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Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care

Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes...

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Autores principales: Sheffield, Brandon S., Beharry, Andrea, Diep, Joanne, Perdrizet, Kirstin, Iafolla, Marco A. J., Raskin, William, Dudani, Shaan, Brett, Mary Anne, Starova, Blerta, Olsen, Brian, Cheema, Parneet K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8947443/
https://www.ncbi.nlm.nih.gov/pubmed/35323313
http://dx.doi.org/10.3390/curroncol29030113
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author Sheffield, Brandon S.
Beharry, Andrea
Diep, Joanne
Perdrizet, Kirstin
Iafolla, Marco A. J.
Raskin, William
Dudani, Shaan
Brett, Mary Anne
Starova, Blerta
Olsen, Brian
Cheema, Parneet K.
author_facet Sheffield, Brandon S.
Beharry, Andrea
Diep, Joanne
Perdrizet, Kirstin
Iafolla, Marco A. J.
Raskin, William
Dudani, Shaan
Brett, Mary Anne
Starova, Blerta
Olsen, Brian
Cheema, Parneet K.
author_sort Sheffield, Brandon S.
collection PubMed
description Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes. Traditional workflows involve moving specimens through multiple facilities. This study evaluates the feasibility of rapid comprehensive NGS using the Genexus integrated sequencer and a novel streamlined workflow in a community setting. Methods: A retrospective chart review was performed to assess the early experience and performance characteristics of a novel approach to biomarker testing at a large community center. This approach to NGS included an automated workflow utilizing the Genexus integrated sequencer, validated for clinical use. NGS testing was further integrated within a routine immunohistochemistry (IHC) service, utilizing histotechnologists to perform technical aspects of NGS, with results reported directly by anatomic pathologists. Results: Between October 2020 and October 2021, 578 solid tumor samples underwent genomic profiling. Median turnaround time for biomarker results was 3 business days (IQR: 2–5). Four hundred eighty-one (83%) of the cases were resulted in fewer than 5 business days, and 66 (11%) of the cases were resulted simultaneously with diagnosis. Tumor types included lung cancer (310), melanoma (97), and colorectal carcinoma (68), among others. NGS testing detected key driver alterations at expected prevalence rates: lung EGFR (16%), ALK (3%), RET (1%), melanoma BRAF (43%), colorectal RAS/RAF (67%), among others. Conclusion: This is the first study demonstrating clinical implementation of rapid NGS. This supports the feasibility of automated comprehensive NGS performed and interpreted in parallel with diagnostic histopathology and immunohistochemistry. This novel approach to biomarker testing offers considerable advantages to clinical cancer care.
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spelling pubmed-89474432022-03-25 Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care Sheffield, Brandon S. Beharry, Andrea Diep, Joanne Perdrizet, Kirstin Iafolla, Marco A. J. Raskin, William Dudani, Shaan Brett, Mary Anne Starova, Blerta Olsen, Brian Cheema, Parneet K. Curr Oncol Article Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes. Traditional workflows involve moving specimens through multiple facilities. This study evaluates the feasibility of rapid comprehensive NGS using the Genexus integrated sequencer and a novel streamlined workflow in a community setting. Methods: A retrospective chart review was performed to assess the early experience and performance characteristics of a novel approach to biomarker testing at a large community center. This approach to NGS included an automated workflow utilizing the Genexus integrated sequencer, validated for clinical use. NGS testing was further integrated within a routine immunohistochemistry (IHC) service, utilizing histotechnologists to perform technical aspects of NGS, with results reported directly by anatomic pathologists. Results: Between October 2020 and October 2021, 578 solid tumor samples underwent genomic profiling. Median turnaround time for biomarker results was 3 business days (IQR: 2–5). Four hundred eighty-one (83%) of the cases were resulted in fewer than 5 business days, and 66 (11%) of the cases were resulted simultaneously with diagnosis. Tumor types included lung cancer (310), melanoma (97), and colorectal carcinoma (68), among others. NGS testing detected key driver alterations at expected prevalence rates: lung EGFR (16%), ALK (3%), RET (1%), melanoma BRAF (43%), colorectal RAS/RAF (67%), among others. Conclusion: This is the first study demonstrating clinical implementation of rapid NGS. This supports the feasibility of automated comprehensive NGS performed and interpreted in parallel with diagnostic histopathology and immunohistochemistry. This novel approach to biomarker testing offers considerable advantages to clinical cancer care. MDPI 2022-02-23 /pmc/articles/PMC8947443/ /pubmed/35323313 http://dx.doi.org/10.3390/curroncol29030113 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sheffield, Brandon S.
Beharry, Andrea
Diep, Joanne
Perdrizet, Kirstin
Iafolla, Marco A. J.
Raskin, William
Dudani, Shaan
Brett, Mary Anne
Starova, Blerta
Olsen, Brian
Cheema, Parneet K.
Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care
title Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care
title_full Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care
title_fullStr Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care
title_full_unstemmed Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care
title_short Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care
title_sort point of care molecular testing: community-based rapid next-generation sequencing to support cancer care
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8947443/
https://www.ncbi.nlm.nih.gov/pubmed/35323313
http://dx.doi.org/10.3390/curroncol29030113
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