Polygenic Score (PGS) ID: PGS000792

Predicted Trait
Reported Trait Oral cavity and pharyngeal cancers
Mapped Trait(s)
Released in PGS Catalog: May 28, 2021
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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 CC_Oral_IV
Development Method
Name 14 variants from Graff et al (PGS000081) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 14
Effect Weight Type Inverse-variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 66%
Multi-ancestry (including European): 27.3%
  • European
  • Not Reported
Not Reported: 6.7%
41,845 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
 1,183 individuals Not reported 7 cohorts
  • ARCAGE
  • ,CHANCE
  • ,EPIC
  • ,HN5000
  • ,IARC
  • ,IARCCES
  • ,Toronto
GWAS Catalog: GCST003857
Europe PMC: 27749845
 11,436 individuals European, NR 7 cohorts
  • ARCAGE
  • ,CHANCE
  • ,EPIC
  • ,HN5000
  • ,IARC
  • ,IARCCES
  • ,Toronto
GWAS Catalog: GCST003859
Europe PMC: 27749845
 736 individuals Not reported 7 cohorts
  • ARCAGE
  • ,CHANCE
  • ,EPIC
  • ,HN5000
  • ,IARC
  • ,IARCCES
  • ,Toronto
GWAS Catalog: GCST003859
Europe PMC: 27749845
 8,490 individuals European 7 cohorts
  • ARCAGE
  • ,CHANCE
  • ,EPIC
  • ,HN5000
  • ,IARC
  • ,IARCCES
  • ,Toronto
GWAS Catalog: GCST003858
Europe PMC: 27749845
 874 individuals Not reported 7 cohorts
  • ARCAGE
  • ,CHANCE
  • ,EPIC
  • ,HN5000
  • ,IARC
  • ,IARCCES
  • ,Toronto
GWAS Catalog: GCST001011
Europe PMC: 21437268
 10,425 individuals European ARCAGE, B58C, CNG, IARCCES
GWAS Catalog: GCST003858
Europe PMC: 27749845
 8,701 individuals European 7 cohorts
  • ARCAGE
  • ,CHANCE
  • ,EPIC
  • ,HN5000
  • ,IARC
  • ,IARCCES
  • ,Toronto

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
PPM002063 PSS001020|
European Ancestry|
391,479 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident oral cavity and pharyngeal cancer HR: 1.12 [1.02, 1.23] AUROC: 0.702
C-index: 0.687 (0.015)		 R²: 0.356 Age at assessment, sex, genotyping array, PCs(1-15), weekly alcohol intake, cigarettes per day, years of smoking, smoing status (never vs. former vs. current) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001020 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 481 cases
  • , 390,998 controls
]
 — European — UKB —