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

Brandon S Sheffield; Andrea Beharry; Joanne Diep; Kirstin Perdrizet; Marco A J Iafolla; William Raskin; Shaan Dudani; Mary Anne Brett; Blerta Starova; Brian Olsen; Parneet K Cheema

doi:10.3390/curroncol29030113

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

Curr Oncol. 2022 Feb 23;29(3):1326-1334. doi: 10.3390/curroncol29030113.

Authors

Brandon S Sheffield¹, Andrea Beharry¹, Joanne Diep¹, Kirstin Perdrizet^{2

3}, Marco A J Iafolla^{2

3}, William Raskin^{2

3}, Shaan Dudani², Mary Anne Brett¹, Blerta Starova¹, Brian Olsen¹, Parneet K Cheema^{2

3}

Affiliations

¹ Department of Laboratory Medicine, William Osler Health System, Brampton, ON L6R 3J7, Canada.
² Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada.
³ Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada.

Abstract

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.

Keywords: NGS; precision medicine; targeted therapy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers, Tumor / genetics
High-Throughput Nucleotide Sequencing / methods
Humans
Lung Neoplasms* / pathology
Melanoma*
Mutation
Point-of-Care Systems
Retrospective Studies

Substances

Biomarkers, Tumor