Polygenic Score (PGS) ID: PGS004912

Predicted Trait
Reported Trait Colorectal neoplasm
Mapped Trait(s) colorectal carcinoma (EFO_1001951)
Released in PGS Catalog: June 27, 2024
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Score Details

Score Construction
PGS Name PRS183
Development Method
Name Pruning and Thresholding (P+T)
Parameters Construct PRSs in a range of significance thresholds(5 ×10-4, 5 ×10-5, 5 ×10-6, 5 ×10-7, and 5 ×10-8) and a range of LD (r2=0.01, 0.1, 0.2)
Variants
Original Genome Build GRCh37
Number of Variants 183
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000643
Citation (link to publication) Tian J et al. Genome Med (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 76.6%
East Asian: 23.4%
867,727 individuals (100%)
Score Development/Training
East Asian: 100%
3,628 individuals (100%)
PGS Evaluation
East Asian: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003017
[
  • 18,299 cases
  • , 19,656 controls
]
 European
(European)		 CORECT
Europe PMC: 36285626
[
  • 4,957 cases
  • , 238,678 controls
]
 European
(Finnish)		 FinnGen
Europe PMC: 32514122
[
  • 7,062 cases
  • , 195,745 controls
]
 East Asian
(Japanese)		 BBJ
[
  • 5,657 cases
  • , 377,673 controls
]
 European
(British)		 UKB
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
—
[
  • 1,814 cases
  • , 1,814 controls
]
,
67.89 % Male samples
 East Asian
(Chinese)		 ZJCRC — Mean = 62.05 years
Sd = 7.446 years		 — — —

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
PPM021368 PSS011706|
East Asian Ancestry|
2,344 individuals
 PGP000643 |
Tian J et al. Genome Med (2024)
 Reported Trait: Colorectal advanced neoplasm OR: 1.61 [1.33, 1.94] AUROC: 0.591 — age, sex, family history, principal components, genotype platform —
PPM021369 PSS011706|
East Asian Ancestry|
2,344 individuals
 PGP000643 |
Tian J et al. Genome Med (2024)
 Reported Trait: Colorectal non-advanced adenoma OR: 1.25 [1.14, 1.38] AUROC: 0.556 — age, sex, family history, principal components, genotype platform —
PPM021370 PSS011705|
European Ancestry|
24,322 individuals
 PGP000643 |
Tian J et al. Genome Med (2024)
 Reported Trait: Colorectal advanced neoplasm OR: 1.34 [1.28, 1.4] AUROC: 0.582 — age, sex, family history, principal components, genotype platform —
PPM021371 PSS011705|
European Ancestry|
24,322 individuals
 PGP000643 |
Tian J et al. Genome Med (2024)
 Reported Trait: Colorectal non-advanced adenoma OR: 1.19 [1.15, 1.23] AUROC: 0.546 — age, sex, family history, principal components, genotype platform —

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
PSS011705 — —
[
  • 6,609 cases
  • , 17,713 controls
]
,
55.6 % Male samples
 Mean = 62.07 years
Sd = 5.21 years		 European — PLCO —
PSS011706 — —
[
  • 672 cases
  • , 1,672 controls
]
,
46.72 % Male samples
 Mean = 57.59 years
Sd = 8.47 years		 East Asian
(Chinese)		 — ZJCRC —