Trait: head and neck squamous cell carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000181
Description A squamous cell carcinoma that arises from any of the following anatomic sites: lip and oral cavity, nasal cavity, paranasal sinuses, pharynx, larynx, and salivary glands. [NCIT: C34447]
Trait category
Cancer
Synonyms 10 synonyms
  • HNSCC
  • SCCHN
  • carcinoma of the head and neck
  • craniocervical region squamous cell carcinoma
  • head and neck squamous cell carcinoma
  • squamous cell carcinoma of head and neck
  • squamous cell carcinoma of the head and neck
  • squamous cell carcinoma, head and neck
  • squamous cell carcinoma, head and neck, somatic
  • squamous cell carcinomas of head and neck
Mapped terms 14 mapped terms
  • DOID:5520
  • EFO:0000181
  • GARD:8503
  • MEDGEN:257911
  • MESH:C535575
  • MESH:D000077195
  • MONDO:0010150
  • MedDRA:10060121
  • NCIT:C34447
  • OMIM:275355
  • ONCOTREE:HNSC
  • Orphanet:67037
  • SCTID:716659002
  • UMLS:C1168401

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
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Multi-ancestry (excluding European)
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Additional Asian Ancestries
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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)
PGS003390
(best_HNSC)
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Head and neck squamous cell carcinoma head and neck squamous cell carcinoma 931,477
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003390/ScoringFiles/PGS003390.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
PPM016265 PGS003390
(best_HNSC)
 PSS010079|
European Ancestry|
270,233 individuals
 PGP000413 |
Namba S et al. Cancer Res (2022)
 Reported Trait: head and neck squamous cell carcinoma — AUROC: 0.672 R²: 0.00561 age, sex, top 20 genetic principal components —

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
PSS010079 C01-06, C09, C10, C13, C14 —
[
  • 689 cases
  • , 269,544 controls
]
 — European
(British)		 — UKB Controls were samples without any cancer diagnosis or self-reported cancer