Mark D Ewalt, Sara E DiNapoli, Kerry Mullaney, Alison Urvalek, Minji Kim Uh, Purvil Sukhadia, J Keith Killian, Michael Zaidinski, Hun Jae Jung, Tiffany McFarlane, Kelly Rios-Papachristos, Alexander Drilon, Mark G Kris, Khedoudja Nafa, Maria E Arcila, Marc Ladanyi, Ahmet Zehir, Michael Offin, Ryma Benayed
{"title":"利用DNA提取裂解液中的RNA来拯救“不足”的样本,以便在肿瘤标本稀少的患者中进行更全面的基因组分析。","authors":"Mark D Ewalt, Sara E DiNapoli, Kerry Mullaney, Alison Urvalek, Minji Kim Uh, Purvil Sukhadia, J Keith Killian, Michael Zaidinski, Hun Jae Jung, Tiffany McFarlane, Kelly Rios-Papachristos, Alexander Drilon, Mark G Kris, Khedoudja Nafa, Maria E Arcila, Marc Ladanyi, Ahmet Zehir, Michael Offin, Ryma Benayed","doi":"10.1016/j.jmoldx.2025.04.005","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4000,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Leveraging RNA from DNA Extraction Lysate to Rescue \\\"Insufficient\\\" Samples for More Comprehensive Genomic Profiling in Patients with Scant Tumor Specimens.\",\"authors\":\"Mark D Ewalt, Sara E DiNapoli, Kerry Mullaney, Alison Urvalek, Minji Kim Uh, Purvil Sukhadia, J Keith Killian, Michael Zaidinski, Hun Jae Jung, Tiffany McFarlane, Kelly Rios-Papachristos, Alexander Drilon, Mark G Kris, Khedoudja Nafa, Maria E Arcila, Marc Ladanyi, Ahmet Zehir, Michael Offin, Ryma Benayed\",\"doi\":\"10.1016/j.jmoldx.2025.04.005\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>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. 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Leveraging RNA from DNA Extraction Lysate to Rescue "Insufficient" Samples for More Comprehensive Genomic Profiling in Patients with Scant Tumor Specimens.
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.
期刊介绍:
The Journal of Molecular Diagnostics, the official publication of the Association for Molecular Pathology (AMP), co-owned by the American Society for Investigative Pathology (ASIP), seeks to publish high quality original papers on scientific advances in the translation and validation of molecular discoveries in medicine into the clinical diagnostic setting, and the description and application of technological advances in the field of molecular diagnostic medicine. The editors welcome for review articles that contain: novel discoveries or clinicopathologic correlations including studies in oncology, infectious diseases, inherited diseases, predisposition to disease, clinical informatics, or the description of polymorphisms linked to disease states or normal variations; the application of diagnostic methodologies in clinical trials; or the development of new or improved molecular methods which may be applied to diagnosis or monitoring of disease or disease predisposition.