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(Variants and weights)

Polygenic Score (PGS) ID: PGS000086

Predicted Trait

Reported Trait: Testicular cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): testicular carcinoma Testicular Germ Cell Tumor

Score Details

Name: CC_Testis

Original Genome Build: GRCh37
Number of Variants: 52

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002023
PubMed: 23666239
1,638 individuals European
GWAS Catalog: GCST000416
PubMed: 19483682
1,196 individuals European
GWAS Catalog: GCST003246
PubMed: 26503584
5,932 individuals European
GWAS Catalog: GCST004635
PubMed: 28604728
24,573 individuals European
GWAS Catalog: GCST002022
PubMed: 23666240
5,932 individuals European
GWAS Catalog: GCST004713
PubMed: 28604732
17,528 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000206 PSS000125 Graff RE et al. (2020) Reported Trait: Testicular cancer OR: 2.29 [2.13 - 2.47] Genotyping array, age, 10 PCs.

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000125 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28020 170,680 individuals
[ 713 cases, 169,967 controls]
1.00 % Male samples
European UKB