28. Next-generation sequencing as a tool for precision medicine in clinical oncology

      Next-generation sequencing (NGS) has become the most effective tool in the practice of clinical oncology. The technology allows for rapid detection of variants in DNA/RNA simultaneously in a single run within a few days. The results provide valuable information on diagnostic, prognostic and therapeutic targets, which help physicians determine the treatment strategy for cancer patients. Using Ion Torrent S5 platform, we have implemented the Ion Torrent 52-gene Oncomine Focus Assay (OFA) for solid tumors and 74-gene Oncomine Myeloid Assay (OMA) for hematological malignancies as routine clinical practice. For OFA, we have run 718 cases with 62% abnormality rate. Among these, 73% were lung cancers, 10% were colorectal cancers, 4.2% were melanomas, and 12.8% were other tumors. The common mutations observed include KRAS, EGFR, BRAF, PIK3CA, NRAS and MET. Fusions include MET exon14 skipping, ALK-EML4, FGFR3-TACC3, EGFR vIII, ROS1-EZR and RET-NCOA4. For OMA, we have run 1098 cases with 56% abnormality rate. Among these, 11.4% were MPN, 18.3% were AML, and 70.3% were other myeloid disorders. The most common variants detected include TET2, ASXL1, DNMT3A, RUNX1, TP53, FLT3, IDH1, IDH2, WT1, JAK2, CALR, and CEBPA. The fusions include BCR/ABL1, CBFB-MYH11, KMT2A fusions, RUNX1 fusions, and PML-RARA. These variants are clinically actionable with therapeutic drugs or have prognostic implications. In summary, our results demonstrate that the NGS test is a robust and powerful tool for detecting genetic alterations associated with various types of cancers. This advanced tool will help maximize the benefit of precision medicine in clinical oncology practice for caner.
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