Polygenic Score (PGS) ID: PGS000787

Predicted Trait
Reported Trait Kidney cancer
Mapped Trait(s) renal cell carcinoma (EFO_0000681)
Released in PGS Catalog: May 28, 2021
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Score Details

Score Construction
PGS Name CC_Kidney_IV
Development Method
Name 19 variants from Graff et al (PGS000076) with inverse variant weights
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 19
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%
42,061 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: GCST002835
Europe PMC: 25826619
 10,871 individuals European NCI, UKBS, WTCCC
GWAS Catalog: GCST004710
Europe PMC: 28598434
 31,190 individuals European 29 cohorts
  • AHS
  • ,ASHRAM
  • ,ATBC
  • ,BioVU
  • ,CPSII
  • ,CeRePP
  • ,DFHCC
  • ,EPIC
  • ,HPFS
  • ,HUNT2
  • ,IARC
  • ,Karolinska
  • ,Leeds
  • ,MCCS
  • ,MDARCCS
  • ,Moscow
  • ,NCI
  • ,NHS
  • ,PHS
  • ,PLCO
  • ,SEARCH
  • ,Tromso
  • ,Umea
  • ,VARI
  • ,VITAL
  • ,WHI
  • ,WHS
  • ,WTCCC
  • ,conFIRM

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
PPM002058 PSS001015|
European Ancestry|
391,610 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident kidney cancer HR: 1.15 [1.07, 1.24] AUROC: 0.722
C-index: 0.723 (0.011)		 R²: 0.366 Age at assessment, sex, genotyping array, PCs(1-15), body mass index, smoking status (never vs. former vs. current), cigarette pack-years, ever diagnosed with hypertension 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
PSS001015 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 612 cases
  • , 390,998 controls
]
 — European — UKB —