| 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 |
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 |
|
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 | — | [ ,
0.46 % Male samples |
Mean = 58.0 years | European | — | GERA, UKB | — |