Next-generation sequencing: recent applications to the analysis of colorectal cancer
Since the application of modern technology in medicine, scientists always tried to understand the real nature of nucleic acids. To this end, a great innovation was brought by the pioneer work of Sanger et al. in the late 70s, when they elaborated the most used method to sequence DNA , still considered as the gold standard in molecular diagnostics, even though it is expensive and time-consuming. Growing efforts have been made to widen technical knowledge in this field until the discovery of the “second and third-generation sequencing” methods [2, 3]. They are both part of the next-generation sequencing (NGS) technology, a group of techniques revolutionizing the standard concept of nucleic acids sequencing. The great success of NGS technology is due to the capability of massively sequencing millions of DNA reads, with the possibility to perform, at least, multi-gene analysis, by using very low amount of nucleic acids. NGS technology is suitable for rapid and efficient sequencing of complex genomes too, with consequent time and cost reduction. Furthermore, it can also count on a noteworthy flexibility: in fact, its application has been reported to be successful in different research fields such as molecular diagnostics of genetic diseases, infectious diseases, cancer and pharmacogenomics [4,5,6,7].
Many studies on cancer took advantage of the use of this technology, due to the possibility to detect high numbers of variants, related to complicated mechanisms of oncogenesis and tumor heterogeneity [8, 9]. Today, molecular profiling of tumors can provide information about diagnosis, prognosis, prediction to therapy response, which can drive clinical decision making. Concerning the precision care in cancer, the eligibility for targeted drugs, able to specifically inhibit aberrantly dysregulated mechanisms, is strictly affected by the “mutational status” of specific genes. The adoption of this type of medication refers to FDA-approved drugs for a specific tumor type, off-label therapies for specific molecular lesions in a non-approved tumor type or to clinical trials focused on analyzing the effects of agents based on the presence of well-defined molecular alterations. In this context, deep molecular characterization of tumors is a key element for optimal patient’s management and unified guidelines to detect and classify variants, interpret and report results should be recommended and adopted .
Colorectal cancer (CRC) is one of the most interesting fields of NGS application. CRC is among the most lethal and frequent types of tumors in the industrialized world and is characterized by a great quantity of activating mutations . These features are the reason why the number of studies employing next-gen techniques is rising in the last years. Their use led to the production of significant results about the identification of novel mutations/altered genes or genomic rearrangements and the possible evaluation of therapy response. This review is intended to condense the state of the art about next-gen technologies and their applications in CRC throughout the last years to provide a useful synopsis. We describe and discuss: (i) NGS main applications and platforms, (ii) main features of CRC pathogenesis and therapy, (iii) NGS application in CRC, by taking into consideration diagnostics of actionable genes, novel mutations, less frequently mutant genes, transcriptomics, epigenetics alterations, other possible directions. Finally, we present some concluding remarks.
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Journal of Next Generation Sequencing & Applications
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