Validation of high throughput sequencing and microbial forensics applications

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• 作者：Bruce Budowle (1) (2)
  Nancy D Connell (3)
  Anna Bielecka-Oder (4)
  Rita R Colwell (5) (6) (7) (8)
  Cindi R Corbett (10) (9)
  Jacqueline Fletcher (11)
  Mats Forsman (12)
  Dana R Kadavy (13)
  Alemka Markotic (14)
  Stephen A Morse (15)
  Randall S Murch (16)
  Antti Sajantila (1) (17)
  Sarah E Schmedes (1)
  Krista L Ternus (13)
  Stephen D Turner (18)
  Samuel Minot (13)
  
  1. Department of Molecular and Medical Genetics ; Institute of Applied Genetics ; University of North Texas Health Science Center ; Fort Worth ; Texas ; USA
  2. Center of Excellence in Genomic Medicine Research (CEGMR) ; King Abdulaziz University ; Jeddah ; Saudi Arabia
  3. Rutgers New Jersey Medical School ; Center for Biodefense ; Rutgers University ; Newark ; New Jersey ; USA
  4. Department of Epidemiology ; The General K. Kaczkowski Military Institute of Hygiene and Epidemiology ; Warsaw ; Poland
  5. CosmosID庐 ; 387 Technology Dr ; College Park ; MD ; USA
  6. Maryland Pathogen Research Institute ; University of Maryland ; College Park ; MD ; USA
  7. University of Maryland Institute for Advanced Computer Studies ; University of Maryland ; College Park ; MD ; USA
  8. Bloomberg School of Public Health ; Johns Hopkins University ; Baltimore ; MD ; USA
  10. Department of Medical Microbiology ; University of Manitoba ; Winnipeg ; Canada
  9. Bioforensics Assay Development and DiagnosticsSection ; Science Technology and Core Services Division ; National Microbiology Laboratory ; Winnipeg ; MB ; Canada
  11. National Institute for Microbial Forensics & Food and Agricultural Biosecurity ; Oklahoma State University ; Stillwater ; OK ; USA
  12. Division of CBRN Defence and Security ; Swedish Defence Research Agency ; Ume氓 ; Sweden
  13. Signature Science ; LLC ; Austin ; TX ; USA
  14. University Hospital for Infectious Diseases 鈥淔ran Mihaljevic鈥?and Medical School University of Rijeka ; Zagreb ; Croatia
  15. Division of Foodborne ; Waterborne ; and Environmental Diseases ; National Center for Emerging and Zoonotic Infectious Diseases ; Centers for Disease Control and Prevention ; Atlanta ; Georgia
  16. Virginia Tech ; National Capital Region ; Arlington ; VA ; USA
  17. Department of Forensic Medicine ; Hjelt Institute ; University of Helsinki ; Helsinki ; Finland
  18. Public Health Sciences ; Bioinformatics Core Director ; University of Virginia School of Medicine ; Charlottesville ; VA ; USA
  
• 关键词：Microbial forensics ; Validation ; High throughput sequencing ; Sample preparation ; Library preparation ; Bioinformatics
• 刊名：Investigative Genetics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：5
• 期：1
• 全文大小：734 KB
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• 刊物主题：Human Genetics; Forensic Science; Evolutionary Biology; Microbiology; Forensic Medicine;
• 出版者：BioMed Central
• ISSN：2041-2223

文摘

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security.