Polygenic Score (PGS) ID: PGS000722

Predicted Trait
Reported Trait Kidney cancer
Mapped Trait(s) renal carcinoma (EFO_0002890)
Released in PGS Catalog: Feb. 3, 2021
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Score Details

Score Construction
PGS Name PRS_Kidney
Development Method
Name Genome-wide significant variants
Parameters NR
Variants
Original Genome Build hg19
Number of Variants 15
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000135
Citation (link to publication) Jia G et al. JNCI Cancer Spectr (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
142,756 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 22113997
[
  • 2,278 cases
  • , 3,719 controls
]
 European ATBC, CEERCC, CPSII, PLCO, USKC
GWAS Catalog: GCST001750
Europe PMC: 23184150
 10,781 individuals European 8 cohorts
  • ATBC
  • ,CPSII
  • ,PLCO
  • ,RMHT
  • ,SORCE
  • ,UKBS
  • ,USKC
  • ,WTCCC
GWAS Catalog: GCST002273
Europe PMC: 24220699
 69,230 individuals European ICR, deCODE
GWAS Catalog: GCST000907
Europe PMC: 21131975
 12,277 individuals European 14 cohorts
  • ASHRAM
  • ,ATBC
  • ,CPSII
  • ,CeRePP
  • ,EPIC
  • ,HUNT2
  • ,IARC
  • ,Leeds
  • ,Moscow
  • ,NCI
  • ,PLCO
  • ,SEARCH
  • ,Tromso
  • ,USKC
GWAS Catalog: GCST001283
Europe PMC: 22010048
 2,410 individuals European MDACCS
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
GWAS Catalog: GCST002835
Europe PMC: 25826619
 10,871 individuals European NCI, UKBS, WTCCC

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
PPM001652 PSS000856|
European Ancestry|
400,812 individuals
 PGP000135 |
Jia G et al. JNCI Cancer Spectr (2020)
 Reported Trait: Incident kidney cancer — AUROC: 0.567 [0.543, 0.591] — Genotyping array —

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
PSS000856 Data and diagnoses on site-specific incident cancers were provided by the National Health Service Information Centre for participants from England and Wales (follow-up through March 31, 2016) and by the NHS Central Register Scotland for participants from Scotland (follow-up through October 31, 2015). Cancers were coded by the International Classification of Diseases, Ninth Revision (ICD-9) or the International Classification of Diseases, Tenth Revision (ICD-10). Kidney Cancer=(ICD-9 = 189.0 or ICD-10 = C64) Median = 5.8 years
[
  • 545 cases
  • , 400,267 controls
]
,
46.5 % Male samples
 — European — UKB —