Polygenic Score (PGS) ID: PGS000074

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (EFO_0005842)
Released in PGS: Feb. 12, 2020

Score Details

Score Construction
PGS Name CC_Colorectal
Variants
Original Genome Build GRCh37
Number of Variants 103
Development Method
Name Genome-wide significant SNPs
Parameters P < 5x10-8, MAF > 1%, biallelic SNPs, LD-thin r2 > 0.3
PGS Source
PGS Catalog Publication (PGP) ID PGP000050
Citation (link to publication) Graff RE et al. bioRxiv (2020) Preprint

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST002919
EuropePMC: 25990418
17,556 individuals European
GWAS Catalog: GCST001544
EuropePMC: 22634755
17,780 individuals European
GWAS Catalog: GCST000270
EuropePMC: 19011631
3,831 individuals European
GWAS Catalog: GCST000843
EuropePMC: 20972440
30,420 individuals European
GWAS Catalog: GCST000843
EuropePMC: 20972440
7,962 individuals European
GWAS Catalog: GCST007856
EuropePMC: 30510241
120,184 individuals European
GWAS Catalog: GCST007856
EuropePMC: 30510241
5,294 individuals East Asian
GWAS Catalog: GCST001787
EuropePMC: 23266556
27,809 individuals European
GWAS Catalog: GCST002512
EuropePMC: 24978480
1,281 individuals European
(Spain)
GWAS Catalog: GCST002528
EuropePMC: 25023989
983 individuals Other
GWAS Catalog: GCST002528
EuropePMC: 25023989
2,976 individuals European
GWAS Catalog: GCST006131
EuropePMC: 29917119
6,597 individuals African American or Afro-Caribbean
GWAS Catalog: GCST006131
EuropePMC: 29917119
67,812 individuals European
GWAS Catalog: GCST003017
EuropePMC: 26151821
37,955 individuals European
GWAS Catalog: GCST004895
EuropePMC: 28960316
15,783 individuals European
GWAS Catalog: GCST002411
EuropePMC: 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 ID
(PPM ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000194 PSS000113 PGP000050
Graff RE et al. (2020)
Pre
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 Sample Set ID
(PSS ID)
Detailed Phenotype Description 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
]
,
0.46 % Male samples
Mean = 58.0 years European GERA, UKB