Polygenic Score (PGS) ID: PGS003433

Predicted Trait
Reported Trait Colorectal cancer
Mapped Trait(s) colorectal cancer (MONDO_0005575)
Released in PGS Catalog: March 3, 2023
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Score Details

Score Construction
PGS Name LDPred2-grid-sp
Development Method
Name LDpred2
Parameters proportion of causal variants 0.01; heritability 0.1602; sparsity 0.44137
Variants
Original Genome Build hg19
Number of Variants 616,956
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000438
Citation (link to publication) Briggs SEW et al. BMJ (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
67,878 individuals (100%)
Score Development/Training
European: 100%
30,000 individuals (100%)
PGS Evaluation
European: 50%
Multi-ancestry (excluding European): 50%
  • Additional Diverse Ancestries
  • Not Reported
8 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST007992
[
  • 26,397 cases
  • , 41,481 controls
]
 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
—
[
  • 446 cases
  • , 29,554 controls
]
 European
(British)		 UKB Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. — — — —

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
PPM017107 PSS010130|
European Ancestry|
280,664 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: Colorectal cancer OR: 1.571 [1.524, 1.62] AUROC: 0.716 [0.71, 0.723] R²: 6.2 [5.8, 6.7] age, sex, PC1-4, array Apparent performance presented, results for internal validation presented in source publication. Dxy and scaled Brier available in source publication
PPM017119 PSS010132|
European Ancestry|
34,152 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: Colorectal cancer — AUROC: 0.733 [0.71, 0.753] R²: 7.6 [6.1, 8.9] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017125 PSS010133|
European Ancestry|
33,893 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: Incident Colorectal cancer — C-index: 0.725 [0.696, 0.752] R²: 28.5 [23.4, 33.7] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017131 PSS010134|
Multi-ancestry (excluding European)|
27,503 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: Colorectal cancer — AUROC: 0.601 [0.559, 0.64] — age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017137 PSS010135|
Multi-ancestry (excluding European)|
27,310 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: Incident Colorectal cancer — C-index: 0.664 [0.609, 0.718] R²: 20.2 [11.4, 30.7] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017141 PSS010129|
Multi-ancestry (excluding European)|
196,091 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: Incident Colorectal cancer in men — C-index: 0.73 [0.72, 0.741] R²: 28.2 [26.3, 30.1]
For top 20% absolute risk sensitivity: 47.8 %
specificty: 80.3 %		 QCancer-10 score Apparent performance presented, results for internal validation presented in source publication. Dxy, D statistic, and scaled Brier available in source publication
PPM017142 PSS010128|
Multi-ancestry (excluding European)|
238,496 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: incident Colorectal cancer in females — C-index: 0.687 [0.673, 0.702] R²: 21.0 [18.7, 23.7]
For top 20% absolute risk sensitivity: 42.7 %
specificty: 80.1 %		 QCancer-10 score Apparent performance presented, results for internal validation presented in source publication. Dxy, D statistic, and scaled Brier available in source publication
PPM017113 PSS010131|
European Ancestry|
278,493 individuals
 PGP000438 |
Briggs SEW et al. BMJ (2022)
 Reported Trait: incident Colorectal cancer HR: 1.545 [1.48, 1.612] C-index: 0.712 [0.702, 0.723] R²: 25.3 [23.4, 27.3] age, sex, PC1-4, array Apparent performance presented, results for internal validation presented in source publication. Dxy, D statistic, and scaled Brier available in source publication

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
PSS010134 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. —
[
  • 255 cases
  • , 27,248 controls
]
 — Other, NR Scottish UKB participants self-identifying as diverse ethnic groups other than "British", "Irish", "white" or "any other white background|" UKB Cohort for logistic regression model validation (minority ethnic population)
PSS010135 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. Median = 7.0 years
[
  • 155 cases
  • , 27,155 controls
]
 — Other, NR Scottish UKB participants self-identifying as diverse ethnic groups other than "British", "Irish", "white" or "any other white background|" UKB Cohort for cox regression model validation (minority ethnic population)
PSS010128 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. Median = 7.0 years
[
  • 1,458 cases
  • , 237,038 controls
]
 Median = 57.0 years Other, NR All ancestral backgrounds within UKB UKB Cohort for integrated model development in women
PSS010129 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. Median = 7.0 years
[
  • 1,895 cases
  • , 194,196 controls
]
 Median = 58.0 years Other, NR All ancestral backgrounds within UKB UKB Cohort for integrated model development in men
PSS010130 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. —
[
  • 4,230 cases
  • , 276,434 controls
]
 — European
(British)		 — UKB Cohort for logistic regression model testing
PSS010131 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. —
[
  • 2,127 cases
  • , 276,366 controls
]
 — European
(British)		 — UKB Cohort for logistic regression model testing
PSS010132 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. —
[
  • 611 cases
  • , 33,541 controls
]
 — European Scottish UKB participants self-identifying as "British", "Irish", "white" or "any other white background|" UKB Cohort for logistic regression model validation (European populations)
PSS010133 Colorectal cancer identified through self-report at UK Biobank study enrolment visit and ICD-9 (153, 154.0, 154.1) and ICD-10 (C18-C20) codes in linked cancer and death registries and hospital data. Median = 7.0 years
[
  • 363 cases
  • , 33,530 controls
]
 — European Scottish UKB participants self-identifying as "British", "Irish", "white" or "any other white background|" UKB Cohort for cox regression model validation (European populations)