Background: DNAseq, RNAseq and determination of microsatellite instability (MSI) are now routine analyses in precision medicine for management of cancer patients. Analyzing DNA/RNA requires reliable assays often performed in two separate runs. Faced with limited quantity of total nucleic acids (TNA) extracted from FFPE this can be challenging. Sequential approaches (i.e. DNAseq followed by RNAseq) increase the turnaround time and cost, delaying treatment. Here, we evaluated a novel NGS approach developed by Invitae (San Francisco, USA). Using TNA from FFPE tissue, we detected SNVs, indels, MSI and structural rearrangements in one single NGS run.Methods: 24 samples from patients with various cancers were included, previously characterized using conventional methods: DNAseq, RNAseq, PCR, IHC or FISH. The study was approved by ICL ethical and scientific committee-all patients gave their consent. FFPE samples were qualified, selected followed by tumor cell content evaluation by a pathologist. After microdissection, TNAs were extracted and libraries were prepared using a parallel VariantPlex (DNA) and FusionPlex (RNA) kit from Invitae. Kits were designed to detect known and novel fusions in gene targets commonly encountered in solid tumors, MSI, and variants using a panel of 156 cancer-relevant target genes (71 DNA, 136 RNA).Results: Among 9 previous SNVs/indels and 11 MSI samples identified by orthogonal methods, NGS approach confirmed all (100%). Among 12 fusions, 11 were detected by NGS (91.7%). Single ROS1 fusion scored low (1+) using IHC. Further analyses are conducted to determine whether the ROS1 fusion is false positive by IHC, or false negative by NGS.Conclusions: Novel, all-in-one NGS approach from Invitae shows promising results by comprehensively detecting SNVs, indels, MSI and structural variants. Analyses of DNA and RNA using the novel NGS strategy improves the overall turn-around-time and cost-effectiveness. This can potentially aid clinicians and patients to take timely decisions regarding treatment modalities.
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