Trait: larynx cancer

Trait Information
Identifier MONDO_0002352
Description A primary or metastatic malignant neoplasm involving the larynx. The majority are carcinomas. [NCIT: C7484]
Trait category
Other trait
Synonyms 14 synonyms
  • cancer of larynx
  • larynx cancer
  • malignant laryngeal neoplasm
  • malignant laryngeal tumor
  • malignant laryngeal tumour
  • malignant larynx neoplasm
  • malignant larynx tumor
  • malignant larynx tumour
  • malignant neoplasm of larynx
  • malignant neoplasm of the larynx
  • malignant tumor of larynx
  • malignant tumor of the larynx
  • malignant tumour of larynx
  • malignant tumour of the larynx

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)
PGS000360
(PRSWEB_PHECODE149.4_C32_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Laryngeal cancer larynx cancer 25,920
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000360/ScoringFiles/PGS000360.txt.gz
PGS000361
(PRSWEB_PHECODE149.4_C3-LARYNX_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Laryngeal cancer larynx cancer 87,893
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000361/ScoringFiles/PGS000361.txt.gz
PGS000362
(PRSWEB_PHECODE149.4_UKBB-SAIGE-HRC-X149.4_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Laryngeal cancer larynx cancer 53
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000362/ScoringFiles/PGS000362.txt.gz
PGS018465
(TPMI_149_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of larynx pharynx nasal cavities larynx cancer 4
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018465/ScoringFiles/PGS018465.txt.gz
PGS018466
(TPMI_149_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of larynx pharynx nasal cavities larynx cancer 939,820
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018466/ScoringFiles/PGS018466.txt.gz
PGS018467
(TPMI_149_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of larynx pharynx nasal cavities larynx cancer 15,690
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018467/ScoringFiles/PGS018467.txt.gz
PGS018468
(TPMI_149_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of larynx pharynx nasal cavities larynx cancer 983,777
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018468/ScoringFiles/PGS018468.txt.gz
PGS018469
(TPMI_149_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Cancer of larynx pharynx nasal cavities larynx cancer 1,000,712
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018469/ScoringFiles/PGS018469.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
PPM001045 PGS000360
(PRSWEB_PHECODE149.4_C32_LASSOSUM_MGI_20200608)
 PSS000536|
European Ancestry|
1,738 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of larynx OR: 1.282 [1.09, 1.508]
β: 0.249 (0.0827)		 AUROC: 0.57 [0.522, 0.618] Nagelkerke's Pseudo-R²: 0.0112
Brier score: 0.0822
Odds Ratio (OR, top 1% vs. Rest): 2.14 [0.649, 7.06]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE149.4_C32_LASSOSUM_MGI_20200608
PPM001046 PGS000361
(PRSWEB_PHECODE149.4_C3-LARYNX_LASSOSUM_MGI_20200608)
 PSS000536|
European Ancestry|
1,738 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of larynx OR: 1.195 [1.014, 1.408]
β: 0.178 (0.0836)		 AUROC: 0.55 [0.504, 0.593] Nagelkerke's Pseudo-R²: 0.00551
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 1.51 [0.382, 5.94]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE149.4_C3-LARYNX_LASSOSUM_MGI_20200608
PPM001047 PGS000362
(PRSWEB_PHECODE149.4_UKBB-SAIGE-HRC-X149.4_PT_MGI_20200608)
 PSS000536|
European Ancestry|
1,738 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of larynx OR: 1.195 [1.023, 1.396]
β: 0.178 (0.0793)		 AUROC: 0.543 [0.494, 0.59] Nagelkerke's Pseudo-R²: 0.00609
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 1.52 [0.384, 5.98]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE149.4_UKBB-SAIGE-HRC-X149.4_PT_MGI_20200608
PPM036647 PGS018465
(TPMI_149_Lassosum2)
 PSS012373|
East Asian Ancestry|
19,194 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of larynx pharynx nasal cavities — AUROC: 0.72273 R²: 0.03266 sex, age, array, PCs 1-10 —
PPM036648 PGS018466
(TPMI_149_LDpred2)
 PSS012372|
East Asian Ancestry|
19,194 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of larynx pharynx nasal cavities — AUROC: 0.72128 R²: 0.03204 sex, age, array, PCs 1-10 —
PPM036649 PGS018467
(TPMI_149_MegaPRS)
 PSS012374|
East Asian Ancestry|
19,194 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of larynx pharynx nasal cavities — AUROC: 0.7201 R²: 0.03195 sex, age, array, PCs 1-10 —
PPM036650 PGS018468
(TPMI_149_PRS-CS)
 PSS012375|
East Asian Ancestry|
19,194 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of larynx pharynx nasal cavities — AUROC: 0.71945 R²: 0.03162 sex, age, array, PCs 1-10 —
PPM036651 PGS018469
(TPMI_149_SBayesR)
 PSS012376|
East Asian Ancestry|
19,194 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Cancer of larynx pharynx nasal cavities — AUROC: 0.71838 R²: 0.03124 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
PSS000536 PheCode:149.4; ICD9CM:161.0, 161.1, 161.2, 161.3, 161.8, 161.9, 231.0, V10.21; ICD10CM:C32, C32.0, C32.1, C32.2, C32.3, C32.8, C32.9, D02.0 —
[
  • 158 cases
  • , 1,580 controls
]
 — European — MGI —
PSS012372 146, 147, 148, 149, 160, 161, 231.0, V10.02, V10.21, V10.22,C09, C10, C11, C12, C13, C14, C30.0, C30.1, C31, C32, D02.0 —
[
  • 335 cases
  • , 18,859 controls
]
,
45.45 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012373 146, 147, 148, 149, 160, 161, 231.0, V10.02, V10.21, V10.22,C09, C10, C11, C12, C13, C14, C30.0, C30.1, C31, C32, D02.0 —
[
  • 335 cases
  • , 18,859 controls
]
,
45.45 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012374 146, 147, 148, 149, 160, 161, 231.0, V10.02, V10.21, V10.22,C09, C10, C11, C12, C13, C14, C30.0, C30.1, C31, C32, D02.0 —
[
  • 335 cases
  • , 18,859 controls
]
,
45.45 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012375 146, 147, 148, 149, 160, 161, 231.0, V10.02, V10.21, V10.22,C09, C10, C11, C12, C13, C14, C30.0, C30.1, C31, C32, D02.0 —
[
  • 335 cases
  • , 18,859 controls
]
,
45.45 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012376 146, 147, 148, 149, 160, 161, 231.0, V10.02, V10.21, V10.22,C09, C10, C11, C12, C13, C14, C30.0, C30.1, C31, C32, D02.0 —
[
  • 335 cases
  • , 18,859 controls
]
,
45.45 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —