Polygenic Score (PGS) ID: PGS000076

Predicted Trait
Reported Trait Kidney cancer
Mapped Trait(s) renal cell carcinoma (EFO_0000681)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name CC_Kidney
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 19
Effect Weight Type NR
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%
42,061 individuals (100%)
PGS Evaluation
European: 100%
3 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
PPM000196 PSS000115|
European Ancestry|
411,695 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Kidney cancer OR: 1.21 [1.14, 1.27] — — Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB
PPM002042 PSS001015|
European Ancestry|
391,610 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident kidney cancer HR: 1.16 [1.08, 1.26] AUROC: 0.722
C-index: 0.724 (0.011)		 — 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.
PPM017169 PSS010145|
European Ancestry|
547 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Kidney cancer HR: 1.14 [1.05, 1.24] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —

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
PSS010145 — —
[
  • 28 cases
  • , 519 controls
]
 — European — UKB —
PSS000115 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): 29020 —
[
  • 1,341 cases
  • , 410,354 controls
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —
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 —