SLAS Technology (Apr 2025)
Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors
- 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
Affiliations
- Kristopher Amirault
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Michael Collins
- Labcorp, Buffalo, NY 14203, United States of America
- Luca Beker
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Brandon Mills
- Labcorp, Buffalo, NY 14203, United States of America
- Martina Werner
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Jonathan Andreas
- Labcorp, Buffalo, NY 14203, United States of America
- Daniel Hartman
- Hamilton Company, Reno, NV 89502, United States of America
- Jordan Dargert
- Hamilton Company, Reno, NV 89502, United States of America
- Vanessa Process
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Sean Cederlund
- Hamilton Company, Reno, NV 89502, United States of America
- Thuy Dao
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Linnea Menin
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Molly Ferrara
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Andrew Briggs
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Joshua Shreve
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Daniel Metzger
- Labcorp, Buffalo, NY 14203, United States of America
- Angela Stout
- Labcorp, Buffalo, NY 14203, United States of America
- Erin Deblasi
- Labcorp, Buffalo, NY 14203, United States of America
- Jie An
- Labcorp, Buffalo, NY 14203, United States of America
- Taylor Jensen
- Labcorp, Buffalo, NY 14203, United States of America
- Shengle Zhang
- Labcorp, Buffalo, NY 14203, United States of America
- Vinesh Rana
- Hamilton Company, Reno, NV 89502, United States of America
- Bryn Burlingame
- Hamilton Company, Reno, NV 89502, United States of America
- Ulrich Thomann
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America
- Durga Prasad Dash
- Labcorp, Buffalo, NY 14203, United States of America
- Sha Liao
- Hamilton Company, Reno, NV 89502, United States of America
- Jeffrey M. Conroy
- Labcorp, Buffalo, NY 14203, United States of America
- Eugenio Daviso
- Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America; Corresponding author.
- Journal volume & issue
-
Vol. 31
p. 100252
Abstract
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.