| Publication Information (EuropePMC) | |
| Title | Colorectal cancer susceptibility variants and risk of conventional adenomas and serrated polyps: results from three cohort studies. |
| PubMed ID | 31038671(Europe PMC) |
| doi | 10.1093/ije/dyz096 |
| Publication Date | Feb. 1, 2020 |
| Journal | Int J Epidemiol |
| Author(s) | Hang D, Joshi AD, He X, Chan AT, Jovani M, Gala MK, Ogino S, Kraft P, Turman C, Peters U, Bien SA, Lin Y, Hu Z, Shen H, Wu K, Giovannucci EL, Song M. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000801 (GRS40_CRC) |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Colorectal cancer | colorectal cancer | 40 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000801/ScoringFiles/PGS000801.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM002087 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Advanced conventional adenoma | OR: 1.22 [1.16, 1.28] | — | Odds Ratio (OR, top 20% vs bottom 20%): 1.91 [1.59, 2.29] | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002092 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Multiple conventional adenomas | OR: 1.25 [1.17, 1.34] | — | — | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002093 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Multiple serrated polyps | OR: 1.09 [1.01, 1.18] | — | — | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002085 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Conventional adeonma | OR: 1.17 [1.12, 1.21] | — | Odds Ratio (OR, top 20% vs bottom 20%): 1.63 [1.44, 1.83] | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002086 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Non-advanced conventional adenoma | OR: 1.12 [1.07, 1.18] | — | Odds Ratio (OR, top 20% vs bottom 20%): 1.44 [1.23, 1.68] | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002088 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Serrated polyp | OR: 1.09 [1.03, 1.14] | — | Odds Ratio (OR, top 20% vs bottom 20%): 1.24 [1.06, 1.45] | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002089 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Serrated polyp with high risk of malignancy | OR: 1.1 [1.01, 1.19] | — | — | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002090 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Serrated polyp with low risk of malignancy | OR: 1.08 [1.02, 1.15] | — | Odds Ratio (OR, top 20% vs bottom 20%): 1.25 [1.03, 1.53] | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
| PPM002091 | PGS000801 (GRS40_CRC) |
PSS001030| European Ancestry| 27,426 individuals |
PGP000190 | Hang D et al. Int J Epidemiol (2020) |
Reported Trait: Synchronous conventional adenoma and serrated polyp | OR: 1.24 [1.16, 1.32] | — | Odds Ratio (OR, top 20% vs bottom 20%): 1.96 [1.54, 2.49] | Study cohort (NHS, NHSII, HPFS), time period of endoscopy (in 2-year interval), number of previous endoscopies, time in years since the most recent endoscopy, age, PCs(1-3) | Effect weights for SNPs within the PGS were obtained using the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) dataset. The GECCO dataset had no overlap with the dataset used to evaluate the score. |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS001030 | Cases included individuals with polyps. Of the 5331 cases, 2952 had conventional adenomas (CAs), 1585 had serrated polyps (SAs) and 794 had sychronous CAs and SPs. CAs were defined as tubular, tubulovillous and villous adenomas and adenomas with high-grade dysplasia. Advanced CAs were defined by at least one CA ≥10 mm in diameter or with advanced histology (tubulovillous/villous histological features or high-grade/severe dysplasia) or ≥3 CAs regardless of histology or size. SPs were defined as hyperplastic polyps and mixed/serrated adenomas. Individuals at high risk of malignancy were defined as having SPs located in the proximal colon or with a size of ≥10 mm. Mixed/serrated ademonas were defined as both mixed polyps (those with both adenomatous and hyperplastic changes in histology) and polyps with any serrated diagnosis (e.g. serrated adenomas, serrated polyps and SSA/Ps). If a participant had both CAs and SPs in an endoscopy, each type of the polyps were recorded separately, and considered the patient as a synchronous SP and CA case. | — | [ ,
30.0 % Male samples |
Mean = 63.2 years Sd = 10.0 years |
European | — | HPFS, NHS, NHS2 | — |