The CDC/APHL next generation sequencing quality initiative: practical guidance to implementing quality management systems in laboratories performing next generation sequencing (phase 2).

Whenever next generation sequencing is used in clinical and public health laboratories, rigorous quality control and quality assurance are key components of a quality management system. However, both the development and maintenance of a quality management system encompassing next generation sequencing present significant challenges, such as selection of appropriate sequencing platforms, complex workflows, allocation of time and resources, kit and reagent management, potential discontinuation of technical support, specialized bioinformatic workflows, compliance with regulatory and/or accreditation bodies, and the necessity of highly trained personnel. In an effort to address such challenges, the Centers for Disease Control and Prevention collaborated with public health partners to establish the Next Generation Sequencing Quality Initiative, which focuses on the development of a sequencing-focused quality management system. Here, we describe the ongoing efforts of the Next Generation Sequencing Quality Initiative to develop a foundational quality management system specific to next generation sequencing, as well as collaborations aimed to assist partners in addressing ongoing and emerging quality-related challenges associated with assay implementation in laboratories for surveillance and diagnostic applications.