1.23]AUROC: 0.702
C-index: 0.687 (0.015)
: 0.356Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, year... s of smoking, smoing status (never vs. former vs. current)Show moreC-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017173PGS000081
(CC_Oral)
PSS010150|
European Ancestry|
415 individuals
PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.
Reported Trait: Oral cavity and pharyngeal cancersHR: 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 covariatesShow more
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Evaluated Samples

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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
PSS000120Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 code... s 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 20100Show more
[
  • 1,223 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 yearsEuropeanGERA, UKB
PSS000535PheCode: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, D00.08Show more
[
  • 578 cases
  • , 5,750 controls
]
EuropeanMGI
PSS001020Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant pri... mary cancer were defined as cases.Show more
[
  • 481 cases
  • , 390,998 controls
]
EuropeanUKB
PSS010150
[
  • 26 cases
  • , 389 controls
]
EuropeanUKB
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