Polygenic Score (PGS) ID: PGS003390

Predicted Trait
Reported Trait Head and neck squamous cell carcinoma
Mapped Trait(s) head and neck squamous cell carcinoma (EFO_0000181)
Released in PGS Catalog: Jan. 19, 2023
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Score Details

Score Construction
PGS Name best_HNSC
Development Method
Parameters PRS-CS-auto
Original Genome Build GRCh37
Number of Variants 931,477
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000413
Citation (link to publication) Namba S et al. Cancer Res (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 90.6%
  • European
  • Not Reported
Not Reported: 9.4%
12,619 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003857
Europe PMC: 27749845
11,436 individuals European, NR NR
GWAS Catalog: GCST003857
Europe PMC: 27749845
1,183 individuals Not reported NR

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
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM016265 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 : 0.00561 age, sex, top 20 genetic principal components

Evaluated Samples

PGS Sample Set ID
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
UKB Controls were samples without any cancer diagnosis or self-reported cancer