Trait: tongue neoplasm

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003871
Description A neoplasm (disease) that involves the tongue. [MONDO: patterns/location]
Trait categories
Cancer
Digestive system disorder
Synonyms 31 synonyms
  • Cancer of Tongue
  • Cancer of the Tongue
  • Cancer, Oral
  • Cancer, Tongue
  • Cancers, Oral
  • Cancers, Tongue
  • NEOPL ORAL
  • NEOPL TONGUE
  • Neoplasm, Oral
  • Neoplasm, Tongue
  • Neoplasms, Oral
  • Neoplasms, Tongue
  • ORAL NEOPL
  • Oral Cancer
  • Oral Cancers
  • Oral Neoplasm
  • Oral Neoplasms
  • TONGUE NEOPL
  • Tongue Cancer
  • Tongue Cancers
  • Tongue Neoplasms
  • neoplasm of the tongue
  • neoplasm of tongue
  • tongue neoplasm
  • tongue neoplasm (disease)
  • tongue tumor
  • tongue tumour
  • tumor of the tongue
  • tumor of tongue
  • tumour of the tongue
  • tumour of tongue
Mapped terms 11 mapped terms
  • DOID:8649
  • ICD10:C02
  • MEDGEN:52778
  • MONDO:0021240
  • MeSH:D014062
  • MedDRA:10061325
  • MedDRA:10062129
  • NCIT:C3416
  • NCIt:C3416
  • SCTID:126778001
  • UMLS:C0040411

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)
PGS000359
(PRSWEB_PHECODE145.2_C3-TONGUENAS_PRS-CS_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Tongue cancer tongue neoplasm 931,954
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000359/ScoringFiles/PGS000359.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
PPM001044 PGS000359
(PRSWEB_PHECODE145.2_C3-TONGUENAS_PRS-CS_MGI_20200608)
 PSS000534|
European Ancestry|
2,841 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of tongue OR: 1.142 [1.006, 1.297]
β: 0.133 (0.0647)		 AUROC: 0.538 [0.501, 0.575] Nagelkerke's Pseudo-R²: 0.00325
Brier score: 0.0827
Odds Ratio (OR, top 1% vs. Rest): 1.69 [0.61, 4.71]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE145.2_C3-TONGUENAS_PRS-CS_MGI_20200608

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
PSS000534 PheCode:145.2; ICD9CM:141.0, 141.1, 141.2, 141.3, 141.4, 141.5, 141.6, 141.8, 141.9, V10.01; ICD10CM:C01, C02, C02.0, C02.1, C02.2, C02.3, C02.4, C02.8, C02.9 —
[
  • 259 cases
  • , 2,582 controls
]
 — European — MGI —