Trait: pharynx cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005577
Description A primary or metastatic malignant neoplasm that affects the pharynx. [NCIT: C7545]
Trait category
Cancer
Digestive system disorder
Synonyms 20 synonyms
  • Malignant Pharyngeal Neoplasm
  • Malignant Pharyngeal Tumor
  • Malignant Pharynx Neoplasm
  • Malignant Pharynx Tumor
  • Malignant Tumor of Pharynx
  • Malignant Tumor of the Pharynx
  • cancer of chordate pharynx
  • cancer of pharynx
  • chordate pharynx cancer
  • malignant chordate pharynx neoplasm
  • malignant neoplasm of chordate pharynx
  • malignant neoplasm of pharynx
  • malignant pharyngeal neoplasm
  • malignant pharyngeal tumor
  • malignant pharynx neoplasm
  • malignant pharynx tumor
  • malignant tumor of pharynx
  • malignant tumor of the pharynx
  • pharyngeal neoplasm
  • pharynx cancer
Mapped term(s) 6 mapped terms
  • DOID:0060119
  • MESH:D010610
  • MONDO:0005517
  • NCIT:C7545
  • NCIt:C7545
  • SNOMEDCT:363507003

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 PGS Scoring File (FTP Link)
PGS000081
(CC_Oral)
PGP000050 |
Graff RE et al. Nat Commun (2021)
Oral cavity and pharyngeal cancers pharynx cancer,
oral cavity cancer
14
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000081/ScoringFiles/PGS000081.txt.gz
PGS000792
(CC_Oral_IV)
PGP000186 |
Kachuri L et al. Nat Commun (2020)
Oral cavity and pharyngeal cancers pharynx cancer,
oral cavity cancer
14
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000792/ScoringFiles/PGS000792.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
PPM000201 PGS000081
(CC_Oral)
PSS000120|
European Ancestry|
411,577 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
Reported Trait: Oral cavity and pharyngeal cancers OR: 1.08 [1.02, 1.14] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002047 PGS000081
(CC_Oral)
PSS001020|
European Ancestry|
391,479 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.
Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.11 [1.01, 1.21] AUROC: 0.702
C-index: 0.686 (0.015)
Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM002063 PGS000792
(CC_Oral_IV)
PSS001020|
European Ancestry|
391,479 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.12 [1.02, 1.23] AUROC: 0.702
C-index: 0.687 (0.015)
: 0.356 Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS000120 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 20010, 20020, 20030, 20040, 20050, 20060, 20070, 20080, 20090, and 20100
[
  • 1,223 cases
  • , 410,354 controls
]
,
46.0 % Male samples
Mean = 58.0 years European GERA, UKB
PSS001020 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases.
[
  • 481 cases
  • , 390,998 controls
]
European UKB