Polygenic Score (PGS) ID: PGS005275

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal carcinoma (EFO_1001951)
Released in PGS Catalog: Aug. 6, 2025
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Score Details

Score Construction
PGS Name CRC_PRS_JPHC_JPGWAS
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (r^2 <= 0.8) & P<=0.05
Variants
Original Genome Build GRCh37
Number of Variants 104,677
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000749
Citation (link to publication) Nakano S et al. Cancer Epidemiol (2025)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
33,870 individuals (100%)
Score Development/Training
East Asian: 100%
4,003 individuals (100%)
PGS Evaluation
East Asian: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 29471430
[
  • 6,692 cases
  • , 27,178 controls
]
 East Asian
(Japanese)		 NR
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
—
[
  • 200 cases
  • , 3,803 controls
]
,
42.59 % Male samples
 East Asian
(Japanese)		 JPHC — Mean (Male Cases) = 56.4 years
Sd = 6.9 years		 — — mean (male subcohorts) = 53.4 years; sd = 7.5; mean (female cases) = 54.6 years; sd = 6.4; mean (female subcohorts) = 52.5 years; sd = 7.3

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
PPM022759 PSS012071|
East Asian Ancestry|
7,943 individuals
 PGP000749 |
Nakano S et al. Cancer Epidemiol (2025)
 Reported Trait: incident colorectal cancer HR: 1.411 [1.229, 1.621] — HR of the top quintile compared to the bottom quintile: 2.27 [1.49, 3.46] age —
PPM022758 PSS012070|
East Asian Ancestry|
4,444 individuals
 PGP000749 |
Nakano S et al. Cancer Epidemiol (2025)
 Reported Trait: incident colorectal cancer HR: 1.475 [1.283, 1.696] — HR of the top quintile compared to the bottom quintile: 2.94 [1.94, 4.45] age —

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
PSS012071 — —
[
  • 341 cases
  • , 7,602 controls
]
,
0.0 % Male samples
 Mean (Cases) = 56.0 years
Sd = 7.3 years		 East Asian
(Japanese)		 — JPHC mean (subcohorts) = 53.8 years; sd = 7.8
PSS012070 — —
[
  • 352 cases
  • , 4,092 controls
]
,
100.0 % Male samples
 Mean (Cases) = 56.7 years
Sd = 7.6 years		 East Asian
(Japanese)		 — JPHC mean (subcohorts) = 54.0 years; sd = 8.2