Polygenic Score (PGS) ID: PGS000148

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Released in PGS Catalog: April 29, 2020
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Score Details

Score Construction
PGS Name CRC63
Development Method
Name Genome-wide significant variants
Parameters Weights were estimated regression coefficients obtained from a multivariable logistic regression that included 63 previously identified SNPs adjusting for age, sex, genotype platform, and up to 6 principal components (PCs)
Variants
Original Genome Build NR
Number of Variants 63
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000071
Citation (link to publication) Jeon J et al. Gastroenterology (2018)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
65,764 individuals (100%)
Score Development/Training
European: 100%
10,166 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001787
Europe PMC: 23266556
 27,809 individuals European NR
GWAS Catalog: GCST003017
Europe PMC: 26151821
 37,955 individuals European 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
—
[
  • 48 cases
  • , 70 controls
]
,
51.0 % Male samples
 European Hawaiian_Colo2&3 — Mean = 64.0 years
Range = [38.0, 84.0] years		 — — Case/Control
—
[
  • 279 cases
  • , 275 controls
]
,
51.0 % Male samples
 European CPSII — Mean = 75.0 years
Range = [58.0, 94.0] years		 — — Cohort Study
—
[
  • 1,187 cases
  • , 1,092 controls
]
,
60.0 % Male samples
 European DALS — Mean = 68.0 years
Range = [33.0, 99.0] years		 — — Case/Control
—
[
  • 579 cases
  • , 570 controls
]
,
56.0 % Male samples
 European DALS — Mean = 65.0 years
Range = [30.0, 79.0] years		 — — Case/Control
—
[
  • 74 cases
  • , 57 controls
]
,
100.0 % Male samples
 European HPFS — Mean = 70.0 years
Range = [50.0, 89.0] years		 — — Cohort Study
—
[
  • 505 cases
  • , 586 controls
]
,
47.0 % Male samples
 European KCCS — Mean = 65.0 years
Range = [21.0, 95.0] years		 — — Case/Control
—
[
  • 125 cases
  • , 226 controls
]
,
52.0 % Male samples
 European MCCS — Mean = 68.0 years
Range = [45.0, 87.0] years		 — — Cohort Study
—
[
  • 120 cases
  • , 187 controls
]
,
54.0 % Male samples
 European MEC — Mean = 70.0 years
Range = [47.0, 89.0] years		 — — Cohort Study
—
[
  • 540 cases
  • , 393 controls
]
,
52.0 % Male samples
 European MECC — Mean = 72.0 years
Range = [25.0, 95.0] years		 — — Case/Control
—
[
  • 99 cases
  • , 234 controls
]
,
62.0 % Male samples
 European NFCCR — Mean = 62.0 years
Range = [23.0, 76.0] years		 — — Case/Control
—
[
  • 118 cases
  • , 273 controls
]
,
0.0 % Male samples
 European NHS — Mean = 66.0 years
Range = [46.0, 83.0] years		 — — Cohort Study
—
[
  • 426 cases
  • , 414 controls
]
,
58.0 % Male samples
 European PLCO — Mean = 70.0 years
Range = [55.0, 87.0] years		 — — Cohort Study
—
[
  • 151 cases
  • , 138 controls
]
,
51.0 % Male samples
 European VITAL — Mean = 70.0 years
Range = [51.0, 83.0] years		 — — Cohort Study
—
[
  • 624 cases
  • , 776 controls
]
,
0.0 % Male samples
 European WHI — Mean = 72.0 years
Range = [52.0, 89.0] years		 — — Cohort Study

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
PPM000452 PSS000260|
European Ancestry|
5,500 individuals
 PGP000071 |
Jeon J et al. Gastroenterology (2018)
 Reported Trait: Colorectal cancer — AUROC: 0.59 [0.58, 0.6] — age, family history, study, endoscopy history Risk prediction using Model III (Family History & G-score)
PPM000451 PSS000261|
European Ancestry|
4,666 individuals
 PGP000071 |
Jeon J et al. Gastroenterology (2018)
 Reported Trait: Colorectal cancer — AUROC: 0.63 [0.62, 0.64] — age, family history, study, endoscopy history, E-score (height, body mass index, education, history of type 2 diabetes mellitus, smoking status, alcohol consumption, regular aspirin use, regular NSAIDs use, smoking pack-years, dietary factors, total-energy, physical activity) Risk prediction using Model IV (Family history & E-score & G-score)
PPM000450 PSS000261|
European Ancestry|
4,666 individuals
 PGP000071 |
Jeon J et al. Gastroenterology (2018)
 Reported Trait: Colorectal cancer — AUROC: 0.59 [0.58, 0.6] — age, family history, study, endoscopy history Risk prediction using Model III (Family History & G-score)
PPM000453 PSS000260|
European Ancestry|
5,500 individuals
 PGP000071 |
Jeon J et al. Gastroenterology (2018)
 Reported Trait: Colorectal cancer — AUROC: 0.62 [0.61, 0.63] — age, family history, study, endoscopy history, E-score (height, body mass index, education, history of type 2 diabetes mellitus, smoking status, alcohol consumption, regular aspirin use, regular NSAIDs use, regular use of post-menopausal hormones, smoking pack-years, dietary factors, total-energy, physical activity) Risk prediction using Model IV (Family history & E-score & G-score)

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
PSS000260 — —
[
  • 2,568 cases
  • , 2,932 controls
]
,
0.0 % Male samples
 Mean (Cases) = 68.8 years
Sd (Cases) = 9.7 years		 European — 14 cohorts
  • CPSII
  • ,DACHS
  • ,DALS
  • ,HPFS
  • ,Hawaiian_Colo2&3
  • ,KCCS
  • ,MCCS
  • ,MEC
  • ,MECC
  • ,NFCCR
  • ,NHS
  • ,PLCO
  • ,VITAL
  • ,WHI
 —
PSS000261 — —
[
  • 2,307 cases
  • , 2,359 controls
]
,
100.0 % Male samples
 Mean (Cases) = 67.8 years
Sd (Cases) = 9.7 years		 European — 14 cohorts
  • CPSII
  • ,DACHS
  • ,DALS
  • ,HPFS
  • ,Hawaiian_Colo2&3
  • ,KCCS
  • ,MCCS
  • ,MEC
  • ,MECC
  • ,NFCCR
  • ,NHS
  • ,PLCO
  • ,VITAL
  • ,WHI
 —