Polygenic Score (PGS) ID: PGS000603

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_GWAS-Catalog-r2019-05-03-X187.2_PT_MGI_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=2.51e-11
Variants
Original Genome Build GRCh37
Number of Variants 22
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%
77,639 individuals (100%)
Score Development/Training
European: 100%
776 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000414
Europe PMC: 19483681
 2,165 individuals European NR
GWAS Catalog: GCST000701
Europe PMC: 20543847
 5,926 individuals European NR
GWAS Catalog: GCST002022
Europe PMC: 23666240
 5,932 individuals European NR
GWAS Catalog: GCST002023
Europe PMC: 23666239
 1,638 individuals European NR
GWAS Catalog: GCST002855
Europe PMC: 25877299
 8,013 individuals European NR
GWAS Catalog: GCST003246
Europe PMC: 26503584
 5,932 individuals European NR
GWAS Catalog: GCST003247
Europe PMC: 26503584
 5,932 individuals European NR
GWAS Catalog: GCST004635
Europe PMC: 28604728
 24,573 individuals European NR
GWAS Catalog: GCST004713
Europe PMC: 28604732
 17,528 individuals 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
[
  • 71 cases
  • , 705 controls
]
 European MGI 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 — — — —

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
PPM001288 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.625 [1.27, 2.079]
β: 0.485 (0.126)		 AUROC: 0.625 [0.557, 0.693] Nagelkerke's Pseudo-R²: 0.044
Brier score: 0.084
Odds Ratio (OR, top 1% vs. Rest): 6.05 [1.73, 21.2]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_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
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 —