Polygenic Score (PGS) ID: PGS000372

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Additional Trait Information PheCode 153
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE153_GWAS-Catalog-r2019-05-03-X153_PT_UKB_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=7e-06
Variants
Original Genome Build GRCh37
Number of Variants 27
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%
122,140 individuals (100%)
Score Development/Training
European: 100%
25,383 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: GCST000113
Europe PMC: 17934461
 1,890 individuals European NR
GWAS Catalog: GCST000168
Europe PMC: 18372901
 1,983 individuals European
(U.K.)		 NR
GWAS Catalog: GCST000270
Europe PMC: 19011631
 3,831 individuals European NR
GWAS Catalog: GCST001787
Europe PMC: 23266556
 27,809 individuals European NR
GWAS Catalog: GCST002411
Europe PMC: 24737748
 13,443 individuals European NR
GWAS Catalog: GCST002919
Europe PMC: 25990418
 17,556 individuals European NR
GWAS Catalog: GCST003017
Europe PMC: 26151821
 37,955 individuals European NR
GWAS Catalog: GCST004895
Europe PMC: 28960316
 15,783 individuals European
(Finnish)		 NR
GWAS Catalog: GCST000053
Europe PMC: 17618284
 1,890 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
[
  • 2,309 cases
  • , 23,074 controls
]
 European UKB PheCode:153; ICD9:154.8; ICD10: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, C21.8, C26.0, D01.0, D01.1, D01.2, D01.3 — — — —

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
PPM001057 PSS000564|
European Ancestry|
24,996 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Colorectal cancer OR: 1.279 [1.225, 1.335]
β: 0.246 (0.0218)		 AUROC: 0.565 [0.551, 0.577] Nagelkerke's Pseudo-R²: 0.0111
Brier score: 0.0822
Odds Ratio (OR, top 1% vs. Rest): 2.1 [1.53, 2.89]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE153_GWAS-Catalog-r2019-05-03-X153_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
PSS000564 PheCode:153; ICD9:154.8; ICD10: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, C21.8, C26.0, D01.0, D01.1, D01.2, D01.3 —
[
  • 2,271 cases
  • , 22,725 controls
]
 — European — UKB —