Trait: tongue neoplasm

Trait Information
Identifier MONDO_0021240
Description A neoplasm (disease) that involves the tongue. [MONDO: patterns/location]
Trait category
Other trait
Synonyms 9 synonyms
  • neoplasm of the tongue
  • neoplasm of tongue
  • tongue neoplasm (disease)
  • tongue tumor
  • tongue tumour
  • tumor of the tongue
  • tumor of tongue
  • tumour of the tongue
  • tumour of tongue
Child trait(s) tongue cancer

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
Note: This table shows all PGS for "tongue neoplasm" and any child terms of this trait in the EFO hierarchy by default.
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
PGS018460
(TPMI_145.2_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 11
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018460/ScoringFiles/PGS018460.txt.gz
PGS018461
(TPMI_145.2_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 34,059
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018461/ScoringFiles/PGS018461.txt.gz
PGS018462
(TPMI_145.2_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 570,182
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018462/ScoringFiles/PGS018462.txt.gz
PGS018463
(TPMI_145.2_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 983,776
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018463/ScoringFiles/PGS018463.txt.gz
PGS018464
(TPMI_145.2_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Tongue cancer tongue cancer 1,003,968
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018464/ScoringFiles/PGS018464.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
PPM036642 PGS018460
(TPMI_145.2_Lassosum2)
 PSS012358|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68616 R²: 0.01171 sex, age, array, PCs 1-10 —
PPM036643 PGS018461
(TPMI_145.2_LDpred2)
 PSS012357|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68599 R²: 0.01168 sex, age, array, PCs 1-10 —
PPM036644 PGS018462
(TPMI_145.2_MegaPRS)
 PSS012359|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68604 R²: 0.0117 sex, age, array, PCs 1-10 —
PPM036645 PGS018463
(TPMI_145.2_PRS-CS)
 PSS012360|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68622 R²: 0.0117 sex, age, array, PCs 1-10 —
PPM036646 PGS018464
(TPMI_145.2_SBayesR)
 PSS012361|
East Asian Ancestry|
19,060 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of tongue — AUROC: 0.68563 R²: 0.01173 sex, age, array, PCs 1-10 —

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
PSS012357 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012358 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012359 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012360 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
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 —
PSS012361 141, V10.01,C01, C02, Z85.810 —
[
  • 201 cases
  • , 18,859 controls
]
,
45.19 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —