Polygenic Score (PGS) ID: PGS000154

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (EFO_0005842)
Released in PGS: April 29, 2020

Score Details

Score Construction
PGS Name cGRS_Colorectal
Variants
Original Genome Build NR
Number of Variants 30
Development Method
Name Pruning + Thresholding
Parameters GWAS significant and r2 < 0.2. PGS levels were computed as product(dosage*weight/expected risk effect), where the expected risk effect for each variant was calculated based on the risk allele frequence (f) and risk allele weight (OR) as f^2*OR^2 + 2f(1-f)OR + (1-f)^2.
PGS Source
PGS Catalog Publication (PGP) ID PGP000075
Citation (link to publication) Shi Z et al. Cancer Med (2019)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST006131
EuropePMC: 29917119
6,597 individuals African American or Afro-Caribbean
GWAS Catalog: GCST006131
EuropePMC: 29917119
67,812 individuals European
GWAS Catalog: GCST000843
EuropePMC: 2097244
30,420 individuals European
GWAS Catalog: GCST000843
EuropePMC: 2097244
7,962 individuals European
GWAS Catalog: GCST001787
EuropePMC: 23266556
27,809 individuals European
GWAS Catalog: GCST001544
EuropePMC: 22634755
17,780 individuals European
GWAS Catalog: GCST000169
EuropePMC: 18372905
1,849 individuals European
GWAS Catalog: GCST000053
EuropePMC: 17618284
1,890 individuals European
GWAS Catalog: GCST000168
EuropePMC: 18372901
1,983 individuals European
(U.K.)
GWAS Catalog: GCST003017
EuropePMC: 26151821
37,955 individuals European
GWAS Catalog: GCST001161
EuropePMC: 21761138
6,322 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
PPM000474 PSS000274 PGP000075
Shi Z et al. (2019)
Reported Trait: Colorectal cancer Mean realative risk: 1.08[1.04, 1.12]
Wilcoxon test (case vs. control) p-value: 8.29e-06
PPM000485 PSS000274 PGP000075
Shi Z et al. (2019)
Reported Trait: Colorectal cancer Odds Ratio (OR; high vs. average risk groups): 1.18[0.87, 1.61]

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
PSS000274 Primary tumor samples from TCGA
[
  • 387 cases
  • , 0 controls
]
Mean = 68.0 years
Sd = 13.0 years
European TCGA
PSS000274
[
  • 0 cases
  • , 13,427 controls
]
European eMERGE