Polygenic Score (PGS) ID: PGS000369

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (EFO_0005842)
Additional Trait Information PheCode 153
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE153_CRC-Huyghe_PT_MGI_20200608
Variants
Original Genome Build GRCh37
Number of Variants 81
Development Method
Name P&T
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=3.98e-07
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%
63,920 individuals (100%)
Score Development/Training
European: 100%
6,445 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
Europe PMC: 30510241
[
  • 34,869 cases
  • , 29,051 controls
]
European
Score Development/Training
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
PheCode:153; ICD9CM:153.0, 153.1, 153.2, 153.3, 153.4, 153.5, 153.6, 153.7, 153.8, 153.9, 154.0, 154.1, 154.2, 154.3, 154.8, 159.0, 209.10, 209.11, 209.12, 209.13, 209.14, 209.15, 209.16, 209.17, 230.3, 230.4, 230.5, 230.6, 796.70, 796.71, 796.72, 796.73, 796.74, 796.76, V10.05, V10.06; ICD10CM:C18, C18.0, C18.1, C18.2, C18.3, C18.4, C18.5, C18.6, C18.7, C18.8, C18.9, C19, C20, C21.0, C21.1, C21.2, C21.8, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.026, C7A.029, D01.0, D01.1, D01.2, D01.3, R85.610, R85.611, R85.612, R85.613, R85.614, R85.619
[
  • 589 cases
  • , 5,856 controls
]
European MGI

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
PPM001054 PSS000540|
European Ancestry|
6,633 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
Reported Trait: Colorectal cancer OR: 1.214 [1.117, 1.32]
β: 0.194 (0.0426)
AUROC: 0.553 [0.525, 0.577] Nagelkerke's Pseudo-R²: 0.00671
Brier score: 0.0828
Odds Ratio (OR, top 1% vs. Rest): 3.04 [1.79, 5.17]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153_CRC-Huyghe_PT_MGI_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
PSS000540 PheCode:153; ICD9CM:153.0, 153.1, 153.2, 153.3, 153.4, 153.5, 153.6, 153.7, 153.8, 153.9, 154.0, 154.1, 154.2, 154.3, 154.8, 159.0, 209.10, 209.11, 209.12, 209.13, 209.14, 209.15, 209.16, 209.17, 230.3, 230.4, 230.5, 230.6, 796.70, 796.71, 796.72, 796.73, 796.74, 796.76, V10.05, V10.06; ICD10CM:C18, C18.0, C18.1, C18.2, C18.3, C18.4, C18.5, C18.6, C18.7, C18.8, C18.9, C19, C20, C21.0, C21.1, C21.2, C21.8, C26.0, C7A.020, C7A.021, C7A.022, C7A.023, C7A.024, C7A.025, C7A.026, C7A.029, D01.0, D01.1, D01.2, D01.3, R85.610, R85.611, R85.612, R85.613, R85.614, R85.619
[
  • 607 cases
  • , 6,026 controls
]
European MGI