| Publication Information (EuropePMC) | |
| Title | Prevalence and Effect of Genetic Risk of Thromboembolic Disease in Inflammatory Bowel Disease. |
| PubMed ID | 33098885(Europe PMC) |
| doi | 10.1053/j.gastro.2020.10.019 |
| Publication Date | Oct. 21, 2020 |
| Journal | Gastroenterology |
| Author(s) | Naito T, Botwin GJ, Haritunians T, Li D, Yang S, Khrom M, Braun J, NIDDK IBD Genetics Consortium, Abbou L, Mengesha E, Stevens C, Masamune A, Daly M, McGovern DPB. |
| 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) |
|---|---|---|---|---|---|---|
| PGS000043 (PRS_VTE) |
PGP000030 | Klarin D et al. Nat Genet (2019) |
Venous thromboembolism | venous thromboembolism | 297 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000043/ScoringFiles/PGS000043.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM001639 | PGS000043 (PRS_VTE) |
PSS000850| European Ancestry| 715 individuals |
PGP000133 | Naito T et al. Gastroenterology (2020) |Ext. |
Reported Trait: Thromboembolic disease event in individuals with inflammatory bowel disease | — | — | Odds Ratio (OR, top 5% vs. remaining 95%): 2.7 [1.03, 7.09] | Age at last visit, PCs(1-2) | Included 265/297 variants from the original score |
| PPM001640 | PGS000043 (PRS_VTE) |
PSS000850| European Ancestry| 715 individuals |
PGP000133 | Naito T et al. Gastroenterology (2020) |Ext. |
Reported Trait: Thromboembolic disease event in individuals with inflammatory bowel disease | — | — | Odds Ratio (OR, top 5% vs. remaining 95%): 3.13 [1.37, 7.18] | Disease duration, age at disease onset, PCs(1-2) | Included 265/297 variants from the original score |
| PPM001641 | PGS000043 (PRS_VTE) |
PSS000850| European Ancestry| 715 individuals |
PGP000133 | Naito T et al. Gastroenterology (2020) |Ext. |
Reported Trait: Thromboembolic disease event in in individuals of inflammatory bowel disease that are carriers of at least 1 thrombophillia pathogenic variant | — | — | Odds Ratio (OR, top 5% vs. remaining 95%): 8.56 [1.76, 41.57] | Age at last visit, PCs(1-2) | Included 265/297 variants from the original 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 |
|---|---|---|---|---|---|---|---|---|
| PSS000850 | All individuals had inflammatory bowel disease, defined on the basis of clinical symptoms as well as standard endoscopic, radiographic and histologic findings. Cases are individuals with a thromboembolic disease (TED) event. Disease activity at the time of TED for Chron's disease was measured by the Harvey-Bradshaw Index and colonoscopy report at the time of clotting event (when available). Patients were considered to have active disease if they had Harvey-Bradshaw Index scores !5 and/or endoscopy showed active disease, Disease activity at the time of TED for Ulcerative Colitis was evaluated by the full Mayo score. A full Mayo score >2 was considered as active disease. | — | [ ,
53.3 % Male samples |
— | European | — | CSMC | — |