Polygenic Score (PGS) ID: PGS012586

Predicted Trait
Reported Trait Head and neck squamous cell carcinoma
Mapped Trait(s) head and neck squamous cell carcinoma (MONDO_0010150)
Released in PGS Catalog: June 17, 2026
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRS_HNC_all
Development Method
Name PRS-CS
Parameters NR
Variants
Original Genome Build NR
Number of Variants 972,182
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000822
Citation (link to publication) Lee YC et al. BMC Med (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
9,986 individuals (100%)
PGS Evaluation
European: 50%
Multi-ancestry (including European): 50%
  • European
  • African
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 27749845
[
  • 5,974 cases
  • , 4,012 controls
]
 European EPIC, HN5000, INHANCE

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) 		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
PPM030758 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 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 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 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 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 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 — —
[
  • 657 cases
  • , 27,276 controls
]
 — European — PMB —
PSS012280 — —
[
  • 74 cases
  • , 10,394 controls
]
 — African American or Afro-Caribbean — PMB —