The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care

Kaul, Karen L.; Sabatini, Linda M.; Tsongalis, Gregory J.; Caliendo, Angela M.; Olsen, Randall J.; Ashwood, Edward R.; Bale, Sherri; Benirschke, Robert; Carlow, Dean; Funke, Birgit H.; Grody, Wayne W.; Hayden, Randall T.; Hegde, Madhuri; Lyon, Elaine; Murata, Kazunori; Pessin, Melissa; Press, Richard D.; Thomson, Richard B.

The complexity of cancer biology and the ever-evolving therapeutic approach to management of the patient with cancer more often requires expanded knowledge of the tumor beyond single-gene mutation status. Over the past several years, the laboratory's ability to multiplex testing for several genes or genetic variants has been limited by the available technologies. Next-generation sequencing or massively parallel sequencing has allowed the laboratory to provide a more comprehensive genomic profile of tumor cells in a single assay than previous methods. The ability to detect numerous mutations in multiple genes results in information that can allow the oncologist to develop a more accurate treatment strategy including therapies selected based on a "responsive" tumor profile and those not selected based on the presence of resistance mutations. [79] [80] [81] Instrumentation from Thermo Fisher (Thermo Fisher Life-Technologies, Carlsbad, CA, USA) and Illumina (Illumina, San Diego, CA, USA), the Personal Genome Machine (PGM), and MiSeq, have made NGS suitable for routine clinical laboratory testing. [82] [83] [84] In 2015, the MiSeq Dx obtained FDA approval. Despite this approval and the routine use of NGS in LDPs setting, there are no currently FDA-approved NGS tests for application in oncology. Although many drug package inserts require or allude to the use of a companion diagnostic for eligibility, very few companion diagnostic tests are FDA approved and none using NGS technology. As an LDP, clinical laboratories are required to demonstrate rigorous performance criteria for wet-bench testing and analysis pipelines to ensure the test is functioning properly for its intended clinical purpose. 73, [85] [86] [87] Most NGS testing for therapeutic selection in cancer consists of panels of genes that range from 10 to 400 or more genes. Each test can be designed to detect hotspots of known mutations in those genes, to sequence the entire coding region of the genes, or to sequence the entire gene. The end result is a comprehensive profile of the tumor genome that can then be used to tailor therapy for the individual patient. Although NGS assays cost more than single-gene assays, the cost per gene sequence is dramatically reduced and results in cost savings over using multiple single-gene tests. Furthermore, NGS panels can be applied to very small specimen samples, using as little as 10 to 250 ng of input DNA depending on the analytic platform utilized. Since evaluation of therapeutic biomarkers is usually needed in the setting of advanced disease and such patients often have only limited tissue samples available for testing, NGS assays allow for much more extensive genomic information to be obtained compared to single-gene assays, each of which can require DNA input comparable to that of an entire NGS panel.