Trait: head and neck squamous cell carcinoma

Trait Information
Identifier MONDO_0010150
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
Other trait
Synonyms 9 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

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
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