title: Unsolved challenges of clinical whole-exome sequencing: a systematic literature review of end-users' views.
abstract: Whole-exome sequencing (WES) consists in the capture, sequencing and analysis of all exons in the human genome. Originally developed in the research context, this technology is now increasingly used clinically to inform patient care. The implementation of WES into healthcare poses significant organizational, regulatory, and ethical hurdles, which are widely discussed in the literature.
  
  
  
  In order to inform future policy decisions on the integration of WES into standard clinical practice, we performed a systematic literature review to identify the most important challenges directly reported by technology users.
  
  
  
  Out of 2094 articles, we selected and analyzed 147 which reported a total of 23 different challenges linked to the production, analysis, reporting and sharing of patients' WES data. Interpretation of variants of unknown significance, incidental findings, and the cost and reimbursement of WES-based tests were the most reported challenges across all articles.
  
  
  
  WES is already used in the clinical setting, and may soon be considered the standard of care for specific medical conditions. Yet, technology users are calling for certain standards and guidelines to be published before this technology replaces more focused approaches such as gene panels sequencing. In addition, a number of infrastructural adjustments will have to be made for clinics to store, process and analyze the amounts of data produced by WES.
authors: Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada. gabrielle.bertier@mail.mcgill.ca.|UMR 1027, Inserm, University of Toulouse III - Paul Sabatier, 37 allées Jules Guesde, F-31000, Toulouse, France. gabrielle.bertier@mail.mcgill.ca.
authors: Gabrielle
authors: 0000-0002-3319-3721
authors: G
authors: Bertier
authors: Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada.
authors: Martin
authors: M
authors: Hétu
authors: Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada.
authors: Yann
authors: Y
authors: Joly
mesh_terms: D059472:Exome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*