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
Cancer
Synonyms 10 synonyms
  • cancer of larynx
  • larynx cancer
  • malignant laryngeal neoplasm
  • malignant laryngeal tumor
  • malignant larynx neoplasm
  • malignant larynx tumor
  • malignant neoplasm of larynx
  • malignant neoplasm of the larynx
  • malignant tumor of larynx
  • malignant tumor of the larynx
Mapped term(s) 10 mapped terms
  • DOID:2596
  • EFO:1000354
  • ICD10:C32
  • ICD10:C32.9
  • ICD9:161
  • ICD9:161.8
  • ICD9:161.9
  • NCIT:C7484
  • SCTID:363429002
  • UMLS:C0007107

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)
PGS000360 PRSWEB_PHECODE149.4_C32_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Cancer of larynx larynx cancer 25,920 http://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) Cancer of larynx larynx cancer 87,893 http://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) Cancer of larynx larynx cancer 53 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000362/ScoringFiles/PGS000362.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
PPM001047 PGS000362 (PRSWEB_PHECODE149.4_UKBB-SAIGE-HRC-X149.4_PT_MGI_20200608) PSS000536 PGP000118
Fritsche LG et al. (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
PPM001046 PGS000361 (PRSWEB_PHECODE149.4_C3-LARYNX_LASSOSUM_MGI_20200608) PSS000536 PGP000118
Fritsche LG et al. (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
PPM001045 PGS000360 (PRSWEB_PHECODE149.4_C32_LASSOSUM_MGI_20200608) PSS000536 PGP000118
Fritsche LG et al. (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

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
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