Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity
Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity
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DOI：
10.1093/infdis/jiz286
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发表时间：
2020-04-15
影响因子：
6.4
通讯作者：
Jarman, Richard G.
中科院分区：
文献类型：
--
作者：
Berry, Irina Maljkovic;Melendrez, Melanie C.;Jarman, Richard G.
与生物信息学相结合的新一代测序技术已经成功地应用于与公共卫生相关的传染病研究的大量分析中。例如，NGS和生物信息学方法已用于确定疫情起源、追踪传播、调查流行动态、确定疾病的病原以及发现新的人类病原体。然而，在研究和公共卫生实验室实施高质量的NGS和生物信息学可能具有挑战性。这些挑战主要包括测序平台和测序方法的选择，生物信息学方法的选择，获得适当的计算和信息技术基础设施，以及招聘和留住具有该领域专业技能和经验的人员。在本文中，我们总结了传染病基因组监测和病原体发现中最常见的NGS和生物信息学工作流程，并强调了建立一个以NGS和生物信息学为重点的传染病研究公共卫生实验室的主要挑战和考虑因素。我们描述了最常用的测序平台，并回顾了它们的优点和缺点。我们回顾了用于各种病原体和研究问题的测序方法，以及在公共卫生或研究环境中实施这些方法时应考虑的与这些方法相关的最常见困难。此外，我们还提供了一些用于病原体发现和基因组组装的常见生物信息学工具和程序的综述，以及最常见的挑战和解决方案。最后，我们总结了高级病毒、细菌和寄生虫病原体表征的生物信息学，包括利用NGS和生物信息学可以回答的研究问题类型。
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.