Polygenic Score (PGS) ID: PGS000081

Predicted Trait
Reported Trait Oral cavity and pharyngeal cancers
Mapped Trait(s)
Released in PGS: Feb. 12, 2020

Score Details

Score Construction
PGS Name CC_Oral
Variants
Original Genome Build GRCh37
Number of Variants 14
Development Method
Name Genome-wide significant SNPs
Parameters P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. bioRxiv (2020) Preprint

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003858
EuropePMC: 27749845
874 individuals NR
GWAS Catalog: GCST003858
EuropePMC: 27749845
8,701 individuals European
GWAS Catalog: GCST001011
EuropePMC: 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 ID
(PPM ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000201 PSS000120 PGP000050
Graff RE et al. (2020)
Pre
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 Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants 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
[
  • 1,223 cases
  • , 410,354 controls
]
,
0.46 % Male samples
Mean = 58.0 years European GERA, UKB