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