Polygenic Score (PGS) ID: PGS000086

Predicted Trait
Reported Trait Testicular cancer
Mapped Trait(s)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name CC_Testis
Variants
Original Genome Build GRCh37
Number of Variants 52
Development Method
Name Genome-wide significant SNPs
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
56,799 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002023
Europe PMC: 23666239
1,638 individuals European
GWAS Catalog: GCST000416
Europe PMC: 19483682
1,196 individuals European
GWAS Catalog: GCST003246
Europe PMC: 26503584
5,932 individuals European
GWAS Catalog: GCST004635
Europe PMC: 28604728
24,573 individuals European
GWAS Catalog: GCST002022
Europe PMC: 2366624
5,932 individuals European
GWAS Catalog: GCST004713
Europe PMC: 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 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
PPM000206 PSS000125|
European Ancestry|
170,680 individuals
PGP000050 |
Graff RE et al. Nat Commun (2021)
Reported Trait: Testicular cancer OR: 2.29 [2.13, 2.47] Genotyping array, age, 10 PCs.
PPM002051 PSS001024|
European Ancestry|
179,537 individuals
PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.
Reported Trait: Incident testicular cancer HR: 2.18 [1.66, 2.87] AUROC: 0.783
C-index: 0.749 (0.034)
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
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
[
  • 713 cases
  • , 169,967 controls
]
,
100.0 % Male samples
European UKB