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(Variants and weights)

Polygenic Score (PGS) ID: PGS000074

Predicted Trait

Reported Trait: Colorectal cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): colorectal cancer

Score Details

Name: CC_Colorectal

Original Genome Build: GRCh37
Number of Variants: 103

PGS Development Method: Genome-wide significant SNPs
PGS Development Details/Relevant Parameters: P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3

Citation: Graff RE et al. bioRxiv (2020) | PGS Catalog Publication ID: PGP000050

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002919
PubMed: 25990418
17,556 individuals European
GWAS Catalog: GCST001544
PubMed: 22634755
17,780 individuals European
GWAS Catalog: GCST000270
PubMed: 19011631
3,831 individuals European
GWAS Catalog: GCST000843
PubMed: 20972440
30,420 individuals European
GWAS Catalog: GCST000843
PubMed: 20972440
7,962 individuals European
GWAS Catalog: GCST007856
PubMed: 30510241
120,184 individuals European
GWAS Catalog: GCST007856
PubMed: 30510241
5,294 individuals East Asian
GWAS Catalog: GCST001787
PubMed: 23266556
27,809 individuals European
GWAS Catalog: GCST002512
PubMed: 24978480
1,281 individuals European
(Spain)
GWAS Catalog: GCST002528
PubMed: 25023989
983 individuals Other
GWAS Catalog: GCST002528
PubMed: 25023989
2,976 individuals European
GWAS Catalog: GCST006131
PubMed: 29917119
6,597 individuals African American or Afro-Caribbean
GWAS Catalog: GCST006131
PubMed: 29917119
67,812 individuals European
GWAS Catalog: GCST003017
PubMed: 26151821
37,955 individuals European
GWAS Catalog: GCST004895
PubMed: 28960316
15,783 individuals European
GWAS Catalog: GCST002411
PubMed: 24737748
13,443 individuals European

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 (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000194 PSS000113 Graff RE et al. (2020) Reported Trait: Colorectal cancer OR: 1.37 [1.33 - 1.4] Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. Results from meta-analysis of GERA and UKB

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000113 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 21041 - 21049, 21051, 21052, and 21060 416,249 individuals
[ 5,895 cases, 410,354 controls]
0.46 % Male samples
European GERA, UKB