Liquid Biopsy and Automated Next-Generation Sequencing - Achieving Results in 27 Hours Within a Community Setting

Sep 30, 2026

Uploaded by Oliver

Conventional next-generation sequencing (NGS) workflows often require more than two weeks, delaying treatment decisions and limiting precision oncology access in community settings. This case report demonstrates the feasibility of rapid, comprehensive cell-free DNA (cfDNA)-based genomic profiling using a fully automated NGS workflow in a community hospital environment. Postoperative pancreatic ductal adenocarcinoma with liver metastasis underwent cfDNA liquid biopsy, generating results in about 27 hours with 40 minutes of hands-on time.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages12

Reading Time30 min

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Abstract

Background/Objectives

Case Presentation

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Introduction

Case Report Liquid Biopsy and Automated Next-Generation Sequencing: Achieving Results in 27 Hours Within a Community Setting Tomomi Yajima 1,2, *, Fumitake Hata 1, Sei Kurokawa 3, Kanan Sawamoto 2, Akiko Yajima 4, Daisuke Furuya 5 and Noriyuki Sato 6 Academic Editor: ConsolatoM. Sergi Received: 28 October 2025 Revised: 16 December 2025 Accepted: 16 December 2025 Published: 22 December 2025 Copyright: © 2025 by the authors. 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. 1 Department of Surgery, Sapporo Dohto Hospital, 14-3-2 Kita 17-jo Higashi, Higashi-ku, Sapporo 065-0017, Japan; [fhata@sdhmc.jp](fhata@sdhmc.jp) 2 Department of Clinical Laboratory, Sapporo Dohto Hospital, 14-3-2 Kita 17-jo Higashi, Higashi-ku, Sapporo 065-0017, Japan; [k-sawamoto@sdhmc.jp](k-sawamoto@sdhmc.jp) 3 Department of Internal Medicine, Sapporo Dohto Hospital, 14-3-2 Kita 17-jo Higashi, Higashi-ku, Sapporo 065-0017, Japan; [s-kurokawa@sdhmc.jp](s-kurokawa@sdhmc.jp) 4 Sapporo Female Clinic, 3-2-5 Kita 21-jo Higashi, Higashi-ku, Sapporo 065-0021, Japan; [akiko@sapporo-fc.jp](akiko@sapporo-fc.jp) [5](5 Department of Clinical Engineering)[ Department of Clinical Engineering](5 Department of Clinical Engineering), [Faculty of Health Sciences](Faculty of Health Sciences), [Hokkaido University of Science](Hokkaido University of Science), [15-4-1](15-4-1)[ ](15-4-1)Maeda 7-jo, Teine-ku, Sapporo 006-8585, Japan; [furuya-d@hus.ac.jp](furuya-d@hus.ac.jp) 6 Academic Center, Sapporo Dohto Hospital, 14-3-2 Kita 17-jo Higashi, Higashi-ku, Sapporo 065-0017, Japan; [nsatou@sapmed.ac.jp](nsatou@sapmed.ac.jp) * Correspondence: [tomomiy@sdhmc.jp](tomomiy@sdhmc.jp); Tel.: +81-11-731-1155 Abstract Background/Objectives: Conventional next-generation sequencing (NGS) workflows often require more than two weeks to complete, delaying treatment decisions and limiting access to precision oncology in community settings. This report aimed to demonstrate the feasibility of performing rapid, comprehensive cell-free DNA (cfDNA)-based genomic profiling by introducing a fully automated NGS workflow in a community hospital environment. Case Presentation: A postoperative patient with pancreatic ductal adenocarcinoma and liver metastasis underwent cfDNA-based liquid biopsy using plasma collected in PAXgene® Blood ccfDNA Tubes. Gene analysis was performed using the Oncomine Precision Assay GX5 on the Ion Torrent Genexus™ System (Thermo Fisher Scientific) . Three pathogenic hotspot mutations—KRAS G12R, TP53 M246I/M246K, and GNA11—and one copy number gain in PIK3CA were identified, whereas no variants were detected in a healthy volunteer control. The total turnaround time from plasma separation to report generation was approximately 27 h, requiring only 40 min of total hands-on time. Discussion: This rapid, automated workflow enabled comprehensive cfDNA analysis within a clinically practical timeframe, overcoming key limitations of conventional multi-step NGS workflows that typically require external sample shipment and specialized personnel. The results confirm the technical feasibility of conducting high-quality molecular testing ina regional hospital setting. Conclusions: This report demonstrates that fully automated cfDNA-based NGS can achieve clinically meaningful genomic profiling within 27 h in a community hospital. This advancement addresses the time and cost barriers of traditional NGS analysis and represents a significant step toward promoting precision medicine in community healthcare. Keywords: liquid biopsy; next-generation sequencing; community setting 1. Introduction Biomarker analysis plays a central role in precision cancer treatment strategies. Nextgeneration sequencing (NGS) enables rapid, large-scale gene panel analysis, allowing the identification and detection of a wide variety of actionable biomarkers that gui

FAQs

Why is rapid NGS important in community settings?

Conventional NGS workflows often take more than two weeks, which delays treatment decisions and restricts access to precision oncology. The report targets a timeframe compatible with clinical decision-making in community hospitals.

How was the liquid biopsy performed in the case?

Plasma was collected in PAXgene Blood ccfDNA Tubes and analyzed using the Oncomine Precision Assay GX5 on the Ion Torrent Genexus system. The study identified specific hotspot mutations and a copy number gain in PIK3CA.

What turnaround time and hands-on time were achieved?

The total turnaround time from plasma separation to report generation was approximately 27 hours, with about 40 minutes of total hands-on time. This supports clinically practical molecular testing in a regional hospital environment.

Sep 30, 2026

Uploaded by Oliver