|
2
|
Ruan E, Nemeth E, Moffitt R, Sandoval L, Machiela MJ, Freedman ND, Huang WY, Wong W, Chen KL, Park B, Jiang K, Hicks B, Liu J, Russ D, Minasian L, Pinsky P, Chanock SJ, Garcia-Closas M, Almeida JS. PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project. Bioinformatics 2022; 38:4434-4436. [PMID: 35900159 PMCID: PMC9890300 DOI: 10.1093/bioinformatics/btac531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION The Division of Cancer Epidemiology and Genetics (DCEG) and the Division of Cancer Prevention (DCP) at the National Cancer Institute (NCI) have recently generated genome-wide association study (GWAS) data for multiple traits in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Genomic Atlas project. The GWAS included 110 000 participants. The dissemination of the genetic association data through a data portal called GWAS Explorer, in a manner that addresses the modern expectations of FAIR reusability by data scientists and engineers, is the main motivation for the development of the open-source JavaScript software development kit (SDK) reported here. RESULTS The PLCO GWAS Explorer resource relies on a public stateless HTTP application programming interface (API) deployed as the sole backend service for both the landing page's web application and third-party analytical workflows. The core PLCOjs SDK is mapped to each of the API methods, and also to each of the reference graphic visualizations in the GWAS Explorer. A few additional visualization methods extend it. As is the norm with web SDKs, no download or installation is needed and modularization supports targeted code injection for web applications, reactive notebooks (Observable) and node-based web services. AVAILABILITY AND IMPLEMENTATION code at https://github.com/episphere/plco; project page at https://episphere.github.io/plco.
Collapse
Affiliation(s)
- Eric Ruan
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Erika Nemeth
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Richard Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Lorena Sandoval
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Wendy Wong
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Kai-Ling Chen
- Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA
| | - Brian Park
- Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA
| | - Kevin Jiang
- Center for Biomedical Informatics and Information Technology (CBIIT), National Cancer Institute, Rockville, MD 20850, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Jia Liu
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Daniel Russ
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Lori Minasian
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Paul Pinsky
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, Rockville, MD 20850, USA
| | | |
Collapse
|
|
3
|
Reyes Nieva H, Ruan E, Schiff G. ISQUA18-2032Primary Care Physician-Patient Boundaries: Results of a National US Survey and Polling on Views and Practices. Int J Qual Health Care 2018. [DOI: 10.1093/intqhc/mzy167.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- H Reyes Nieva
- Brigham and Women’s Hospital
- Harvard Medical School, Boston
- Johns Hopkins Bloomberg School of Public Health, Baltimore
| | - E Ruan
- Brigham and Women’s Hospital
- Tufts University School of Medicine, Boston, United States
| | - G Schiff
- Brigham and Women’s Hospital
- Harvard Medical School, Boston
| |
Collapse
|
|
4
|
Abstract
Antioxidants may delay or prevent neural diseases. Depletion of the non-enzymatic antioxidant, glutathione, in a mouse model was produced by inhibiting its rate-limiting enzyme, gamma-glutamylcysteine synthetase, for 7 weeks. Ileum and colon were obtained from treated and control (saline) mice. Glutathione levels and nicotinamide adenine dinucleotide phosphate (NADPH) diaphorase activity were determined by spectrophotometric assays; vasoactive intestinal peptide (VIP) levels were measured by radioimmunoassay. Glutathione levels were higher in ileum than colon. Colonic glutathione was decreased in treated mice compared to controls; there were no differences in ileal glutathione levels. VIP was decreased in ileum compared to controls, while NADPH diaphorase activity was decreased in colon compared to controls. In this chronic mouse model, glutathione appeared to regulate expression of enteric inhibitory nerve cell products.
Collapse
Affiliation(s)
- T R Koch
- Department of Medicine, LA Johnson VA Medical Center, West Virginia University, Morgantown 26506-9161, USA
| | | | | | | | | |
Collapse
|