Lab Matters Summer 2016 | Page 6

infectious diseases Focus Groups Identify Common NGS Challenges and Obstacles by Christin L. Hanigan, PhD, senior specialist, Advanced Molecular Detection In the past two years, an increasing number of state and local public health laboratories (PHLs) have implemented or are planning to implement next generation sequencing (NGS) in their laboratories. In May 2016, APHL convened three focus groups with 18 participating state and local PHLs to discuss challenges and potential solutions surrounding the implementation and use of NGS technologies. The purpose of these groups was to engage states that have recently adopted NGS technology; gain a better understanding of the current challenges and barriers that the participants have faced incorporating it into their laboratory workflow; and identify strategies to overcome those challenges. The focus groups consisted of five to six PHL members and were facilitated by PHL leaders with well-established NGS programs. The Advance Molecular Detection Initiative has brought increased funding and urgency to implementation of next generation sequencing in public health laboratories. CHALLENGES IDENTIFIED POTENTIAL SOLUTIONS Participants provided valuable insight into challenges that laboratories have been facing throughout the NGS implementation process, including the initial procurement of an instrument, staff training and incorporation with current workflows. Common discussion themes included the challenges around adopting new molecular based technologies, the need for bioinformatics tools and support, training/guidance for best practices and protocols, and data storage needs. Several PHL members shared ways they have addressed challenges, as well as resources that they would like to see as they move forward. Multiple participants spoke of benefits gained through collaboration with other PHLs. For example, one laboratory spoke of establishing a relationship with a “mentor lab” during the set-up process, describing how much easier and faster it was to have expertise located in a similar geographic region and able to give more practical and real-time assistance. The basic question of “what to do with the data?” was a common topic among the focus groups. Also, as laboratories expanded beyond foodborne pathogens, the data analysis tools and NGS applications for other pathogens were not as well known or understood. Getting support from jurisdictional epidemiologists and training them to understand how to utilize the data was identified as a critical step in making full use of NGS data. Collaboration was also noted as a valuable resource for bioinformatics support. Collaboration with other PHLs with those capabilities or with local universities was suggested as a potential solution. However, some laboratories noted they had difficulties finding collaborators at academic institutions. There seemed to be a great desire for more mechanisms for collaboration between states to share experience and knowledge, and synergistically tackle some common issues. Funding is another common challenge for PHLs. The cost of implementation often goes beyond the cost of the instrument itself and includes the ancillary equipment, the added cost of reagents and staff time. As laboratories look to the future and how this technology can be incorporated and utilized to its fullest potential, sustainable funding is a definite need. 4 LAB MATTERS Summer 2016 Regardless of the challenges facing laboratories, all were excited about the potential that NGS technology brings to the public health arena. As one participant noted, “NGS [is] the future, and if we don’t bring it on and figure it out, there’s no future for the state labs.” PublicHealthLabs @APHL APHL.org