PGS Publication: PGP000822

Publication Information (EuropePMC)
Title Polygenic risk score-based phenome-wide association study of head and neck cancer across two large biobanks.
PubMed ID 38486201(Europe PMC)
doi 10.1186/s12916-024-03305-2
Publication Date March 14, 2024
Journal BMC Med
Author(s) Lee YC, Jung SH, Shivakumar M, Cha S, Park WY, Won HH, Eun YG, Biobank PM, Kim D.
Released in PGS Catalog: June 17, 2026

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

PGS Developed By This Publication

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)
PGS012587
(PRS_HNC_OC)
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Oral cavity cancer oral cavity cancer 972,182
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS012587/ScoringFiles/PGS012587.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
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
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 —
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 —
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 —
PPM030756 PGS012587
(PRS_HNC_OC)
 PSS012282|
European Ancestry|
307,595 individuals
 PGP000822 |
Lee YC et al. BMC Med (2024)
 Reported Trait: Oral cavity cancer OR: 1.2 [1.1, 1.31] — — age, sex, genotype array, 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 —
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
PSS012280 — —
[
  • 657 cases
  • , 27,276 controls
]
 — European — PMB —
PSS012280 — —
[
  • 74 cases
  • , 10,394 controls
]
 — African American or Afro-Caribbean — PMB —
PSS012281 — —
[
  • 1,753 cases
  • , 306,739 controls
]
,
45.5 % Male samples
 Mean = 58.0 years
Sd = 7.9 years		 European — UKB —
PSS012282 — —
[
  • 856 cases
  • , 306,739 controls
]
 — European — UKB —
PSS012283 — —
[
  • 231 cases
  • , 37,670 controls
]
 — European, African American or Afro-Caribbean — PMB —
PSS012284 — —
[
  • 556 cases
  • , 306,739 controls
]
 — European — UKB —