PGS Publication: PGP000438

Publication Information (EuropePMC)
Title Integrating genome-wide polygenic risk scores and non-genetic risk to predict colorectal cancer diagnosis using UK Biobank data: population based cohort study.
PubMed ID 36351667(Europe PMC)
doi 10.1136/bmj-2022-071707
Publication Date Nov. 9, 2022
Journal BMJ
Author(s) Briggs SEW, Law P, East JE, Wordsworth S, Dunlop M, Houlston R, Hippisley-Cox J, Tomlinson I.
Released in PGS Catalog: March 3, 2023

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
Scoring File (FTP Link)
PGS003431
(LDPred2-inf)
PGP000438 |
Briggs SEW et al. BMJ (2022)
Colorectal cancer colorectal cancer 1,104,409
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003431/ScoringFiles/PGS003431.txt.gz
PGS003432
(LDPred2-grid)
PGP000438 |
Briggs SEW et al. BMJ (2022)
Colorectal cancer colorectal cancer 1,104,409
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003432/ScoringFiles/PGS003432.txt.gz
PGS003433
(LDPred2-grid-sp)
PGP000438 |
Briggs SEW et al. BMJ (2022)
Colorectal cancer colorectal cancer 616,956
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003433/ScoringFiles/PGS003433.txt.gz
PGS003434
(SCT)
PGP000438 |
Briggs SEW et al. BMJ (2022)
Colorectal cancer colorectal cancer 194,756
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003434/ScoringFiles/PGS003434.txt.gz
PGS003435
(CT)
PGP000438 |
Briggs SEW et al. BMJ (2022)
Colorectal cancer colorectal cancer 13,446
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003435/ScoringFiles/PGS003435.txt.gz
PGS003436
(GWAS-sig)
PGP000438 |
Briggs SEW et al. BMJ (2022)
Colorectal cancer colorectal cancer 50
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003436/ScoringFiles/PGS003436.txt.gz

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)
Evaluated Score 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
PPM017106 PGS003432
(LDPred2-grid)
PSS010130|
European Ancestry|
280,664 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer OR: 1.584 [1.536, 1.633] AUROC: 0.717 [0.711, 0.725] : 6.3 [5.9, 6.8] age, sex, PC1-4, array Apparent performance presented, results for internal validation presented in source publication. Dxy and scaled Brier available in source publication
PPM017107 PGS003433
(LDPred2-grid-sp)
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] : 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
PPM017108 PGS003434
(SCT)
PSS010130|
European Ancestry|
280,664 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer OR: 1.417 [1.375, 1.461] AUROC: 0.702 [0.695, 0.711] : 5.4 [5.0, 5.9] age, sex, PC1-4, array Apparent performance presented, results for internal validation presented in source publication. Dxy and scaled Brier available in source publication
PPM017109 PGS003435
(CT)
PSS010130|
European Ancestry|
280,664 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer OR: 1.425 [1.382, 1.47] AUROC: 0.704 [0.697, 0.711] : 5.4 [5.1, 5.9] age, sex, PC1-4, array Apparent performance presented, results for internal validation presented in source publication. Dxy and scaled Brier available in source publication
PPM017110 PGS003436
(GWAS-sig)
PSS010130|
European Ancestry|
280,664 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer OR: 1.39 [1.348, 1.433] AUROC: 0.7 [0.693, 0.707] : 5.3 [4.9, 5.7] age, sex, PC1-4, array Apparent performance presented, results for internal validation presented in source publication. Dxy and scaled Brier available in source publication
PPM017114 PGS003434
(SCT)
PSS010131|
European Ancestry|
278,493 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: incident Colorectal cancer HR: 1.378 [1.321, 1.438] C-index: 0.695 [0.685, 0.706] : 22.3 [20.3, 24.4] 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
PPM017115 PGS003435
(CT)
PSS010131|
European Ancestry|
278,493 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: incident Colorectal cancer HR: 1.397 [1.338, 1.459] C-index: 0.698 [0.689, 0.709] : 22.4 [20.6, 24.4] 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
PPM017116 PGS003436
(GWAS-sig)
PSS010131|
European Ancestry|
278,493 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: incident Colorectal cancer HR: 1.377 [1.32, 1.436] C-index: 0.695 [0.685, 0.706] : 22.2 [20.2, 24.4] 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
PPM017117 PGS003431
(LDPred2-inf)
PSS010132|
European Ancestry|
34,152 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.726 [0.704, 0.748] : 7.0 [5.7, 8.4] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017118 PGS003432
(LDPred2-grid)
PSS010132|
European Ancestry|
34,152 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.732 [0.71, 0.752] : 7.6 [6.1, 8.9] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017119 PGS003433
(LDPred2-grid-sp)
PSS010132|
European Ancestry|
34,152 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.733 [0.71, 0.753] : 7.6 [6.1, 8.9] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017120 PGS003434
(SCT)
PSS010132|
European Ancestry|
34,152 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.718 [0.696, 0.739] : 6.4 [5.0, 7.7] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017121 PGS003435
(CT)
PSS010132|
European Ancestry|
34,152 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.719 [0.696, 0.74] : 6.6 [5.2, 7.9] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017122 PGS003436
(GWAS-sig)
PSS010132|
European Ancestry|
34,152 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.703 [0.679, 0.724] : 5.4 [4.0, 6.7] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017123 PGS003431
(LDPred2-inf)
PSS010133|
European Ancestry|
33,893 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.715 [0.686, 0.743] : 27.0 [21.7, 32.1] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017124 PGS003432
(LDPred2-grid)
PSS010133|
European Ancestry|
33,893 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.724 [0.696, 0.751] : 28.3 [23.2, 33.3] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017125 PGS003433
(LDPred2-grid-sp)
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] : 28.5 [23.4, 33.7] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017126 PGS003434
(SCT)
PSS010133|
European Ancestry|
33,893 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.713 [0.686, 0.74] : 25.1 [20.2, 30.2] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017127 PGS003435
(CT)
PSS010133|
European Ancestry|
33,893 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.707 [0.681, 0.734] : 25.1 [20.0, 30.3] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017128 PGS003436
(GWAS-sig)
PSS010133|
European Ancestry|
33,893 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.701 [0.675, 0.729] : 23.8 [19.0, 29.4] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017129 PGS003431
(LDPred2-inf)
PSS010134|
Multi-ancestry (excluding European)|
27,503 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.588 [0.545, 0.627] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017130 PGS003432
(LDPred2-grid)
PSS010134|
Multi-ancestry (excluding European)|
27,503 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.602 [0.558, 0.64] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017131 PGS003433
(LDPred2-grid-sp)
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
PPM017132 PGS003434
(SCT)
PSS010134|
Multi-ancestry (excluding European)|
27,503 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.589 [0.546, 0.626] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017133 PGS003435
(CT)
PSS010134|
Multi-ancestry (excluding European)|
27,503 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.597 [0.554, 0.636] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017134 PGS003436
(GWAS-sig)
PSS010134|
Multi-ancestry (excluding European)|
27,503 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer AUROC: 0.587 [0.543, 0.624] age, sex, PC1-4, array Dxy, scaled Brier, calibration slope and CITL available in source publication
PPM017135 PGS003431
(LDPred2-inf)
PSS010135|
Multi-ancestry (excluding European)|
27,310 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.647 [0.593, 0.7] : 17.2 [9.2, 27.9] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017136 PGS003432
(LDPred2-grid)
PSS010135|
Multi-ancestry (excluding European)|
27,310 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.666 [0.61, 0.72] : 20.3 [11.5, 31.1] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017137 PGS003433
(LDPred2-grid-sp)
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] : 20.2 [11.4, 30.7] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017138 PGS003434
(SCT)
PSS010135|
Multi-ancestry (excluding European)|
27,310 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.65 [0.596, 0.705] : 17.4 [8.9, 28.1] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017139 PGS003435
(CT)
PSS010135|
Multi-ancestry (excluding European)|
27,310 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.658 [0.606, 0.71] : 18.7 [10.0, 29.4] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017140 PGS003436
(GWAS-sig)
PSS010135|
Multi-ancestry (excluding European)|
27,310 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer C-index: 0.659 [0.605, 0.715] : 19.1 [10.3, 29.9] age, sex, PC1-4, array Dxy, D statistic, scaled Brier, calibration slope, available in source publication
PPM017141 PGS003433
(LDPred2-grid-sp)
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] : 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 PGS003433
(LDPred2-grid-sp)
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] : 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
PPM017143 PGS003436
(GWAS-sig)
PSS010129|
Multi-ancestry (excluding European)|
196,091 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Incident Colorectal cancer in men C-index: 0.715 [0.706, 0.726] : 25.6 [23.9, 27.5]
For top 20% absolute risk sensitivity: 44.4 %
specificty: 80.2 %
QCancer-10 score Apparent performance presented, results for internal validation presented in source publication. Dxy, D statistic, and scaled Brier available in source publication
PPM017144 PGS003436
(GWAS-sig)
PSS010128|
Multi-ancestry (excluding European)|
238,496 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: incident Colorectal cancer in females C-index: 0.669 [0.655, 0.683] : 17.0 [14.8, 19.3]
For top 20% absolute risk sensitivity: 39.2 %
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
PPM017105 PGS003431
(LDPred2-inf)
PSS010130|
European Ancestry|
280,664 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: Colorectal cancer OR: 1.435 [1.391, 1.48] AUROC: 0.704 [0.697, 0.712] : 5.5 [5.1, 5.9] age, sex, PC1-4, array Apparent performance presented, results for internal validation presented in source publication. Dxy and scaled Brier available in source publication
PPM017111 PGS003431
(LDPred2-inf)
PSS010131|
European Ancestry|
278,493 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: incident Colorectal cancer HR: 1.368 [1.31, 1.428] C-index: 0.696 [0.685, 0.707] : 22.0 [20.1, 24.0] 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
PPM017112 PGS003432
(LDPred2-grid)
PSS010131|
European Ancestry|
278,493 individuals
PGP000438 |
Briggs SEW et al. BMJ (2022)
Reported Trait: incident Colorectal cancer HR: 1.563 [1.498, 1.631] C-index: 0.714 [0.704, 0.726] : 25.6 [23.8, 27.8] 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
PPM017113 PGS003433
(LDPred2-grid-sp)
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] : 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)