Polygenic Score (PGS) ID: PGS000074

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Released in PGS Catalog: Feb. 12, 2020
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Score Details

Score Construction
PGS Name CC_Colorectal
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
Variants
Original Genome Build GRCh37
Number of Variants 103
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 96.6%
African: 1.7%
East Asian: 1.4%
Additional Diverse Ancestries: 0.3%
377,666 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST002919
Europe PMC: 25990418
 17,556 individuals European NR
GWAS Catalog: GCST000270
Europe PMC: 19011631
 3,831 individuals European COGS, CoRGI
GWAS Catalog: GCST000843
Europe PMC: 20972440
 30,420 individuals European NR
GWAS Catalog: GCST007856
Europe PMC: 30510241
 120,184 individuals European NR
GWAS Catalog: GCST007856
Europe PMC: 30510241
 5,294 individuals East Asian NR
GWAS Catalog: GCST002528
Europe PMC: 25023989
 983 individuals Other CCFR, MECC
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: GCST004895
Europe PMC: 28960316
 15,783 individuals European
(Finnish)		 NR
GWAS Catalog: GCST000843
Europe PMC: 20972440
 7,962 individuals European NR
GWAS Catalog: GCST001544
Europe PMC: 22634755
 17,780 individuals European COGS, CoRGI, NSCCG, SOCCS, VICTOR
GWAS Catalog: GCST001787
Europe PMC: 23266556
 27,809 individuals European NR
GWAS Catalog: GCST002411
Europe PMC: 24737748
 13,443 individuals European NR
GWAS Catalog: GCST002512
Europe PMC: 2497848
 1,281 individuals European
(Spain)		 NR
GWAS Catalog: GCST002528
Europe PMC: 25023989
 2,976 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
PPM000194 PSS000113|
European Ancestry|
416,249 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 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
PPM002040 PSS001013|
European Ancestry|
393,723 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident colorectal cancer HR: 1.32 [1.27, 1.37] AUROC: 0.704
C-index: 0.704 (0.006)		 — Age at assessment, sex, family history of bowel cancer, genotyping array, PCs(1-15), wasit to hip ratio, cigarette pack years, frequency of processed meat intake (<1 per week vs. ≥1 per week), moderate and/or strenuous physical activity (days per week), alcohol intake C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM017164 PSS010144|
European Ancestry|
2,150 individuals
 PGP000443 |
Byrne S et al. Int J Epidemiol (2023)
|Ext.		 Reported Trait: Colorectal cancer HR: 1.36 [1.31, 1.42] — — age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates —

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
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 —
[
  • 5,895 cases
  • , 410,354 controls
]
,
46.0 % Male samples
 Mean = 58.0 years European — GERA, UKB —
PSS001013 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 2,725 cases
  • , 390,998 controls
]
 — European — UKB —
PSS010144 — —
[
  • 180 cases
  • , 1,970 controls
]
 — European — UKB —