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(Variants and weights)

Polygenic Score (PGS) ID: PGS000081

Predicted Trait

Reported Trait: Oral cavity and pharyngeal cancers
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): oral cavity cancer carcinoma of pharynx

Score Details

Name: CC_Oral

Original Genome Build: GRCh37
Number of Variants: 14

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003858
PubMed: 27749845
874 individuals NR
GWAS Catalog: GCST003858
PubMed: 27749845
8,701 individuals European
GWAS Catalog: GCST001011
PubMed: 21437268
10,425 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000201 PSS000120 Graff RE et al. (2020) Reported Trait: Oral cavity and pharyngeal cancers OR: 1.08 [1.02 - 1.14] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000120 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 20010, 20020, 20030, 20040, 20050, 20060, 20070, 20080, 20090, and 20100 411,577 individuals
[ 1,223 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB