| Predicted Trait | |
| Reported Trait | Oral cavity and pharyngeal cancers |
| Mapped Trait(s) | |
| Score Construction | |
| PGS Name | CC_Oral |
| Development Method | |
| Name | Genome-wide significant variants |
| Parameters | P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3 |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 14 |
| Effect Weight Type | log(OR) |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000050 |
| Citation (link to publication) | Graff RE et al. Nat Commun (2021) |
| Ancestry Distribution | |
| Source of Variant Associations (GWAS) | European: 95.6% Not Reported: 4.4% 20,000 individuals (100%) |
| PGS Evaluation | European: 100% 3 Sample Sets |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST003858 Europe PMC: 27749845 |
874 individuals | NR | NR |
GWAS Catalog: GCST003858 Europe PMC: 27749845 |
8,701 individuals | European | 7 cohorts
|
GWAS Catalog: GCST001011 Europe PMC: 21437268 |
10,425 individuals | European | NR |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM000201 | PSS000120| European Ancestry| 411,577 individuals |
PGP000050 | Graff RE et al. Nat Commun (2021) |
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 |
| PPM002047 | PSS001020| European Ancestry| 391,479 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |Ext. |
Reported Trait: Incident oral cavity and pharyngeal cancer | HR: 1.11 [1.01, 1.21] | AUROC: 0.702 C-index: 0.686 (0.015) |
— | 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. |
| PPM017173 | PSS010150| European Ancestry| 415 individuals |
PGP000443 | Byrne S et al. Int J Epidemiol (2023) |Ext. |
Reported Trait: Oral cavity and pharyngeal cancers | HR: 1.03 [0.94, 1.14] | — | — | age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| 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 | — |
| PSS001020 | Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. | — | [
|
— | European | — | UKB | — |
| PSS010150 | — | — | [
|
— | European | — | UKB | — |