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High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research An Official American Thoracic Society Workshop Report
journal contribution
posted on 2020-03-06, 15:48 authored by Craig P. Hersh, Ian M. Adcock, Juan C. Celedon, Michael H. Cho, David C. Christiani, Blanca E. Himes, Naftali Kaminski, Rasika A. Mathias, Deborah A. Meyers, John Quackenbush, Susan Redline, Katrina A. Steiling, Holly K. Tabor, Martin D. Tobin, Mark M. Wurfel, Ivana V. Yang, Gerard H. KoppelmanHigh-throughput, “next-generation” sequencing methods are now being broadly applied across all fields of biomedical research, including respiratory disease, critical care, and sleep medicine. Although there are numerous review articles and best practice guidelines related to sequencing methods and data analysis, there are fewer resources summarizing issues related to study design and interpretation, especially as applied to common, complex, nonmalignant diseases. To address these gaps, a single-day workshop was held at the American Thoracic Society meeting in May 2017, led by the American Thoracic Society Section on Genetics and Genomics. The aim of this workshop was to review the design, analysis, interpretation, and functional follow-up of high-throughput sequencing studies in respiratory, critical care, and sleep medicine research. This workshop brought together experts in multiple fields, including genetic epidemiology, biobanking bioinformatics, and research ethics, along with physician-scientists with expertise in a range of relevant diseases. The workshop focused on application of DNA and RNA sequencing research in common chronic diseases and did not cover sequencing studies in lung cancer, monogenic diseases (e.g., cystic fibrosis), or microbiome sequencing. Participants reviewed and discussed study design, data analysis and presentation, interpretation, functional follow-up, and reporting of results. This report summarizes the main conclusions of the workshop, specifically addressing the application of these methods in respiratory, critical care, and sleep medicine research. This workshop report may serve as a resource for our research community as well as for journal editors and reviewers of sequencing-based manuscript submissions in our research field.
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Citation
Ann Am Thorac Soc. 2019 Jan;16(1):1-16Author affiliation
Department of Health SciencesVersion
- VoR (Version of Record)
Published in
Annals of the American Thoracic SocietyVolume
16Issue
1Pagination
1 - 16 (16)Publisher
American Thoracic Societyissn
1546-3222eissn
2325-6621Copyright date
2019Available date
2019-01-01Publisher DOI
Publisher version
https://www.atsjournals.org/doi/full/10.1513/AnnalsATS.201810-716WSSpatial coverage
United StatesLanguage
EnglishUsage metrics
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Keywords
Science & TechnologyLife Sciences & BiomedicineRespiratory Systembioinformaticsfunctional genomicsgenetic epidemiologyRNA sequencingwhole-genome sequencingGENOME-WIDE ASSOCIATIONOBSTRUCTIVE PULMONARY-DISEASEDIFFERENTIALLY EXPRESSED GENESRNA-SEQ DATALUNG-FUNCTIONDISTRESS-SYNDROMEQUALITY-CONTROLREAD ALIGNMENTEXOMEGENERATION
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