Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors

Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors

Comprehensive Genomic Profiling (CGP) has emerged as a progressive standard of care for the understanding clinical oncology and treatment of solid tumors (Conroy, Pabla et al. 2021). By identifying actionable mutations through next-generation sequencing of solid tumors CGP enables targeted therapy d...

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Main Authors: Kristopher Amirault, Michael Collins, Luca Beker, Brandon Mills, Martina Werner, Jonathan Andreas, Daniel Hartman, Jordan Dargert, Vanessa Process, Sean Cederlund, Thuy Dao, Linnea Menin, Molly Ferrara, Andrew Briggs, Joshua Shreve, Daniel Metzger, Angela Stout, Erin Deblasi, Jie An, Taylor Jensen, Shengle Zhang, Vinesh Rana, Bryn Burlingame, Ulrich Thomann, Durga Prasad Dash, Sha Liao, Jeffrey M. Conroy, Eugenio Daviso
Format: Article
Language:English
Published: Elsevier 2025-04-01
Series:SLAS Technology
Subjects:
Laboratory automation
Comprehensive genomic profiling
Clinical oncology
Formalin-fixed paraffin-embedded
Precision medicine
Nucleic acid extraction
Online Access:http://www.sciencedirect.com/science/article/pii/S247263032500010X
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Summary:Comprehensive Genomic Profiling (CGP) has emerged as a progressive standard of care for the understanding clinical oncology and treatment of solid tumors (Conroy, Pabla et al. 2021). By identifying actionable mutations through next-generation sequencing of solid tumors CGP enables targeted therapy decisions. Formalin-fixed paraffin-embedded tissues are notoriously difficult samples in respect to reliably extracting high-quality nucleic acids and sufficient genetic material to meet sequencing input requirements. In this work we present an automated solution for upstream sample processing of solid tumors to enable high throughput and scalable CGP workflows by eliminating bottlenecks and enhancing results. The Sonication STAR automated DNA and RNA methods from FFPE Tissues was created as a collaboration between Hamilton Company, Covaris, and Labcorp and it offers the potential reduction in quantity not sufficient (QNS) samples and sequencing performance improvements resulting in a 16 % increase in fully reported tumor profiles for patients. This automated approach offers potential saving in workflow costs, improved efficiency, and a reduction in re-extraction and re-sequencing of tumors.
ISSN:2472-6303

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