Next-Generation Sequencing: Targeting Targeted Therapies

Abstract

Next-generation sequencing (NGS) has given new perspective in oncology. With the ongoing development of targeted therapies, NGS is evolving molecular diagnostics by providing comprehensive interrogation of clinically actionable genomic aberrations in tumors. Having this assay as the primary testing method produces clinically beneficial results. See related article by Drilon et al., p. 3631 In this issue of Clinical Cancer Research, Drilon and colleagues (1) demonstrate the significant role of next-generation sequencing (NGS) as the primary testing method in molecular diagnostics. Thirty one previously tested lung adenocarcinoma patients assessed by single non-NGS molecular tests, such as fluorescence in situ hybridization (FISH), multiplex mass spectrometry, and sizing assays, produced "negative" results for known lung adenocarcinoma genomic alterations in the genes EGFR, ERBB2, KRAS, NRAS, BRAF, MAP2K1, PIK3CA, AKT1, ALK, ROS1, and RET. By retesting these patients with a broad, hybrid capturebased NGS assay, Drilon and colleagues (1) revealed actionable genomic alterations present in 65% of the patients that were formerly deemed "driver negative." NGS technologies are rapidly evolving and are being increasingly used in research settings as well as clinical settings, to replace older and less-sensitive technologies. As opposed to classic Sanger sequencing, NGS technology uses clonally amplified or singlemolecule templates that are sequenced in a massively parallel fashion, allowing examination of numerous amounts of large protein coding regions, which makes NGS assays suitable for a comprehensive interrogation of cancer drivers (2). Whereas current non-NGS tests mostly examine only one variant type, NGS technology allows the patient's tumor to be tested in a single run for all types of variants, including single-nucleotide variations (SNV), insertions, deletions, exon duplications, gene copy number changes, and known translocations (3).In recent years, the advancement of NGS technology in the clinical setting has been rapidly progressing and will soon likely replace older technologies. Lung cancer, the leading cause of cancer-related death in the world, comprises a complex mutational spectrum, and the discoveries of many oncogenic drivers in the tumors have led to the development and evolution of targeted therapy, especially in the adenocarcinoma of the lung, the most prevalent type of lung cancer (4, 5). Among these targeted therapies are the tyrosine kinase inhibitors (TKI); the FDA approved TKIs in lung adenocarcinoma treatment to target EGFR and ALK. Sensitizing mutations and rearrangements in the EGFR and ALK genes, respectively, are responsible for the constitutively activated kinase, and render tumors exquisitely sensitive to TKIs. In the case of EGFR and ALK inhibitors, response rates and progression-free survival are dramatically improved compared with standard chemotherapy (6). Although TKIs are initially very effective in the majority of patients whose tumors harbor the genetic alteration, acquired...

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“…During the past decade, next-generation sequencing (NGS) has become an efficient and accurate method in molecular diagnostics by providing comprehensive genomic aberrations in tumors for both research and clinical purposes2930. NGS encompasses a set of different techniques including whole genome/exome sequencing, RNA sequencing (RNA-Seq) and targeted sequencing of specific panels of genes31.…”

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“…Given the heterogeneous nature of cancer, the quality of the biopsy can significantly affect the downstream genomic analysis and therefore, the ability to direct therapy to the appropriate oncologic pathway [10–14]. As novel therapeutics begins to be routinely introduced with companion biomarkers, it is expected that molecular biomarker testing will become the standard of care.…”

“…While only one hot-spot sequence is examined at a time in the uniplex methods, multiple hot-spot mutations are examined simultaneously using multiplex techniques. Multiplex methodologies, including NGS platforms, are available in several testing laboratories capable of high-throughput molecular analysis including the ability to fully sequence large numbers of genes in a single test while simultaneously detecting deletions, insertions, copy number alterations, translocations, and exome-wide base substitutions (including known hot-spot mutations) in all known cancer-related genes [14,18]. Currently, NGS platforms, including whole genome, whole exome and targeted gene sequencing, represent emerging diagnostic methodologies for the detection of oncogene fusions and mutations in tumor tissue specimens, including FFPE samples.…”

Novel BCR-ABL1 fusion and leukemic mutations of SETBP1, PAX5, and TP53 detected by next generation sequencing in chronic myeloid leukemia

“…Moreover, targeted NGS applications have been developed and have greatly facilitated the usage of this technology as a daily diagnostic tool. 16 In this study, we described a case of CML patient carried a novel variant BCR-ABL fusion that has never been described. Although Fluorescent In Situ Hybridization (FISH) suggested the incidence of BCR-ABL1 rearrangement, a functional mRNA transcript was unable to be detected using qRT-PCR-based diagnostic methods, which are designed for detecting those well-known and previously identified BCR-ABL1 fusion transcripts.…”

“…16 Using the NGS platform, both whole genome sequencing (WGS) and whole exome sequencing (WES) are powerful tools for the discovery of new disease genes and for the diagnosis of many hematological conditions, such as leukemia, with complex phenotypic and genotypic variations. 17,18 While conventional diagnostic technologies, such as PCR-based and antibody-based detection methods, are still useful to detect known targets, NGS can be used for detecting both identified and novel mutations.…”