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• W2896161553 abstract "Variants associated with non-small cell lung cancer (NSCLC) initiation and progression include DNA mutations, copy number variants, RNA fusions and splicing isoforms. Co-detection of DNA and RNA variants has become increasingly important to shorten time from samples to results and optimize personalized medicine for NSCLC. Here we describe the unification of next-generation sequencing (NGS) workflows using library pooling to reliably and sensitively quantify both DNA and RNA variants from tumor FFPE nucleic acids. Total nucleic acid (TNA) and DNA were isolated from residual FFPE NSCLC biopsies and cancer cell lines. The QuantideX® NGS RNA Lung Cancer Kit (RUO, Asuragen) and QuantideX® NGS DNA Hotspot 21 Kit (Prototype, Asuragen) were evaluated on the MiSeq® System. DNA and RNA libraries were sequenced on a single MiSeq flow cell. Multiple library pooling strategies were assessed to provide workflow flexibility. All data was analyzed using QuantideX® NGS Reporter 3.0 software. The average time from sample QC to MiSeq loading was 10 hours. Including 40-hour instrument run time and data processing and analysis, the sample-to-answer time was less than three days. Library pooling experiments evaluated sample run capacity, coverage uniformity, and variant call accuracy from FFPE TNA and DNA. For example, a single pool of 8 RNA and 16 DNA libraries yielded >500,000 reads for each library, with RNA fusions called with 189 to 11,274 reads and DNA mutations detected down to 5% variant allele frequency. Variant calls were 100% concordant with independent results and included mutations in EGFR, RAS, PIK3CA, and BRAF, along with fusions in ALK, RET, and NRG1 and skipped METex14. The co-detection strategy generated reliable quantitative information from low-input tumor FFPE DNA and TNA within three days. The simplicity and speed of the approach, coupled with a standardized workflow, has the potential to increase the accessibility of NGS analysis and accelerate the return of results for NSCLC patients." @default.
• W2896161553 created "2018-10-26" @default.
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• W2896161553 date "2018-10-01" @default.
• W2896161553 modified "2023-09-26" @default.
• W2896161553 title "P3.09-20 A Simple and Versatile Next-Generation Sequencing Technology for Co-Detection of RNA Structural Variants and DNA Mutations in Lung Cancer" @default.
• W2896161553 doi "https://doi.org/10.1016/j.jtho.2018.08.1789" @default.
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