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. |
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 |
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] | R²: 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] | 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 |
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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | 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 | 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] | 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 |
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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | R²: 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] | 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 |
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. | — | [
|
— | 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 | [
|
— | 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 | [
|
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 | [
|
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. | — | [
|
— | 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. | — | [
|
— | 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. | — | [
|
— | 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 | [
|
— | European | Scottish UKB participants self-identifying as "British", "Irish", "white" or "any other white background|" | UKB | Cohort for cox regression model validation (European populations) |