A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya.
Irina Maljkovic Berry, Wiriya Rutvisuttinunt, Logan J Voegtly, Karla Prieto, Simon Pollett, Regina Z Cer, Jeffrey R Kugelman, Kimberly A Bishop-Lilly, Lindsay Morton, John Waitumbi, Richard G Jarman
Author Information
Irina Maljkovic Berry: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.
Wiriya Rutvisuttinunt: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.
Logan J Voegtly: Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.
Karla Prieto: College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States.
Simon Pollett: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.
Regina Z Cer: Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.
Jeffrey R Kugelman: Center for Genomic Studies, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, United States.
Kimberly A Bishop-Lilly: Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.
Lindsay Morton: Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, MD, United States.
John Waitumbi: Basic Science Laboratory, US Army Medical Research Directorate-Africa/Kenya Medical Research Institute, Kisumu, Kenya.
Richard G Jarman: Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.
Epidemics of emerging and re-emerging infectious diseases are a danger to civilian and military populations worldwide. Health security and mitigation of infectious disease threats is a priority of the United States Government and the Department of Defense (DoD). Next generation sequencing (NGS) and Bioinformatics (BI) enhances traditional biosurveillance by providing additional data to understand transmission, identify resistance and virulence factors, make predictions, and update risk assessments. As more and more laboratories adopt NGS and BI technologies they encounter challenges in building local capacity. In addition to choosing the right sequencing platform and approach, considerations must also be made for the complexity of bioinformatics analyses, data storage, as well as personnel and computational requirements. To address these needs, a comprehensive training program was developed covering wet lab and bioinformatics approaches to NGS. The program is meant to be modular and adaptive to meet both common and individualized needs of medical research and public health laboratories across the DoD. The training program was first deployed internationally to the Basic Science Laboratory of the US Army Medical Research Directorate-Africa in Kisumu, Kenya, which is an overseas Lab of the Walter Reed Army Institute of Research (WRAIR). A week-long workshop with intensive focus on targeted sequencing and the bioinformatics of genome assembly ( = 24 participants) was held. Post-workshop self-assessment (completed by 21 participants) noted significant median gains in knowledge domains related to NGS targeted sequencing, bioinformatics for genome assembly, and sequence quality assessment. The participants also reported that the information on study design, sample preparation, sequencing quality control, data quality assessment, reporting, and basic and advanced bioinformatics analysis were the most useful information presented in the training. While longer-term evaluations are planned, the training resulted in significant short-term improvement of a laboratory's self-reported wet lab and bioinformatics capabilities. This framework can be used for future DoD laboratory development in the area of NGS and BI for infectious disease surveillance, ultimately enhancing this global DoD capability.
