Next generation sequencing (NGS) promises to transform the delivery of health care by providing in one test diagnostic and prognostic information that had previously only been available in multiple analyses. One application of the information obtained from NGS is as a companion diagnostic for a therapeutic. A significant reduction in the overall cost to sequence the complete genome, most notably Illumina’s announcement of the “$1,000 genome,” makes NGS an attractive alternative to current locus-by-locus genetic analysis, and raises the prospect of near-term adoption of NGS in clinical medicine. This post will review some current opinions on NGS and whether the technology is ready for use in diagnostic and therapeutic development.
Translating Genomic-Based Research for Health
The potential for, and the challenges with, incorporating NGS into the co-development of targeted therapeutics and companion molecular tests was addressed in depth by a variety of stakeholders in Refining Processes for the Co-Development of Genome-Based Therapeutics and Companion Diagnostic Tests: Workshop Summary (Workshop) and the findings summarized in its recently published report (Report).
The Workshop was an outgrowth of the National Academies of Science’s prior work regarding the establishment of clinical utility data for genomic technologies by the Academies’ Roundtable on Translating Genomic-Based Research for Health. The Workshop was convened last year to examine and discuss potential solutions for the co-development of diagnostics and therapeutics. A wide range of perspectives were represented: patients, providers, clinical laboratories, the Food and Drug Administration (FDA), and payers.
A Regulatory Perspective
Elizabeth Mansfield, director of the personalized medicine staff in the Office of In Vitro Diagnostics and Radiologic Health at the FDA was a key participant representing a perspective on the regulatory challenges facing the use of NGS in diagnostic and therapeutic co-development. Dr. Mansfield remarked that the FDA understood the importance of NGS in clinical care and the opportunities it provides. In addition, but remarking on behalf of herself and not the FDA, she noted that “in the future, next-generation sequencing could report only mutations that have known drug safety or efficacy correlations,.. with additional data being retained for investigational use… As new information becomes available, new drugs could be approved, which would greatly increase the efficiency of the approval process.” She added that however “even in co-development… not everyone who has [a particular] marker actually benefits from the drug. So we’re still not there yet, even with next-generation sequencing.”
Patients, Providers and Laboratories
Representatives from these end users commented that NGS may solve some of the issues around cost and reimbursement that impede current diagnostic development. John Pfeifer, vice chair for clinical affairs, pathology and professor at Washington University School of Medicine stated that NGS could be the ultimate companion diagnostic but that several threshold issues need to be addressed prior to adoption, such as how to select the appropriate technology, how to improve reproducibility of the bioinformatics analysis, and how NGS would be regulated.
Mark Robson, clinical director of the clinical genetics service in the Department of Human Genetics at Memorial Sloan-Kettering Cancer Center noted that Memorial Sloan-Kettering is currently using NGS where potential germline predispositions are difficult to define phenotypically. He remarked that NGS is useful for diseases that are due to a number of factors which are difficult to sort out and very expensive to test serially.
The Report noted an interesting observation with respect to cost. It may be assumed that because sequencing and analysis is accomplished for the complete genome at one time, NGS and its application should reduce health care costs. That is not necessarily true. Wylie Burke, professor and chair, Department of Bioethics and Humanities, University of Washington, noted that “while genomic technology could improve quality of care and reduce costs, it also has the potential to drive costs upward because there is a temptation to acquire as much data as possible…The health care system cannot afford to pay for all of the research that needs to be done to determine the utility of genomic information.” Pfeifer observed other ways genomics can add costs, for example, tests being ordered for patients that are not well enough to benefit from the results.
Payers and Regulators
Sharon Terry, president and chief executive officer of the Genetic Alliance, opined that NGS would provide unique regulatory and reimbursement challenges because it provides more information than just a single companion diagnostic. Joanne Armstrong, a senior medical director for Aetna, remarked that “when payers evaluate technologies, they do it individually. If a biomarker is safe, effective, and has clinical utility, it will be covered.” However, with a panel of tests that contains multiple biomarkers, only those markers that have been shown to be safe, effective and useful will be covered by insurance.
The Report highlights the perspectives of stakeholders on whether NGS can be effectively integrated into the co-development of diagnosis and therapeutics. Similar to current technologies, the issues are complex and require coordination among numerous stakeholders as well as a clear regulatory pathway for development and application of the technology.
 Next generation sequencing includes whole genome sequencing and whole exome sequencing.
 IOM (Institute of Medicine) 2014. Refining Processes for the Co-Development of Genome-Based Therapeutics and Companion Diagnostic Tests: Workshop summary. Washington DC: The National Academies Press, at page 15.
 IOM (Institute of Medicine) 2014. Refining Processes for the Co-Development of Genome-Based Therapeutics and Companion Diagnostic Tests: Workshop summary. Washington DC: The National Academies Press, available at: http://www.nap.edu/catalog.php?record_id=18617.
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