BIOTECHNOLOGY
PRECISION MEDICINE
REVOLUTIONISING Advances in oncology research
Courtney Tomas PhD is with Integrated DNA Technologies
P
recision medicine has created a paradigm shift in oncology research, allowing scientists to identify individualised cancer-
associated biomarkers. In this space, next generation sequencing (NGS) has emerged as a transformative tool, offering a range of insights from single nucleotide variants (SNVs) to comprehensive profiles of cancer genomes. This knowledge can be further used to streamline laboratory workflows and resources, optimising assay content and protocols for efficient and accurate genomic profiling of tumours. The integration of NGS data with real-time monitoring approaches fosters a dynamic approach to understanding genetic variations associated with cancer and can contribute to the discovery of new cancer targets biomarkers. Despite this, there are several factors, e.g., cost and accessibility, that have slowed progress in this field [1]. Investing in equipment for NGS can be prohibitive. Additionally, the large amount of data generated with NGS often requires advanced bioinformatic analyses and interpretation. Accessibility to the latest oncology research NGS approaches varies drastically by country. In some, like Germany, NGS for oncology precision medicine has been adopted as standard alongside a commitment to
making whole genome sequencing a widely accessible tool. Other countries are working towards integrating small, targeted gene panels into their standard practices [1]. There is a clear need to improve availability of NGS tools globally and to standardise implementation of these approaches. IDT has long recognised the power of NGS and made a commitment to empowering oncology research labs in their pursuit of important insights in precision medicine. “Over its more than 35-year-history, IDT has been innovating alongside its customers to equip them with the right tools when they need them,” said Steven Henck, PhD, Vice President, R&D at Integrated DNA Technologies. “Our NGS portfolio, which is comprised of stand-alone library preparation, target enrichment, and normalisation chemistries, as well as connected NGS solutions with secondary analysis software support, have been foundational to some of the world’s greatest genomic discoveries. We’re proud to make these solutions widely available to the research community, which depends on IDT to deliver the critical tools they need to continue advancing cancer breakthroughs.” This article discusses the spectrum of approaches used in oncology research and highlights the benefits and the limitations of each technique.
Figure 1. Continuum of approaches used by oncology researchers in precision medicine
SINGLE GENE TESTING Single gene techniques (also referred to as whole gene testing) are among the most widely available methods. Examples include fluorescence and chromogenic in situ hybridization (FISH), PCR, and micro-satellite instability (MSI) tests [1]. They are well established, allow for streamlined analyses and are also cost-effective, making them widely accessible. For certain types of cancers, PCR and other single gene targeting approaches focus on known mutations that drive oncogenesis –e.g., BRCA1/2 in breast cancer [2,3]. These approaches can fail to capture the full picture of mutations driving tumourigenesis since some cancers are the result of an accumulation of mutations across multiple genes.
SMALL TO LARGE PANEL TESTING The limitations presented by single gene targeting approaches can be largely overcome using small to large gene panel testing. Panels rely on NGS to obtain information about specific genes consolidating relevant targets into a multi gene panel. Small panels (less than 50 genes), and large panels (more than 50 genes) [1] provide more information per sample than a single gene approach. Small gene panels target a select set of genes that were previously identified as having relevant mutations in specific cancer types. This focused sequencing of a limited number of genes helps streamline data analyses and interpretation, while also providing more accessibility with less cost than large gene panels [1]. Small gene panels can be employed before samples are analysed using approaches that target more genes like large gene panels or comprehensive genomic profiling (CGP). Large gene panels target a wider
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