Polygenic Score (PGS) ID: PGS000357

Predicted Trait
Reported Trait Oral cavity cancer
Mapped Trait(s) oral cavity cancer (EFO_0005570)
Additional Trait Information PheCode 145
Released in PGS Catalog: Dec. 15, 2020
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name PRSWEB_PHECODE145_C3-LIP-ORAL-PHARYNX_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=2e-05
Variants
Original Genome Build GRCh37
Number of Variants 45
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
361,194 individuals (100%)
Score Development/Training
European: 100%
6,613 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 790 cases
  • , 360,404 controls
]
 European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 32991828
[
  • 604 cases
  • , 6,009 controls
]
 European MGI PheCode:145; ICD9CM:140.0, 140.1, 140.3, 140.4, 140.5, 140.6, 140.8, 140.9, 141.0, 141.1, 141.2, 141.3, 141.4, 141.5, 141.6, 141.8, 141.9, 142.0, 142.1, 142.2, 142.8, 142.9, 143.0, 143.1, 143.8, 143.9, 144.0, 144.1, 144.8, 144.9, 145.0, 145.1, 145.2, 145.3, 145.4, 145.5, 145.6, 145.8, 145.9, 230.0, V10.01; ICD10CM:C00, C00.0, C00.1, C00.2, C00.3, C00.4, C00.5, C00.6, C00.8, C00.9, C01, C02, C02.0, C02.1, C02.2, C02.3, C02.4, C02.8, C02.9, C03, C03.0, C03.1, C03.9, C04, C04.0, C04.1, C04.8, C04.9, C05, C05.0, C05.1, C05.2, C05.8, C05.9, C06, C06.0, C06.1, C06.2, C06.8, C06.80, C06.89, C06.9, C07, C08, C08.0, C08.1, C08.9, D00.0, D00.00, D00.01, D00.02, D00.03, D00.04, D00.05, D00.06, D00.07, D00.08 — — — —

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) 		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
PPM001042 PSS000535|
European Ancestry|
6,328 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of mouth OR: 1.111 [1.021, 1.208]
β: 0.105 (0.0427)		 AUROC: 0.519 [0.498, 0.542] Nagelkerke's Pseudo-R²: 0.0021
Brier score: 0.0829
Odds Ratio (OR, top 1% vs. Rest): 1.26 [0.585, 2.73]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE145_C3-LIP-ORAL-PHARYNX_PT_MGI_20200608

Evaluated Samples

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
PSS000535 PheCode:145; ICD9CM:140.0, 140.1, 140.3, 140.4, 140.5, 140.6, 140.8, 140.9, 141.0, 141.1, 141.2, 141.3, 141.4, 141.5, 141.6, 141.8, 141.9, 142.0, 142.1, 142.2, 142.8, 142.9, 143.0, 143.1, 143.8, 143.9, 144.0, 144.1, 144.8, 144.9, 145.0, 145.1, 145.2, 145.3, 145.4, 145.5, 145.6, 145.8, 145.9, 230.0, V10.01; ICD10CM:C00, C00.0, C00.1, C00.2, C00.3, C00.4, C00.5, C00.6, C00.8, C00.9, C01, C02, C02.0, C02.1, C02.2, C02.3, C02.4, C02.8, C02.9, C03, C03.0, C03.1, C03.9, C04, C04.0, C04.1, C04.8, C04.9, C05, C05.0, C05.1, C05.2, C05.8, C05.9, C06, C06.0, C06.1, C06.2, C06.8, C06.80, C06.89, C06.9, C07, C08, C08.0, C08.1, C08.9, D00.0, D00.00, D00.01, D00.02, D00.03, D00.04, D00.05, D00.06, D00.07, D00.08 —
[
  • 578 cases
  • , 5,750 controls
]
 — European — MGI —