Leveraging RNA from DNA Extraction Lysate to Rescue "Insufficient" Samples for More Comprehensive Genomic Profiling...

Area of Science:

• Oncology
• Genomics
• Molecular Biology

Background:

• Limited tissue availability hinders comprehensive genomic profiling for actionable oncogenic drivers in cancer patients.
• Complementary DNA and RNA sequencing can identify targetable gene fusions.

Purpose of the Study:

• To evaluate the utility of RNA recovered from tumor lysate for targeted RNA sequencing.
• To identify gene fusions and oncogenic transcript variants in a large cohort of solid tumors.
• To compare the performance of lysate-extracted RNA with direct formalin-fixed, paraffin-embedded (FFPE) extracted RNA.

Main Methods:

• Targeted RNA sequencing was performed on RNA extracted from tumor lysate.
• RNA sequencing results from lysate-extracted RNA were compared to those from direct FFPE-extracted RNA from the same tumors.
• The approach was validated in a large cohort across diverse solid tumor types.

Main Results:

• Lysate-extracted RNA demonstrated comparable performance to direct FFPE-extracted RNA, with success rates of 97% and 96%, respectively.
• In 42% of tested samples (n=1862), lysate was the only available material for RNA extraction.
• Within the lysate-only group, 20% (364 samples) were positive for actionable fusions or oncogenic isoforms.

Conclusions:

• RNA recovered from tumor lysate is a viable method for comprehensive DNA/RNA sequencing.
• This approach enhances the identification of actionable oncogenic gene fusions, particularly from scant FFPE samples.
• It offers a solution for laboratories where dual sample extraction is not logistically feasible, improving patient care.