11/23/2023 0 Comments Dna to rna sequence![]() To address this need, our laboratory has validated an RNA-based custom solid tumor Fusion-Panel (MSK-Fusion refs. Second, DNA sequencing (DNAseq) assays provide no direct evidence that the rearrangement produces a fusion expressed at the mRNA level ( 28), a particular problem for rearrangements that appear noncanonical at the genomic DNA level. Moreover, some introns harbor repetitive sequence elements also present elsewhere in the genome that therefore cannot be assessed by short-read NGS due to the difficulty in uniquely mapping such reads, resulting in gaps in the coverage of certain introns and hence blind spots in the detection of potential rearrangement breakpoints. Some clinically important fusions arise from rearrangements in very long introns, the tiling of which would significantly compromise coverage of the remainder of the genes on the panel. First, such assays can only identify fusions in genes where the genomic rearrangements occur in typically short introns effectively covered in the panel ( Fig 1). However, there are technical limitations to the ability of such DNA-based assays to detect gene fusions ( 27). ![]() For instance, the FDA-cleared MSK-IMPACT large panel, hybrid capture–based NGS assay ( 21, 26), is designed to detect many common kinase fusions, including those involving ALK, RET, and ROS1, and METex14 skipping mutations, via tiling of the appropriate introns for hybrid capture. Targeted DNA-based NGS techniques specifically designed to detect rearrangements in kinases can effectively detect oncogenic kinase fusions with high confidence ( 23–25). Thus, a rational, algorithmic approach to the use of targeted RNA-based next-generation sequencing (NGS) to complement large panel DNA-based NGS testing can be highly effective in comprehensively uncovering targetable gene fusions or oncogenic isoforms not just in lung cancer but also more generally across different tumor types. In a clinical setting, such patients should be prioritized for RNAseq. Among the driver-negative samples tested by RNAseq, those with low tumor mutation burden (TMB) were significantly enriched for gene fusions when compared with the ones with higher TMB. We found actionable alterations (kinase fusions or MET exon 14 skipping) in 13% of cases apparently driver negative by previous DNAseq testing. Here, we evaluated the incremental benefit of targeted RNA sequencing (RNAseq) in the identification of gene fusions in patients where no clear mitogenic driver alteration is found by DNA sequencing (DNAseq)–based panel testing. Inhibitors targeting kinase fusions have shown dramatic and durable responses in lung cancer patients, making their comprehensive detection critical.
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