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Survey Highlights Successes and Challenges for Early Adopters of Clinical NGS


This article was originally published July 29.

NEW YORK (GenomeWeb) — As interest in using clinical sequencing to personalize medicine begins to expand past the initial vanguard of early adopters, researchers from several institutions participating in a College of American Pathologists workgroup have attempted to tease out some of the decision-making behind the implementation of these pioneering programs in hopes of helping to guide the future spread of genomic medicine.

The team, led by James Crawford, chair of the department of pathology at the North Shore-Long Island Jewish Health System, published results of its survey of 13 academic institutions identified as some of the earliest to move next-gen sequencing into their clinical laboratories this month in Genetics in Medicine.

In the study, the researchers recruited laboratory directors and/or pathology department chairs from these 13 centers to undergo a one-hour telephone interview focused on the business side of implementing genomic medicine, combining a number of pre-set questions with other potential elaborative subquestions, as well as the opportunity for spontaneous discussion.

The survey found that, overall, several themes dominated among those cited by early adopters as an impetus for initiating clinical sequencing. For one, most respondents to the survey said that demand for NGS testing from clinicians, most often oncologists, was a major factor in the decision of their institution to adopt it. An equally dominant catalyst, according to the study authors, was an expectation that NGS testing would, ultimately, be more efficient than single-gene testing methods.

Crawford, the study's first author, told CSN that as chair of the CAP working group, he wanted to make sure that the result of the study was more than just anecdotes.

"It took a long time to think through how to analyze the data," he said. "I think the survey addressed what we wanted to address, but to me, the missing piece that I would still like to see filled in would be to go back to the same people and ask how [things are going] two years on, both in terms of deployment and in terms of efficacy and utility."

Of the group of institutions studied, only four were offering NGS testing clinically at the time of the interviews in 2012, while seven said they expected to begin clinical sequencing within six to 12 months, and one other felt its timeline was uncertain.

Ten of the institutions indicated that cancer genomics was or would be their primary clinical application for NGS, while the remaining three were focused on medical genetics.

With one exception, Crawford and his coauthors reported that early adopter institutions did not expect clinical NGS to be financially self-sustainable in the near future, although most reported having established systems for seeking payor reimbursement. The majority of respondents anticipated that their programs would continue to consume institutional resources, including research funds into the future.

In discussing their strategies for implementing clinical sequencing, the respondents described three main approaches. First, interviewees suggested that NGS might be overlaid on existing or established single-gene tests already in an institution's clinical test menu before the service should be expanded.

Additionally, respondents recommended beginning with commercially validated NGS testing platforms, or with limited NGS panels for specific applications, before expanding a test menu to more customized services. According to the study authors, respondents cited the question of whether to start with commercially available products or custom panels as a critical early decision in the process, and varied in their preference for one strategy or the other.

Twelve of the 13 respondents expressed that they believed adopting clinical NGS gave them a competitive market advantage over other institutions.

Though the survey was not focused on challenges and barriers — only one question asked about "lessons learned" in the process of enacting clinical genomics — respondents frequently mentioned issues they faced off the cuff during their interviews, the authors wrote.

According to the study, a recurrent theme was the challenge of having or acquiring appropriate expertise in informatics. This was mentioned as a significant barrier by seven of the interviewees. Many also responded that rapidly changing technologies offered a challenge.

Respondents also cited lessons learned in their implementation of clinical sequencing, including the fact that deploying a clinical NGS service was more complicated and took longer than they expected, and that a multidisciplinary team is helpful or necessary in this process.

In their own words interviewees highlighted the importance of optimizing an appropriate gene panel. "If you are going to be a leader … these panels must be tested and validated before clinical implementation," one respondent said. "It is a lot easier to generate the data than [to] interpret it," responded another.

Another cited a need to respect the limitations as well as the potential of NGS. "For testing small regions of the genome, NGS may not be the preferred technology," they said.

According to Crawford and his coauthors, the study was not intended to determine whether implementing NGS was a sound or a successful decision for these early adopters, but rather to collect information on the considerations that went into the adoption of genomic medicine for these institutions. Such information could aid those making similar decisions in the future, at least while evidence for the ultimate utility of clinical sequencing to personalize medical treatment remains lacking.

Respondents in the study had relatively little to share on the subject of the ultimate value of clinical NGS, or about how they planned to try to measure the success of their activities.

"They had operational proxies: questions like 'does volume grow?' or 'how do people respond to the service?' But figuring out if this is the right thing to do — it's not yet a mature science," Crawford said.

"The real challenge is in showing that having this genomic information is better than prior testing methods … I think we are better now positioned than we ever have been before to answer those questions, but it's still open," he added.

In the meantime, Crawford said the working group hoped that their survey, focused on the views of clinical NGS mainly from the perspective of laboratory directors and administrators — those in the position to actually decide to bring genomic medicine to their institution or not — alongside other studies that have surveyed clinicians and other genomics professionals, would be a resource for others as interest in clinical implementation of NGS technologies continues to grow.