Chapter 22 - Regulatory Considerations Related to Clinical Next Generation Sequencing

Abstract

Next generation sequencing (NGS) is subject to the same regulatory standards as other molecular genetic tests. The regulatory oversight of clinical laboratories and of clinical NGS testing varies worldwide, but many countries base compliance on standards set by the International Standards Organization (ISO). In the USA, oversight is federally regulated based on the Clinical Laboratory Improvement Amendments act of 1988 (CLIA ’88). In addition, in the USA, the Food and Drug Administration (FDA) regulates the manufacture of equipment, devices, and assay reagent kits used in clinical testing, which in the context of NGS includes the sequencing platforms themselves, the kits used for library preparation and specific tests, and the bioinformatics pipelines to analyze the data; most NGS tests are categorized as laboratory developed tests (LDTs), which are also subject to FDA oversight. Regardless of the regulatory standards, as with other laboratory tests, NGS has a test cycle that includes a preanalytic phase, an analytic phase, and a postanalytic phase, and the quality control (QC) and quality assurance (QA) principles that govern these phases for more traditional molecular genetic tests are also applicable to NGS tests. However, NGS tests are somewhat unique in that the analytic portion of the test consists of three individual components, specifically the sequence platform itself; the so-called wet-bench procedures that are involved in DNA library preparation; and the bioinformatics associated with base calling, reference genome alignment, variant identification, variant annotation, and variant interpretation. The fact that there are three independent aspects of NGS complicates proficiency testing (PT) of NGS assays. While the emphasis to date has been on the development of comprehensive PT surveys that evaluate all three aspects of an NGS test, a novel type of PT has recently been developed (termed in silico-based PT) in order to specifically address the bioinformatics component of the tests.