Polygenic Score (PGS) ID: PGS000148

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 CRC63
Variants
Original Genome Build NR
Number of Variants 63
Development Method
Name GWAS 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)
PGS Source
PGS Catalog Publication (PGP) ID PGP000071
Citation (link to publication) Jeon J et al. Gastroenterology (2018)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST003017
EuropePMC: 26151821
37,955 individuals European
GWAS Catalog: GCST001787
EuropePMC: 23266556
27,809 individuals European
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
[
  • 1,187 cases
  • , 1,092 controls
]
,
60.0 % Male samples
Mean = 68.0 years
Range = [33.0, 99.0] years
European DALS Case/Control
[
  • 118 cases
  • , 273 controls
]
,
0.0 % Male samples
Mean = 66.0 years
Range = [46.0, 83.0] years
European NHS Cohort Study
[
  • 426 cases
  • , 414 controls
]
,
58.0 % Male samples
Mean = 70.0 years
Range = [55.0, 87.0] years
European PLCO Cohort Study
[
  • 151 cases
  • , 138 controls
]
,
51.0 % Male samples
Mean = 70.0 years
Range = [51.0, 83.0] years
European VITAL Cohort Study
[
  • 48 cases
  • , 70 controls
]
,
51.0 % Male samples
Mean = 64.0 years
Range = [38.0, 84.0] years
European Hawaiian Colo2&3 Case/Control
[
  • 279 cases
  • , 275 controls
]
,
51.0 % Male samples
Mean = 75.0 years
Range = [58.0, 94.0] years
European CPSII Cohort Study
[
  • 579 cases
  • , 570 controls
]
,
56.0 % Male samples
Mean = 65.0 years
Range = [30.0, 79.0] years
European DALS Case/Control
[
  • 74 cases
  • , 57 controls
]
,
100.0 % Male samples
Mean = 70.0 years
Range = [50.0, 89.0] years
European HPFS Cohort Study
[
  • 505 cases
  • , 586 controls
]
,
47.0 % Male samples
Mean = 65.0 years
Range = [21.0, 95.0] years
European KCCS Case/Control
[
  • 125 cases
  • , 226 controls
]
,
52.0 % Male samples
Mean = 68.0 years
Range = [45.0, 87.0] years
European MCCS Cohort Study
[
  • 120 cases
  • , 187 controls
]
,
54.0 % Male samples
Mean = 70.0 years
Range = [47.0, 89.0] years
European MEC Cohort Study
[
  • 540 cases
  • , 393 controls
]
,
52.0 % Male samples
Mean = 72.0 years
Range = [25.0, 95.0] years
European MECC Case/Control
[
  • 99 cases
  • , 234 controls
]
,
62.0 % Male samples
Mean = 62.0 years
Range = [23.0, 76.0] years
European NFCCR Case/Control
[
  • 624 cases
  • , 776 controls
]
,
0.0 % Male samples
Mean = 72.0 years
Range = [52.0, 89.0] years
European WHI 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 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
PPM000453 PSS000260 PGP000071
Jeon J et al. (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)
PPM000450 PSS000261 PGP000071
Jeon J et al. (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 PGP000071
Jeon J et al. (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)
PPM000452 PSS000260 PGP000071
Jeon J et al. (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)

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
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