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
Download Score FTP directory
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_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)
JSONXMLCSVTXTMS-Excel
Loading, please wait
Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST000414
Europe PMC: 19483681
2,165 individualsEuropeanNR
GWAS Catalog: GCST000701
Europe PMC: 20543847
5,926 individualsEuropeanNR
GWAS Catalog: GCST002022
Europe PMC: 23666240
5,932 individualsEuropeanNR
GWAS Catalog: GCST002023
Europe PMC: 23666239
1,638 individualsEuropeanNR
GWAS Catalog: GCST002855
Europe PMC: 25877299
8,013 individualsEuropeanNR
GWAS Catalog: GCST003246
Europe PMC: 26503584
5,932 individualsEuropeanNR
GWAS Catalog: GCST003247
Europe PMC: 26503584
5,932 individualsEuropeanNR
GWAS Catalog: GCST004635
Europe PMC: 28604728
24,573 individualsEuropeanNR
GWAS Catalog: GCST004713
Europe PMC: 28604732
17,528 individualsEuropeanNR
Showing 1 to 9 of 9 rows
Score Development/Training
JSONXMLCSVTXTMS-Excel
Loading, please wait
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
]
EuropeanMGIPheCode:187.2; ICD9CM:186.0, 186.9, V10.47; ICD10CM:C62, C62.0, C62.00, C62.01, C62.02, C62.1, C62.1... 0, C62.11, C62.12, C62.9, C62.90, C62.91, C62.92Show more————
Showing 1 to 1 of 1 rows

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.

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PPM001288PSS000553|
European Ancestry|
755 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Malignant neoplasm of testisOR: 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 1-4Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_PT_MGI_20200608
Showing 1 to 1 of 1 rows

Evaluated Samples

JSONXMLCSVTXTMS-Excel
Loading, please wait
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
PSS000553PheCode:187.2; ICD9CM:186.0, 186.9, V10.47; ICD10CM:C62, C62.0, C62.00, C62.01, C62.02, C62.1, C62.1... 0, C62.11, C62.12, C62.9, C62.90, C62.91, C62.92Show more—
[
  • 73 cases
  • , 682 controls
]
—European—MGI—
Showing 1 to 1 of 1 rows