High-throughput sequencing in respiratory, critical care, and sleep medicine research an official American thoracic society workshop report

Craig P. Hersh, Ian M. Adcock, Juan C. Celedón, Michael H. Cho, David C. Christiani, Blanca E. Himes, Naftali Kaminski, Rasika 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. Koppelman

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1-16
Number of pages16
JournalAnnals of the American Thoracic Society
Volume16
Issue number1
DOIs
StatePublished - Jan 1 2019

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Critical Care
Sleep
Thorax
Medicine
Education
Research
Practice Guidelines
Research Ethics
RNA Sequence Analysis
Molecular Epidemiology
Manuscripts
Microbiota
Genomics
Computational Biology
DNA Sequence Analysis
Cystic Fibrosis
Biomedical Research
Lung Neoplasms
Chronic Disease
Physicians

Keywords

  • Bioinformatics
  • Functional genomics
  • Genetic epidemiology
  • RNA sequencing
  • Whole-genome sequencing

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine

Cite this

High-throughput sequencing in respiratory, critical care, and sleep medicine research an official American thoracic society workshop report. / Hersh, Craig P.; Adcock, Ian M.; Celedón, Juan C.; Cho, Michael H.; Christiani, David C.; Himes, Blanca E.; Kaminski, Naftali; Mathias, Rasika; Meyers, Deborah A.; Quackenbush, John; Redline, Susan; Steiling, Katrina A.; Tabor, Holly K.; Tobin, Martin D.; Wurfel, Mark M.; Yang, Ivana V.; Koppelman, Gerard H.

In: Annals of the American Thoracic Society, Vol. 16, No. 1, 01.01.2019, p. 1-16.

Research output: Contribution to journalArticle

Hersh, CP, Adcock, IM, Celedón, JC, Cho, MH, Christiani, DC, Himes, BE, Kaminski, N, Mathias, R, Meyers, DA, Quackenbush, J, Redline, S, Steiling, KA, Tabor, HK, Tobin, MD, Wurfel, MM, Yang, IV & Koppelman, GH 2019, 'High-throughput sequencing in respiratory, critical care, and sleep medicine research an official American thoracic society workshop report', Annals of the American Thoracic Society, vol. 16, no. 1, pp. 1-16. https://doi.org/10.1513/AnnalsATS.201810-716WS
Hersh, Craig P. ; Adcock, Ian M. ; Celedón, Juan C. ; Cho, Michael H. ; Christiani, David C. ; Himes, Blanca E. ; Kaminski, Naftali ; Mathias, Rasika ; Meyers, Deborah A. ; Quackenbush, John ; Redline, Susan ; Steiling, Katrina A. ; Tabor, Holly K. ; Tobin, Martin D. ; Wurfel, Mark M. ; Yang, Ivana V. ; Koppelman, Gerard H. / High-throughput sequencing in respiratory, critical care, and sleep medicine research an official American thoracic society workshop report. In: Annals of the American Thoracic Society. 2019 ; Vol. 16, No. 1. pp. 1-16.
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