Handbook of Targeted Cancer Therapy and Immunotherapy

88 (RNASeq), micro RNA sequencing (miRNASeq), DNA sequencing (DNASeq), single-­ nucleotide polymorphism (SNP)-based platforms, and array-based DNA methylation sequencing for nucleic acid sequencing, as well as reverse-phase protein array (RPPA) for proteomic assessment (6). Subsequently, the TCGA Pan-Cancer project was im plemented and sought to further analyze the molecular profiles of individual tumors, as well as compare genetic aberrations between tumor types (8). Similarly, the ICGC characterized > 50 cancer types, with the goal of discovering highly prevalent mutations, standardizing reporting methods on an international scale, providing granular data at the single-nucleotide level, and to make this data publicly accessible (7). Progress in the field of cancer biology that has stemmed from these efforts cannot be over stated. The field of oncology was previously predominated by a tumor-centric approach to treat ment, but it is now evident that tumors with vastly different origins can have overlapping molecular drivers, and often tumors of the same origin are molecularly distinct (8). Publicly available data from the TCGA and ICGC have allowed researchers around the globe to make progress in iden tifying biomarkers, discovering new targets for therapy, and providing an opportunity to develop bioinformatics tools to better understand the available data, which will ultimately improve the care of cancer patients (6). Detection of Genomic Alterations High-throughput DNASeq can be performed using several molecular biology techniques, including cyclic reversible termination, pyrosequencing, synthesis by ligation, and real-time sequencing (9). Sequences determined by these assays are then mapped onto the human reference genome using bioinformatics tools, which enables the calling of single-nucleotide variants, insertions/deletions, fusions, and copy number variations (Figure 9.1). These NGS technologies are advantageous over first-generation Sanger sequencing, considering that the volume of data that can be produced with one run can exceed 1 billion short reads (9). Tissue input for these assays includes solid tumor tissue, individual tumor cells, and plasma (liquid biopsy). Although fresh frozen tissue provides ad equate tissue for performing NGS, samples are often formalin fixed and paraffin embedded (FFPE), which can lead to the degradation of both DNA and RNA (10). Despite these limitations, most mod ern NGS platforms can utilize FFPE tissue for sequencing analysis.

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