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.

Therapeutic Value of miRNAs in Coronary Artery Disease

“…Currently, next-generation sequencing (NGS) is considered as "the novel and gold-standard" highly reliable technique for the identification of miRNA and is broadly used in clinical laboratory medicine. NGS has the ability to detect the single miRNA, whole genome, and even millions of DNA or RNA sequences simultaneously (Figure 3) [45,46]. Moreover, NGS is also able to detect unknown miRNAs which the other two generally used miRNA methods (RT-qPCR and microarray) are incapable of doing.…”

“…Moreover, NGS is also able to detect unknown miRNAs which the other two generally used miRNA methods (RT-qPCR and microarray) are incapable of doing. Therefore, the NGS technique has been widely used for gene regulation research and profiling of miRNAs in diagnosis, prognosis, and drug development (Table 1) [45,46]. Atherosclerosis is a chronic inflammatory disease of the arterial wall caused by endothelial injury and subendothelial accumulation of lipid and extracellular matrix proteins and calcium, particularly at sites of disturbed blood flow that finally form atherosclerotic plaque [47].…”

Currently Applied Molecular Assays for Identifying ESR1 Mutations in Patients with Advanced Breast Cancer

“…The most used Illumina sequencers in the included studies for ESR1 mutation were HiSeq2000 and Hiseq 2500, launched in 2012 [ 104 ] ( Table 1 ). Both platforms belong to second-generation sequencing technologies and utilize four-channel sequencing using a synthesis system in which each fluorescently labeled base is detected using individual images.…”

“…These sequencing strategies increase the chances of detecting pathogenic variants. Patients with negative results in targeted panel sequencing or complex phenotypes are usually indicated for exome sequencing [ 104 ]. Among the included studies, a study investigating the association between ESR1 mutations and efficacy of ER antagonists [ 87 ] utilized a commercially available MSK-IMPACT assay, a targeted sequencing assay covering all protein-coding exons and introns of 410 key oncogenes.…”

“…Whole genome sequencing is a comprehensive technique for analyzing the entire genome. It can detect variants missed using targeted panel sequencing or whole exome sequencing, providing increased diagnostic yield [ 104 ]. In terms of costs, a single test ranged from 555–5169 USD for exome sequencing and 1906–24,810 USD for whole genome sequencing based on a recently published meta-analysis on the cost-effectiveness of different sequencing platforms [ 132 ].…”