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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| Format: | Article |
| Language: | English |
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Elsevier
2025-04-01
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| Series: | SLAS Technology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S247263032500010X |
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| author | 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 |
| author_facet | 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 |
| author_sort | Kristopher Amirault |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-c9f46a570fc64d36ada65caa55394d7f |
| institution | Kabale University |
| issn | 2472-6303 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SLAS Technology |
| spelling | doaj-art-c9f46a570fc64d36ada65caa55394d7f2025-02-08T05:00:47ZengElsevierSLAS Technology2472-63032025-04-0131100252Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumorsKristopher Amirault0Michael Collins1Luca Beker2Brandon Mills3Martina Werner4Jonathan Andreas5Daniel Hartman6Jordan Dargert7Vanessa Process8Sean Cederlund9Thuy Dao10Linnea Menin11Molly Ferrara12Andrew Briggs13Joshua Shreve14Daniel Metzger15Angela Stout16Erin Deblasi17Jie An18Taylor Jensen19Shengle Zhang20Vinesh Rana21Bryn Burlingame22Ulrich Thomann23Durga Prasad Dash24Sha Liao25Jeffrey M. Conroy26Eugenio Daviso27Covaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaHamilton Company, Reno, NV 89502, United States of AmericaHamilton Company, Reno, NV 89502, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaHamilton Company, Reno, NV 89502, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaHamilton Company, Reno, NV 89502, United States of AmericaHamilton Company, Reno, NV 89502, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaHamilton Company, Reno, NV 89502, United States of AmericaLabcorp, Buffalo, NY 14203, United States of AmericaCovaris a PerkinElmer Company, 14 Gill Street, Woburn, MA 01801, United States of America; Corresponding author.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.http://www.sciencedirect.com/science/article/pii/S247263032500010XLaboratory automationComprehensive genomic profilingClinical oncologyFormalin-fixed paraffin-embeddedPrecision medicineNucleic acid extraction |
| spellingShingle | 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 Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors SLAS Technology Laboratory automation Comprehensive genomic profiling Clinical oncology Formalin-fixed paraffin-embedded Precision medicine Nucleic acid extraction |
| title | Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors |
| title_full | Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors |
| title_fullStr | Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors |
| title_full_unstemmed | Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors |
| title_short | Fully automated extraction of high-quality total nucleic acids from FFPE specimens for comprehensive genomic profiling of solid tumors |
| title_sort | fully automated extraction of high quality total nucleic acids from ffpe specimens for comprehensive genomic profiling of solid tumors |
| topic | Laboratory automation Comprehensive genomic profiling Clinical oncology Formalin-fixed paraffin-embedded Precision medicine Nucleic acid extraction |
| url | http://www.sciencedirect.com/science/article/pii/S247263032500010X |
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