Polygenic Score (PGS) ID: PGS000802

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Released in PGS Catalog: June 11, 2021
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Score Details

Score Construction
PGS Name CRC_19
Development Method
Name LASSO penalized regression
Parameters 10-fold cross-validation, lambda (λ) = 0.012, r^2 < 0.20
Variants
Original Genome Build NR
Number of Variants 19
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000191
Citation (link to publication) He CY et al. Genomics (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 63.6%
East Asian: 36.4%
111,769 individuals (100%)
Score Development/Training
East Asian: 100%
5,606 individuals (100%)
PGS Evaluation
East Asian: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001161
Europe PMC: 21761138
6,322 individuals European CCFR, DALS, PLCO, WHI
Europe PMC: 21655089
[
  • 8,021 cases
  • , 9,253 controls
]
European 8 cohorts
  • B58C
  • ,CoRGI
  • ,EPICOLON
  • ,FCCPS
  • ,NSCCG
  • ,QUASAR2
  • ,SEARCH
  • ,VICTOR
GWAS Catalog: GCST000948
Europe PMC: 21242260
3,481 individuals East Asian BBJ, O-MRC
GWAS Catalog: GCST001792
Europe PMC: 23263487
7,847 individuals East Asian Aichi_Con, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST002454
Europe PMC: 24836286
8,270 individuals East Asian Aichi_Con, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST003799
Europe PMC: 26965516
21,096 individuals East Asian BBJ, Guangzhou, KCPS, Shanghai
GWAS Catalog: GCST001787
Europe PMC: 23266556
27,809 individuals European NR
GWAS Catalog: GCST001544
Europe PMC: 22634755
17,780 individuals European COGS, CoRGI, NSCCG, SOCCS, VICTOR
GWAS Catalog: GCST000113
Europe PMC: 17934461
1,890 individuals European CoRGI
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
[
  • 2,557 cases
  • , 3,049 controls
]
,
54.07 % Male samples
East Asian
(Han-Chinese)
NR Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations. Subjects obtained from Sun Yat-Sen University Cancer Center (SYSUCC)

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
PPM002098 PSS001032|
East Asian Ancestry|
2,566 individuals
PGP000191 |
He CY et al. Genomics (2021)
Reported Trait: Colorectal cancer Odds Ratio (OR, top 75% vs bottom 25%): 2.53 [1.99, 3.22] Gender, age
PPM002099 PSS001031|
East Asian Ancestry|
2,269 individuals
PGP000191 |
He CY et al. Genomics (2021)
Reported Trait: Colorectal cancer Odds Ratio (OR, top 75% vs bottom 25%): 2.12 [1.63, 2.77] Gender, age
PPM002094 PSS001033|
East Asian Ancestry|
5,465 individuals
PGP000191 |
He CY et al. Genomics (2021)
Reported Trait: Colorectal cancer AUROC: 0.59 [0.57, 0.6] Possible overlap with score development samples
PPM002095 PSS001032|
East Asian Ancestry|
2,566 individuals
PGP000191 |
He CY et al. Genomics (2021)
Reported Trait: Colorectal cancer AUROC: 0.61 [0.59, 0.63]
PPM002096 PSS001031|
East Asian Ancestry|
2,269 individuals
PGP000191 |
He CY et al. Genomics (2021)
Reported Trait: Colorectal cancer AUROC: 0.59 [0.57, 0.61]
PPM002097 PSS001033|
East Asian Ancestry|
5,465 individuals
PGP000191 |
He CY et al. Genomics (2021)
Reported Trait: Colorectal cancer Odds Ratio (OR, top 75% vs bottom 25%): 2.27 [1.95, 2.64] Gender, age possible overlap with score development samples

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
PSS001031 Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations.
[
  • 1,027 cases
  • , 1,242 controls
]
,
51.39 % Male samples
East Asian
(Han-Chinese)
NR Subects obtained from First Hospital of China Medical University (CMU)
PSS001032 Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations.
[
  • 1,152 cases
  • , 1,414 controls
]
,
53.86 % Male samples
East Asian
(Han-Chinese)
NR Subjects obtained from Fudan University Shanghai Cancer Center (FUSCC)
PSS001033 Exclusion criteria for healthy controls included subjects with polyposis, adenomas, and diseases related to or causing a predisposition for cancer. Cases included subjects with colorectal cancer, confirmed by endoscopic and histological examinations.
[
  • 2,448 cases
  • , 3,017 controls
]
,
53.72 % Male samples
East Asian
(Han-Chinese)
NR Subjects obtained from Sun Yat-Sen University Cancer Center (SYSUCC)