Comparison of Comprehensive Genomic Profiling Testing "Ion Torrent Genexus Sequencer" With FoundationOne.

IF 1.7 4区医学 Q4 ONCOLOGY

Anticancer research Pub Date : 2025-08-01 DOI:10.21873/anticanres.17709

Kenji Fujiyoshi, Rie Sugihara, Naoki Miyamoto, Yoriko Watanabe, Tomoya Sudo, Sanae Numata, Jun Akiba, Hideyuki Abe, Yuka Ichinose, Kenji Inoue, Shuichi Ozono, Takeharu Ono, Kentaro Orioka, Masaki Kashihara, Ryousuke Kajiwara, Hiroyuki Kawano, Akihiko Kawahara, Ryuta Takase, Uhi Toh, Kazuaki Hashimoto, Toru Hisaka, Shingo Hirai, Masahiro Mitsuoka, Daiki Miyazaki, Fumi Yoshitomi, Ken Yamamoto, Hirohito Umeno, Masahisa Nomura, Yoshiki Naito

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引用次数: 0

Abstract

Background/aim: Comprehensive genomic profiling (CGP) with tissue- and blood-based next-generation sequencing (NGS) is integral to the delivery of personalized medicine for targeted cancer therapy. This study aimed to evaluate the variant concordance for somatic variants using two clinical NGS systems for conducting both tissue- and blood-based analyses: Genexus-OCA v3 (OCA) vs. FoundationOne CDx (F1) for tissues and Genexus OPA (OPA) vs. FoundationOne CDx Liquid (F1L) for blood.

Patients and methods: The concordance of genomic alterations between the two NGS analyses was compared in six patients with breast, head, and neck cancers using tissue and circulating tumor DNA biopsies.

Results: A total of 130 genes were common between F1 and OCA, and 41 between F1L and OPA. When comparing FoundationOne to Genexus for common genes, the sensitivity and specificity of OCA and OPA were 55% and 99%, respectively. Nine single-nucleotide variants (SNVs), one copy number alteration (CNA), and one fusion were detected by both Genexus and FoundationOne. However, one SNV (MAP2K1 F53V), two CNAs (AKT3 and MYC), and one fusion (ESR-CCDC170) were detected only in Genexus, whereas two SNVs (TP53 Q331* and KRAS G12V) were detected only in FoundationOne.

Conclusion: The two cancer genome panels were equivalent but not perfect in terms of the detection of variants using tissue and blood, indicating that different assays and analytical methods may have influenced the results. When performing CGPs, it is important to consider the characteristics of each NGS-based CGP test and the genetic variants associated with each disease.

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综合基因组分析测试“Ion Torrent Genexus Sequencer”与FoundationOne的比较。

背景/目的：综合基因组分析（CGP）与基于组织和血液的下一代测序（NGS）是提供针对癌症治疗的个性化药物不可或缺的一部分。本研究旨在评估体细胞变异的变异一致性，使用两种临床NGS系统进行组织和血液分析：用于组织的Genexus-OCA v3 （OCA）与FoundationOne CDx (F1)，以及用于血液的Genexus OPA （OPA）与FoundationOne CDx Liquid （F1L）。患者和方法：通过组织和循环肿瘤DNA活检，比较了6例乳腺癌、头颈癌患者两种NGS分析之间基因组改变的一致性。结果：F1与OCA共有130个基因，F1L与OPA共有41个基因。比较FoundationOne和Genexus对常见基因的检测，OCA和OPA的敏感性和特异性分别为55%和99%。Genexus和FoundationOne检测到9个单核苷酸变异（SNVs）、1个拷贝数改变（CNA）和1个融合（fusion）。然而，一个SNV （MAP2K1 F53V）、两个CNAs （AKT3和MYC）和一个融合（ESR-CCDC170）仅在Genexus中检测到，而两个SNV （TP53 Q331*和KRAS G12V）仅在FoundationOne中检测到。结论：两种癌症基因组组在使用组织和血液检测变异方面是等同的，但并不完美，这表明不同的测定和分析方法可能会影响结果。在进行CGP时，重要的是要考虑每个基于ngs的CGP测试的特征和与每种疾病相关的遗传变异。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Anticancer research 医学-肿瘤学

CiteScore

3.70

自引率

10.00%

发文量

566

审稿时长

2 months

期刊介绍： ANTICANCER RESEARCH is an independent international peer-reviewed journal devoted to the rapid publication of high quality original articles and reviews on all aspects of experimental and clinical oncology. Prompt evaluation of all submitted articles in confidence and rapid publication within 1-2 months of acceptance are guaranteed. ANTICANCER RESEARCH was established in 1981 and is published monthly (bimonthly until the end of 2008). Each annual volume contains twelve issues and index. Each issue may be divided into three parts (A: Reviews, B: Experimental studies, and C: Clinical and Epidemiological studies). Special issues, presenting the proceedings of meetings or groups of papers on topics of significant progress, will also be included in each volume. There is no limitation to the number of pages per issue.