Polygenic Score (PGS) ID: PGS000161

Predicted Trait
Reported Trait Renal cancer
Mapped Trait(s) renal carcinoma (EFO_0002890)
Released in PGS Catalog: April 29, 2020
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cGRS_Renal
Development Method
Name Pruning and Thresholding (P+T)
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
Variants
Original Genome Build NR
Number of Variants 10
Effect Weight Type Odds Ratio over expected risk
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
67,529 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: 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: 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: GCST001750
Europe PMC: 2318415
 10,781 individuals European NR
GWAS Catalog: GCST001283
Europe PMC: 22010048
 2,410 individuals European MDACCS
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
PPM000492 PSS000281|
European Ancestry|
13,880 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Renal cancer — — Odds Ratio (OR; high vs. average risk groups): 1.58 [1.14, 2.18] — —
PPM000481 PSS000281|
European Ancestry|
13,880 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Renal cancer — — Mean realative risk: 1.09 [1.06, 1.12]
Wilcoxon test (case vs. control) p-value: 8.66e-10		 — —

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
PSS000281 Primary tumor samples from TCGA —
[
  • 453 cases
  • , 0 controls
]
 Mean = 62.0 years
Sd = 12.0 years		 European — TCGA —
PSS000281 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —