Polygenic Score (PGS) ID: PGS000154

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Released in PGS Catalog: April 29, 2020
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Score Details

Score Construction
PGS Name cGRS_Colorectal
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 30
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: 96.8%
African: 3.2%
208,379 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: GCST000053
Europe PMC: 17618284
 1,890 individuals European CoRGI
GWAS Catalog: GCST000169
Europe PMC: 18372905
 1,849 individuals European CoRGI
GWAS Catalog: GCST000843
Europe PMC: 20972440
 7,962 individuals European NR
GWAS Catalog: GCST001161
Europe PMC: 21761138
 6,322 individuals European NR
GWAS Catalog: GCST001544
Europe PMC: 22634755
 17,780 individuals European COGS, CoRGI, NSCCG, SOCCS, VICTOR
GWAS Catalog: GCST006131
Europe PMC: 29917119
 6,597 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST006131
Europe PMC: 29917119
 67,812 individuals European NR
GWAS Catalog: GCST000168
Europe PMC: 18372901
 1,983 individuals European
(U.K.)		 NR
GWAS Catalog: GCST000843
Europe PMC: 20972440
 30,420 individuals European NR
GWAS Catalog: GCST001787
Europe PMC: 23266556
 27,809 individuals European NR
GWAS Catalog: GCST003017
Europe PMC: 26151821
 37,955 individuals European NR

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
PPM000474 PSS000274|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Colorectal cancer — — Mean realative risk: 1.08 [1.04, 1.12]
Wilcoxon test (case vs. control) p-value: 8.29e-06		 — —
PPM000485 PSS000274|
European Ancestry|
13,814 individuals
 PGP000075 |
Shi Z et al. Cancer Med (2019)
 Reported Trait: Colorectal cancer — — Odds Ratio (OR; high vs. average risk groups): 1.18 [0.87, 1.61] — —

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
PSS000274 Primary tumor samples from TCGA —
[
  • 387 cases
  • , 0 controls
]
 Mean = 68.0 years
Sd = 13.0 years		 European — TCGA —
PSS000274 — —
[
  • 0 cases
  • , 13,427 controls
]
 — European — eMERGE —