Polygenic Score (PGS) ID: PGS000362

Predicted Trait
Reported Trait Cancer of larynx
Mapped Trait(s) larynx cancer (MONDO_0002352)
Additional Trait Information PheCode 149.4
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE149.4_UKBB-SAIGE-HRC-X149.4_PT_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 53
Development Method
Name P&T
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=3.98e-05
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%
407,079 individuals (100%)
Score Development/Training
European: 100%
1,908 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
Europe PMC: 32424355
[
  • 258 cases
  • , 406,821 controls
]
European
Score Development/Training
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
PheCode:149.4; ICD9CM:161.0, 161.1, 161.2, 161.3, 161.8, 161.9, 231.0, V10.21; ICD10CM:C32, C32.0, C32.1, C32.2, C32.3, C32.8, C32.9, D02.0
[
  • 174 cases
  • , 1,734 controls
]
European MGI

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
PPM001047 PSS000536|
European Ancestry|
1,738 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of larynx OR: 1.195 [1.023, 1.396]
β: 0.178 (0.0793)
AUROC: 0.543 [0.494, 0.59] Nagelkerke's Pseudo-R²: 0.00609
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 1.52 [0.384, 5.98]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE149.4_UKBB-SAIGE-HRC-X149.4_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
PSS000536 PheCode:149.4; ICD9CM:161.0, 161.1, 161.2, 161.3, 161.8, 161.9, 231.0, V10.21; ICD10CM:C32, C32.0, C32.1, C32.2, C32.3, C32.8, C32.9, D02.0
[
  • 158 cases
  • , 1,580 controls
]
European MGI