Leveraging RNA from DNA extraction lysate to rescue “insufficient” samples for more comprehensive genomic profiling in patients with scant tumor specimens Journal Article
| Authors: | Ewalt, M. D.; DiNapoli, S. E.; Mullaney, K.; Urvalek, A.; Uh, M. K.; Sukhadia, P.; Killian, J. K.; Zaidinski, M.; Jung, H. J.; McFarlane, T.; Rios-Papachristos, K.; Drilon, A.; Kris, M. G.; Nafa, K.; Arcila, M. E.; Ladanyi, M.; Zehir, A.; Offin, M.; Benayed, R. |
| Article Title: | Leveraging RNA from DNA extraction lysate to rescue “insufficient” samples for more comprehensive genomic profiling in patients with scant tumor specimens |
| Abstract: | Tissue availability is often a limiting factor in obtaining comprehensive genomic profiling to identify actionable oncogenic drivers in tumors from patients with cancer. The utility of performing complementary DNA and RNA sequencing to better identify targetable gene fusions was previously reported. Here, we report our experience using RNA recovered from lysate material, following DNA extraction, to perform targeted RNA sequencing and identify gene fusions and oncogenic transcript variants in a large cohort of patients with solid tumors. To validate this approach, RNA-sequencing results of lysate-extracted RNA and direct formalin-fixed, paraffin-embedded (FFPE) extracted RNA from the same tumors were compared. After finding equivalent identification of oncogenic gene fusions and transcript variants, efforts were expanded to a larger cohort across more diverse tumor types. Lysate-extracted RNA performed comparably to freshly FFPE extract RNA, with 97% and 96% success rates, respectively. Within the lysate-extracted group, it was documented that lysate was the only material available for RNA extraction (n = 1862, 42% of all tested samples) and, within this subgroup, 364 (20%) samples were positive for actionable fusions or oncogenic isoforms. Using RNA recovered from lysate can permit sequential or simultaneous comprehensive DNA/RNA sequencing from scant FFPE samples in laboratories where dual sample extraction is not logistically possible, allowing more complete profiling to enhance the identification of actionable oncogenic gene fusions to guide care. © 2025 Association for Molecular Pathology and American Society for Investigative Pathology |
| Journal Title: | Journal of Molecular Diagnostics |
| Volume: | 27 |
| Issue: | 8 |
| ISSN: | 1525-1578 |
| Publisher: | Elsevier Science, Inc. |
| Publication status: | Published |
| Date Published: | 2025-08-01 |
| Start Page: | 713 |
| End Page: | 721 |
| Language: | English |
| DOI: | 10.1016/j.jmoldx.2025.04.005 |
| PUBMED: | 40381915 |
| PROVIDER: | scopus |
| PMCID: | PMC12405906 |
| DOI/URL: | |
| Notes: | The MSK Cancer Center Support Grant (P30 CA008748) is acknowledge in the PDF -- Corresponding authors is MSK author: Mark D. Ewalt -- Source: Scopus |
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