Implementation of next generation sequencing in clinical molecular diagnostic laboratories: advantages, challenges and potential

Next generation sequencing (NGS) technologies have the capacity to perform massively parallel sequencing of the genome. This capacity simultaneously facilitates sequencing large areas of the genome in multiple samples and has revolutionized clinical genomics, both for discovery and diagnostic screening of genomic aberrations. The implementation of these powerful technologies in a Clinical Laboratory Improvement Amendment certified and College of American Pathologists accredited clinical laboratory presents a unique challenge due to their complexity, volume and medico-legal implications of the data generated. Here, with a focus on routine clinical cancer diagnostics, we review recent progress in the implementation of NGS, associated recommendations and guidelines, and the advantages and challenges of implementing NGS. In the light of rapidly increasing acceptance of NGS to replace the classical first generation technologies in the clinical environment, we also discuss the potential of NGS to be the new ‘gold standard’ for genome sequencing and to further improve the implementation of precision medicine.