Archives

  • 2022-08
  • 2022-07
  • 2022-06
  • 2022-05
  • 2022-04
  • 2021-03
  • 2020-08
  • 2020-07
  • 2020-03
  • 2019-11
  • 2019-10
  • 2019-09
  • 2019-08
  • 2019-07
  • br to inform bioinformatics variant detection and interpretation enables the

    2022-05-17

    
    to inform bioinformatics variant detection and interpretation enables the suppression of false-positive variant calls and flags samples at risk of false-negative calls, thus enabling accurate analysis of poorer-quality specimens. The analytical validity of our Artesunate approach is supported by 100% confirmation rates of RNA fusions and MET Artesunate 14 skipping events by qPCR or PCR/CE and high analytical concordance in our analysis of FNA smears from the BATTLE-2 trial with an independent NGS assay on matched surgical resections.
    Joint preanalytical QC analysis of DNA and RNA offered additional insights into the quality distinctions between analytes and specimen types. As expected, FFPE surgical resections were of the highest quality, with 100% of specimens yielding sufficient DNA and RNA for NGS analyses. In contrast, 99% and 86% of CNB specimens offered sufficient material for DNA and RNA NGS analyses, respectively. At the extreme end of the quality spectrum were the FNA smears with 48% and 2% pass rates for DNA and RNA, respectively. Across this continuum of quality, we noticed a general trend with respect to the suitability of a specimen's DNA relative to RNA, namely, that specimens were more likely to offer sufficient DNA for analysis. A parallel and related observation was that analysis of RNA expression trends (analysis of immune checkpoint inhibitor expression markers and CNAs) tended to show more robust associations in the FFPE surgical resections relative to CNBs.
    The longer-term rationale for a conjoined analysis of DNA and RNA is to provide a foundation for integrative, targeted NGS applications that pair genotype with molecular phenotype in order to interpret variants of unknown significance through orthogonal functional evidence. In this paradigm, RNA expression can be viewed as a molecular information bottleneck that can aid in the interpretation of the long tail of genetic and epigenetic variation that underlies tumor evolution. Functional pathway analysis will enable the resolution of cryptic and latent oncogenic driver mutations and shed light onto the “dark matter” that underlies cancer. The NGS workflow presented here offers a foundation for integrative analysis of DNA and RNA compatible with a range of clinical specimen types in a small-footprint format suitable for routine diagnostic and clinical research purposes to enable holistic interpretation of cancer specimens.
    Disclosures
    B. C. H., R. A. B., R. D. C., R. Z., S. G., J. R. T., L. C., and G. J. L. were employed by Asuragen, Inc., at the time that the research was performed. Asuragen employees have or may have stock in Asuragen, Inc. Asuragen markets a for Research Use Only (RUO) test for QuantideX® NGS RNA Lung Cancer Kit as a clinical research tool enabling the simultaneous assessment of biomarkers frequently observed in lung cancer and QuantideX® NGS DNA Hotspot 21 Kit (RUO), a research tool that interrogates hotspot regions within 21 genes that are commonly mutated in a number of solid and hematological malignancies.
    Acknowledgements
    The authors thank Annette Schlageter for assistance with the manuscript.
    References
    [1] Pant S, Weiner R, and Marton MJ (2014). Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays
    844 An Integrated Next-Generation Sequencing System Haynes et al. Translational Oncology Vol. 12, No. 6, 2019
    [15] Drilon A, Wang L, Arcila ME, Balasubramanian S, Greenbowe JR, Ross JS, Stephens P, Lipson D, Miller VA, and Kris MG, et al (2015). Broad, hybrid capture-based next-generation sequencing identifies actionable genomic alter-ations in lung adenocarcinomas otherwise negative for such alterations by other genomic testing approaches. Clin Cancer Res 21, 3631–3639. http://dx.doi. org/10.1158/1078-0432.CCR-14-2683.
    [20] Oliveira DM, Mirante T, Mignogna C, Scrima M, Migliozzi S, Rocco G, Franco R, Corcione F, Viglietto G, and Malanga D, et al (2018). Simultaneous identification of clinically relevant single nucleotide variants, copy number alterations and gene fusions in solid tumors by targeted next-generation sequencing. Oncotarget 9, 22749–22768. http://dx.doi.org/10.18632/ oncotarget.25229.