Polygenic Score (PGS) ID: PGS000796

Predicted Trait
Reported Trait Testicular cancer
Mapped Trait(s)
Released in PGS Catalog: May 28, 2021
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 CC_Testis_IV
Development Method
Name 52 variants from Graff et al (PGS000086) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 52
Effect Weight Type Inverse-variance weighting
PGS Source
PGS Catalog Publication (PGP) ID PGP000186
Citation (link to publication) Kachuri L et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
56,799 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: GCST004635
Europe PMC: 28604728
 24,573 individuals European 6 cohorts
  • B58C
  • ,BCAC
  • ,SEARCH
  • ,UKBS
  • ,UKGPCS
  • ,UKTCC
GWAS Catalog: GCST002022
Europe PMC: 23666240
 5,932 individuals European B58C, UKBS, UKTCC
GWAS Catalog: GCST004713
Europe PMC: 28604732
 17,528 individuals European NCI, Penn, Sweden
GWAS Catalog: GCST002023
Europe PMC: 23666239
 1,638 individuals European FCCC, NCI, UPENN
GWAS Catalog: GCST003246
Europe PMC: 26503584
 5,932 individuals European B58C, UKBS, UKTCC
GWAS Catalog: GCST000416
Europe PMC: 19483682
 1,196 individuals European FCCC, PennCATH, UPENN

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
PPM002067 PSS001024|
European Ancestry|
179,537 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident testicular cancer HR: 2.26 [1.71, 2.99] AUROC: 0.787
C-index: 0.766 (0.033)		 R²: 0.605 Age at assessment, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.

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
PSS001024 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 52 cases
  • , 179,485 controls
]
,
100.0 % Male samples
 — European — UKB —