Polygenic Score (PGS) ID: PGS000606

Predicted Trait
Reported Trait Malignant neoplasm of kidney, except pelvis
Mapped Trait(s) kidney cancer (MONDO_0002367)
Additional Trait Information PheCode 189.11
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_PT_UKB_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08
Variants
Original Genome Build GRCh37
Number of Variants 12
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
33,826 individuals (100%)
Score Development/Training
European: 100%
5,539 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: GCST001500
Europe PMC: 22544364
 2,636 individuals European NR
GWAS Catalog: GCST004710
Europe PMC: 28598434
 31,190 individuals European NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
Europe PMC: 32991828
[
  • 504 cases
  • , 5,035 controls
]
 European UKB PheCode:189.11; ICD9:189.0; ICD10:C64 — — — —

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
PPM001291 PSS000575|
European Ancestry|
5,818 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of kidney, except pelvis OR: 1.154 [1.062, 1.254]
β: 0.143 (0.0426)		 AUROC: 0.517 [0.492, 0.54] Nagelkerke's Pseudo-R²: 0.00398
Brier score: 0.0825
Odds Ratio (OR, top 1% vs. Rest): 2.17 [1.13, 4.14]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE189.11_GWAS-Catalog-r2019-05-03-X189.11_PT_UKB_20200608

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
PSS000575 PheCode:189.11; ICD9:189.0; ICD10:C64 —
[
  • 529 cases
  • , 5,289 controls
]
 — European — UKB —