Trait: tongue neoplasm

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003871
Description A neoplasm (disease) that involves the tongue. [MONDO: patterns/location]
Trait category
Cancer
Digestive system disorder
Synonyms 28 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
  • tumor of the tongue
  • tumor of tongue
Mapped term(s) 7 mapped terms
  • DOID:8649
  • ICD10:C02
  • MONDO:0021240
  • MSH:D014062
  • NCIT:C3416
  • NCIt:C3416
  • SCTID:126778001

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)
PGS000359 PRSWEB_PHECODE145.2_C3-TONGUENAS_PRS-CS_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of tongue tongue neoplasm 931,954 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000359/ScoringFiles/PGS000359.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
PPM001044 PGS000359 (PRSWEB_PHECODE145.2_C3-TONGUENAS_PRS-CS_MGI_20200608) PSS000534 PGP000118
Fritsche LG et al. (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 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
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 —