Trait: head and neck carcinoma

Trait Information
Identifier MONDO_0002038
Description A carcinoma that arises from the head and neck region. Representative examples include oral cavity squamous cell carcinoma, laryngeal squamous cell carcinoma, and salivary gland carcinoma. [NCIT: C35850]
Trait category
Other trait
Synonyms 8 synonyms
  • carcinoma of craniocervical region
  • carcinoma of head and neck
  • carcinoma of neck
  • carcinoma of the head and neck
  • carcinoma of the neck
  • craniocervical region carcinoma
  • head and neck carcinoma
  • neck carcinoma
Child trait(s) head and neck squamous cell carcinoma

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 "head and neck carcinoma" 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)
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
PGS012586
(PRS_HNC_all)
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Head and neck squamous cell carcinoma head and neck squamous cell carcinoma 972,182
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS012586/ScoringFiles/PGS012586.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 —
PPM030758 PGS012586
(PRS_HNC_all)
 PSS012280|
Multi-ancestry (including European)|
38,401 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Head and neck squamous cell carcinoma OR: 1.17 [1.07, 1.26] — — age, sex, ethnicity, and PC 1 to 10 —
PPM030759 PGS012586
(PRS_HNC_all)
 PSS012280|
Multi-ancestry (including European)|
38,401 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oral cavity cancer OR: 1.14 [1.06, 1.23] — — age, sex, ethnicity, and PC 1 to 10 —
PPM030753 PGS012586
(PRS_HNC_all)
 PSS012281|
European Ancestry|
308,492 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Head and neck squamous cell carcinoma OR: 1.12 [1.06, 1.17] — — age, sex, genotype array, and PC 1 to 10 —
PPM030754 PGS012586
(PRS_HNC_all)
 PSS012281|
European Ancestry|
308,492 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oral cavity cancer OR: 1.1 [1.02, 1.17] — — age, sex, genotype array, and PC 1 to 10 —
PPM030755 PGS012586
(PRS_HNC_all)
 PSS012281|
European Ancestry|
308,492 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.18 [1.08, 1.28] — — age, sex, genotype array, and PC 1 to 10 —
PPM030760 PGS012586
(PRS_HNC_all)
 PSS012280|
Multi-ancestry (including European)|
38,401 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oropharynx cancer OR: 1.13 [1.05, 1.22] — — age, sex, ethnicity, 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
PSS012281 — —
[
  • 1,753 cases
  • , 306,739 controls
]
,
45.5 % Male samples
 Mean = 58.0 years
Sd = 7.9 years		 European — UKB —
PSS012280 — —
[
  • 74 cases
  • , 10,394 controls
]
 — African American or Afro-Caribbean — PMB —
PSS012280 — —
[
  • 657 cases
  • , 27,276 controls
]
 — European — PMB —
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