Abstract
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 (n = 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.
Highlights
Development of Next-Generation Sequencing (NGS), or HighThroughput Sequencing (HTS), has revolutionized life sciences, dramatically increasing the variety of questions that can be answered using genomic sequence data
In detail: (i) List of library preparation kits used by core Department of Defense (DoD) for different projects and specimens were highlighted; (ii) Several topics on types of kits for viruses, bacteria and parasite work were heavily discussed throughout the lecture; (iii) Specific library preparation kits were highlighted including TruSeq, QIASeq Fx, Kappa, NexteraXT, RNA Access and DNAFlex; (iv) AmpureXP Beads clean up after PCR reactions and library preparation was emphasized as preferred method; (v) Different library validations, including qPCR, Qubit and TapeStation were highlighted as essentials for quality control (QC); (vi) Library pooling based on TapeStation and Qubit were introduced; (vii) Two exercises of how to calculate amount of each library for pooling were conducted
The wet lab lectures could be adjusted to cover: (i) the theory of targeted sequencing, which is mainly used in response to epidemics and outbreaks of known pathogens; and (ii) the theory of metagenomics, which is usually used for pathogen discovery and identification
Summary
Development of Next-Generation Sequencing (NGS), or HighThroughput Sequencing (HTS), has revolutionized life sciences, dramatically increasing the variety of questions that can be answered using genomic sequence data With this continuously evolving and growing field, the need for adequate computational hardware resources, software, and expertise to analyze large and complex data is increasing. Utilizing a global network of partner DoD medical research and public health laboratories, GEIS funds surveillance activities in over 70 countries to inform force health protection through timely and actionable infectious disease surveillance information (Chakhunashvili et al, 2017; Chang et al, 2018; Coleman et al, 2018; Koka et al, 2018; Anyamba et al, 2019; Guerra et al, 2019; Juma et al, 2019; Rivers et al, 2019; Rocha et al, 2019; Sugiharto et al, 2019). In spite of great interest in this technology, only a few partner laboratories have been adequately equipped to utilize these approaches to their full potential
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