Predicted Trait | |
Reported Trait | Oral cavity and pharyngeal cancers |
Mapped Trait(s) |
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 |
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 |
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 |
PGS Sample Set ID (PSS 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 |
---|---|---|---|---|---|---|---|---|
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 | — | [ ,
46.0 % Male samples |
Mean = 58.0 years | European | — | GERA, UKB | — |