Publication Information (EuropePMC) | |
Title | A model to determine colorectal cancer risk using common genetic susceptibility loci. |
PubMed ID | 25683114(Europe PMC) |
doi | 10.1053/j.gastro.2015.02.010 |
Publication Date | Feb. 13, 2015 |
Journal | Gastroenterology |
Author(s) | Hsu L, Jeon J, Brenner H, Gruber SB, Schoen RE, Berndt SI, Chan AT, Chang-Claude J, Du M, Gong J, Harrison TA, Hayes RB, Hoffmeister M, Hutter CM, Lin Y, Nishihara R, Ogino S, Prentice RL, Schumacher FR, Seminara D, Slattery ML, Thomas DC, Thornquist M, Newcomb PA, Potter JD, Zheng Y, White E, Peters U, Colorectal Transdisciplinary (CORECT) Study, Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). |
Polygenic Score (PGS) ID | PGS Name | PGS Publication (PGP) ID | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | PGS Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000146 | CRC_GRS_27 | PGP000069 Hsu L et al. Gastroenterology (2015) | Colorectal cancer risk | colorectal cancer | 27 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000146/ScoringFiles/PGS000146.txt.gz |
PGS Performance Metric ID (PPM ID) |
Evaluated Score |
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 |
---|---|---|---|---|---|---|---|---|---|
PPM000439 | PGS000146 (CRC_GRS_27) | PSS000252 | PGP000069 Hsu L et al. (2015) | Reported Trait: Distal colon cancer | OR: 1.08 [1.06, 1.11] | — | — | Study, age, endoscopy, family history | — |
PPM000438 | PGS000146 (CRC_GRS_27) | PSS000254 | PGP000069 Hsu L et al. (2015) | Reported Trait: Proximal colon cancer | OR: 1.07 [1.04, 1.1] | — | — | Study, age, endoscopy, family history | — |
PPM000445 | PGS000146 (CRC_GRS_27) | PSS000257 | PGP000069 Hsu L et al. (2015) | Reported Trait: Colorectal cancer | — | AUROC: 0.56 [0.51, 0.61] | — | Age, endoscopy, family history | — |
PPM000444 | PGS000146 (CRC_GRS_27) | PSS000258 | PGP000069 Hsu L et al. (2015) | Reported Trait: Colorectal cancer | — | AUROC: 0.59 [0.54, 0.64] | — | Age, endoscopy, family history | — |
PPM000443 | PGS000146 (CRC_GRS_27) | PSS000255 | PGP000069 Hsu L et al. (2015) | Reported Trait: Rectal cancer | OR: 1.12 [1.08, 1.15] | — | — | Study, age, endoscopy, family history | — |
PPM000442 | PGS000146 (CRC_GRS_27) | PSS000251 | PGP000069 Hsu L et al. (2015) | Reported Trait: Distal colon cancer | OR: 1.08 [1.05, 1.1] | — | — | Study, age, endoscopy, family history | — |
PPM000441 | PGS000146 (CRC_GRS_27) | PSS000253 | PGP000069 Hsu L et al. (2015) | Reported Trait: Proximal colon cancer | OR: 1.06 [1.03, 1.08] | — | — | Study, age, endoscopy, family history | — |
PPM000440 | PGS000146 (CRC_GRS_27) | PSS000256 | PGP000069 Hsu L et al. (2015) | Reported Trait: Rectal cancer | OR: 1.06 [1.03, 1.09] | — | — | Study, age, endoscopy, family history | — |
PGS Sample Set ID (PSS ID) |
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 |
---|---|---|---|---|---|---|---|---|
PSS000251 | Colorectal adenocarcinoma located in the distal colon confirmed by medical records, pathology reports, or death certificate | — | [ ,
0.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |
PSS000252 | Colorectal adenocarcinoma located in the distal colon confirmed by medical records, pathology reports, or death certificate | — | [ ,
100.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |
PSS000253 | Colorectal adenocarcinoma located in the proximal colon confirmed by medical records, pathology reports, or death certificate | — | [ ,
0.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |
PSS000254 | Colorectal adenocarcinoma located in the proximal colon confirmed by medical records, pathology reports, or death certificate | — | [ ,
100.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |
PSS000255 | Colorectal adenocarcinoma located in the rectum confirmed by medical records, pathology reports, or death certificate | — | [ ,
0.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |
PSS000256 | Colorectal adenocarcinoma located in the rectum confirmed by medical records, pathology reports, or death certificate | — | [ ,
100.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |
PSS000257 | Colorectal adenocarcinoma confirmed by medical records, pathology reports, or death certificate | — | [ ,
0.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |
PSS000258 | Colorectal adenocarcinoma confirmed by medical records, pathology reports, or death certificate | — | [ ,
100.0 % Male samples |
— | European | — | 6 cohorts
|
Training and test split not relevant to PGS |