title: Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges.
abstract: The application of next-generation sequencing (NGS) to characterize cancer genomes has resulted in the discovery of numerous genetic markers. Consequently, the number of markers that warrant routine screening in molecular diagnostic laboratories, often from limited tumor material, has increased. This increased demand has been difficult to manage by traditional low- and/or medium-throughput sequencing platforms. Massively parallel sequencing capabilities of NGS provide a much-needed alternative for mutation screening in multiple genes with a single low investment of DNA. However, implementation of NGS technologies, most of which are for research use only (RUO), in a diagnostic laboratory, needs extensive validation in order to establish Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP)-compliant performance characteristics. Here, we have reviewed approaches for validation of NGS technology for routine screening of tumors. We discuss the criteria for selecting gene markers to include in the NGS panel and the deciding factors for selecting target capture approaches and sequencing platforms. We also discuss challenges in result reporting, storage and retrieval of the voluminous sequencing data and the future potential of clinical NGS.
authors.affiliation: Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX 77054, USA. rluthra@mdanderson.org.
authors.forename: Rajyalakshmi
authors.initials: R
authors.lastname: Luthra
authors.affiliation: Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX-77030, USA. hchen7@mdanderson.org.
authors.forename: Hui
authors.initials: H
authors.lastname: Chen
authors.affiliation: Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX-77030, USA. SRoy2@mdanderson.org.
authors.forename: Sinchita
authors.initials: S
authors.lastname: Roy-Chowdhuri
authors.affiliation: Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 8515 Fannin Street, Houston, TX 77054, USA. rsingh@mdanderson.org.
authors.forename: R Rajesh
authors.initials: RR
authors.lastname: Singh
keywords: cancer genomics; guidelines; molecular diagnostics; mutation; next-generation sequencing