Trait: oropharynx cancer

Trait Information
Identifier MONDO_0004608
Description A primary or metastatic malignant neoplasm that affects the oropharynx. [NCIT: C7398]
Trait category
Other trait
Synonyms 22 synonyms
  • cancer of oropharynx
  • malignant neoplasm of junctional region of oropharynx
  • malignant neoplasm of lateral wall of oropharynx
  • malignant neoplasm of oropharynx
  • malignant neoplasm of posterior wall of oropharynx
  • malignant neoplasm of the oropharynx
  • malignant oropharyngeal neoplasm
  • malignant oropharyngeal tumor
  • malignant oropharyngeal tumour
  • malignant oropharynx neoplasm
  • malignant tumor of mesopharynx
  • malignant tumor of oropharynx
  • malignant tumor of posterior wall of oropharynx
  • malignant tumor of the oropharynx
  • malignant tumour of mesopharynx
  • malignant tumour of oropharynx
  • malignant tumour of posterior wall of oropharynx
  • malignant tumour of the oropharynx
  • oropharyngeal cancer
  • oropharyngeal carcinoma
  • oropharynx cancer
  • primary malignant neoplasm of lateral wall of oropharynx

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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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)
PGS012588
(PRS_HNC_OPC)
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Oropharynx cancer oropharynx cancer 972,182
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS012588/ScoringFiles/PGS012588.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
PPM030761 PGS012588
(PRS_HNC_OPC)
 PSS012283|
Multi-ancestry (including European)|
37,901 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.24 [1.08, 1.42] — — age, sex, ethnicity, and PC 1 to 10 —
PPM030757 PGS012588
(PRS_HNC_OPC)
 PSS012284|
European Ancestry|
307,295 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.09 [1.02, 1.17] — — age, sex, genotype array, and PC 1 to 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
PSS012283 — —
[
  • 231 cases
  • , 37,670 controls
]
 — European, African American or Afro-Caribbean — PMB —
PSS012284 — —
[
  • 556 cases
  • , 306,739 controls
]
 — European — UKB —