2381/11816670.v1 Craig P. Hersh Craig P. Hersh Ian M. Adcock Ian M. Adcock Juan C. Celedon Juan C. Celedon Michael H. Cho Michael H. Cho David C. Christiani David C. Christiani Blanca E. Himes Blanca E. Himes Naftali Kaminski Naftali Kaminski Rasika A. Mathias Rasika A. Mathias Deborah A. Meyers Deborah A. Meyers John Quackenbush John Quackenbush Susan Redline Susan Redline Katrina A. Steiling Katrina A. Steiling Holly K. Tabor Holly K. Tabor Martin D. Tobin Martin D. Tobin Mark M. Wurfel Mark M. Wurfel Ivana V. Yang Ivana V. Yang Gerard H. Koppelman Gerard H. Koppelman High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research An Official American Thoracic Society Workshop Report University of Leicester 2020 Science & Technology Life Sciences & Biomedicine Respiratory System bioinformatics functional genomics genetic epidemiology RNA sequencing whole-genome sequencing GENOME-WIDE ASSOCIATION OBSTRUCTIVE PULMONARY-DISEASE DIFFERENTIALLY EXPRESSED GENES RNA-SEQ DATA LUNG-FUNCTION DISTRESS-SYNDROME QUALITY-CONTROL READ ALIGNMENT EXOME GENERATION 2020-03-06 15:48:01 Journal contribution https://figshare.le.ac.uk/articles/journal_contribution/High-Throughput_Sequencing_in_Respiratory_Critical_Care_and_Sleep_Medicine_Research_An_Official_American_Thoracic_Society_Workshop_Report/11816670 High-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.