Trait: laryngeal neoplasm

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003817
Description A benign or malignant neoplasm involving the larynx. [NCIT: C3156]
Trait category
Cancer
Synonyms 33 synonyms
  • Cancer of Larynx
  • Cancer of the Larynx
  • Cancer, Laryngeal
  • Cancer, Larynx
  • Cancers, Laryngeal
  • Cancers, Larynx
  • LARYNGEAL NEOPL
  • LARYNX NEOPL
  • Laryngeal Cancer
  • Laryngeal Cancers
  • Laryngeal Neoplasms
  • Larynx Cancer
  • Larynx Cancers
  • Larynx Neoplasm
  • Larynx Neoplasms
  • NEOPL LARYNGEAL
  • Neoplasm, Laryngeal
  • Neoplasm, Larynx
  • Neoplasms, Laryngeal
  • Neoplasms, Larynx
  • laryngeal neoplasm
  • laryngeal tumor
  • laryngeal tumour
  • larynx neoplasm
  • larynx neoplasm (disease)
  • larynx tumor
  • larynx tumour
  • neoplasm of larynx
  • neoplasm of the larynx
  • tumor of larynx
  • tumor of the larynx
  • tumour of larynx
  • tumour of the larynx
Mapped terms 10 mapped terms
  • DOID:2596
  • MESH:D007822
  • MONDO:0021071
  • MeSH:D007822
  • MedDRA:10023841
  • MedDRA:10028995
  • NCIT:C3156
  • NCIt:C3156
  • SCTID:126692004
  • UMLS:C0023055
Child trait(s) Malignant Laryngeal Neoplasm

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 PGS for child terms of "laryngeal neoplasm" in the EFO hierarchy.
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 Malignant Laryngeal Neoplasm 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 Malignant Laryngeal Neoplasm 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 Malignant Laryngeal Neoplasm 53
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000362/ScoringFiles/PGS000362.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

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 —