Application of Next Generation Sequencing in Laboratory Medicine

Abstract

The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.

Keywords: Constitutional disorders; Infectious diseases; Next-generation sequencing; Oncology.

Fig. 1

Representations of genomic alterations identified by the Children’s Hospital of Philadelphia Division of Genomic Diagnostics NGS tests. (A) A KIAA1549-BRAF fusion detected in the Fusion panel. Red and blue represent forward and reverse sequencing reads. (B) FLT3-ITD identified in the NGS solid tumor panel. (C) CNVs identified by the NGS solid tumor panel. (C-1) CNV analysis based on reading depth. (C-2) B allele frequency analysis demonstrating SNV separation. Red arrows indicate one copy of 11q; green arrows indicate three copies of the 17q genomic region. Abbreviations: NGS, next-generation sequencing; CNV, copy number variation; SNV, single-nucleotide variation.