Polygenic Score (PGS) ID: PGS000361

Predicted Trait
Reported Trait Laryngeal cancer
Mapped Trait(s) Malignant Laryngeal Neoplasm (EFO_1000354)
Additional Trait Information PheCode 149.4
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_PHECODE149.4_C3-LARYNX_LASSOSUM_MGI_20200608
Development Method
Name lassosum
Parameters s=1;Lambda=0.07848
Variants
Original Genome Build GRCh37
Number of Variants 87,893
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%
1,908 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
[
  • 205 cases
  • , 360,989 controls
]
EuropeanNR
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Score Development/Training
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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
[
  • 174 cases
  • , 1,734 controls
]
EuropeanMGIPheCode:149.4; ICD9CM:161.0, 161.1, 161.2, 161.3, 161.8, 161.9, 231.0, V10.21; ICD10CM:C32, C32.0, C... 32.1, C32.2, C32.3, C32.8, C32.9, D02.0Show more————
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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.

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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
PPM001046PSS000536|
European Ancestry|
1,738 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Cancer of larynxOR: 1.195 [1.014, 1.408]
β: 0.178 (0.0836)		AUROC: 0.55 [0.504, 0.593]Nagelkerke's Pseudo-R²: 0.00551
Brier score: 0.0824
Odds Ratio (OR, top 1% vs. Rest): 1.51 [0.382, 5.94]		age, sex, batch PCs 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE149.4_C3-LARYNX_LASSOSUM_MGI_20200608
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Evaluated Samples

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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
PSS000536PheCode:149.4; ICD9CM:161.0, 161.1, 161.2, 161.3, 161.8, 161.9, 231.0, V10.21; ICD10CM:C32, C32.0, C... 32.1, C32.2, C32.3, C32.8, C32.9, D02.0Show more—
[
  • 158 cases
  • , 1,580 controls
]
—European—MGI—
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