Polygenic Score (PGS) ID: PGS000599

Predicted Trait
Reported Trait Malignant neoplasm of testis
Mapped Trait(s) testicular carcinoma (EFO_0005088)
Additional Trait Information PheCode 187.2
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE187.2_C3-TESTIS_PT_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 31
Development Method
Name P&T
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=1e-05
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
EuropePMC: http://www.nealelab.is/uk-biobank
[
  • 432 cases
  • , 166,588 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:187.2; ICD9CM:186.0, 186.9, V10.47; ICD10CM:C62, C62.0, C62.00, C62.01, C62.02, C62.1, C62.10, C62.11, C62.12, C62.9, C62.90, C62.91, C62.92
[
  • 71 cases
  • , 705 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 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
PPM001284 PSS000553 PGP000118 Fritsche LG et al. (2020) Reported Trait: Malignant neoplasm of testis OR: 1.628 [1.281, 2.069]
β: 0.487 (0.122)
AUROC: 0.637 [0.568, 0.703] Nagelkerke's Pseudo-R²: 0.0473
Brier score: 0.0844
Odds Ratio (OR, top 1% vs. Rest): 4.35 [1.08, 17.5]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_C3-TESTIS_PT_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000553 PheCode:187.2; ICD9CM:186.0, 186.9, V10.47; ICD10CM:C62, C62.0, C62.00, C62.01, C62.02, C62.1, C62.10, C62.11, C62.12, C62.9, C62.90, C62.91, C62.92
[
  • 73 cases
  • , 682 controls
]
European MGI