Pepe Francesco, Russo Gianluca, Barraco Nadia, Bono Marco, Listì Angela, Righi Luisella, de Biase Dario, Maloberti Thais, Scimone Claudia, Palumbo Lucia, Rocco Danilo, Roscigno Giuseppina, Gallo Enzo, Buglioni Simonetta, Coco Michelina, Muscarella Lucia Anna, Troncone Giancarlo, Malapelle Umberto
Department of Public Health, Federico II University of Naples, Naples, Italy.
Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), University of Palermo, Palermo, Italy.
Oncol Ther. 2025 Mar;13(1):115-130. doi: 10.1007/s40487-024-00316-0. Epub 2024 Nov 28.
Personalized medicine has revolutionized the clinical management of patients with solid tumors. However, the large volumes of molecular data derived from next-generation sequencing (NGS) and the lack of harmonized bioinformatics pipelines drastically impact the clinical management of patients with solid tumors. A possible solution to streamline the molecular interpretation and reporting of NGS data would be to adopt automated data analysis software. In this study, we tested the clinical efficiency of the Navify Mutation Profiler (nMP) software in improving the interpretation of NGS data analysis in diagnostic routine samples from patients with solid tumors.
This study included one coordinating institution (Federico II University of Naples) and five other Italian institutions. Variant call format (VCF) files from reference standard samples previously tested by the coordinating institution and from n = 8 diagnostic routine samples (n = 2 from colorectal carcinoma; n = 2 from non-small cell lung cancer; n = 2 from advanced melanoma; and n = 2 from patients with gastrointestinal stromal tumors) and previously analyzed by each participating institution (n = 5) with standardized internal analysis workflows were uploaded onto the Navify Mutation Profiler (nMP) system (Roche Sequencing Solutions, Pleasanton, CA, USA) for automated analysis and interpretation of DNA and RNA molecular alterations analytical parameters, molecular profiling, and clinical interpretation were carried out by the nMP system and compared with the standard workflow data analyzed by the participating institutions.
Overall, all VCF files were successfully submitted and interpreted by the nMP system. A concordance agreement rate of 89.6% was observed between the automated and standard workflow systems. In particular, DNA and RNA molecular profiles obtained with the nMP system matched those obtained with standardized approaches in 44 out of 48 patients (91.7%) and in 11 out of 12 (91.7%) cases, respectively. In addition, the nMP system evidenced wild-type variants in 6 out of 7 (85.7%) cases.
The nMP system represents a valid, easily manageable, and clinically useful system to interpret NGS data on diagnostic routine samples from patients with solid tumors.
个性化医疗彻底改变了实体瘤患者的临床管理方式。然而，来自下一代测序（NGS）的大量分子数据以及缺乏统一的生物信息学流程，极大地影响了实体瘤患者的临床管理。简化NGS数据分子解读和报告的一个可能解决方案是采用自动化数据分析软件。在本研究中，我们测试了Navify突变分析器（nMP）软件在改善实体瘤患者诊断常规样本中NGS数据分析解读方面的临床效率。
本研究包括一个协调机构（那不勒斯费德里科二世大学）和其他五个意大利机构。来自协调机构先前检测的参考标准样本以及来自8份诊断常规样本（2份来自结直肠癌；2份来自非小细胞肺癌；2份来自晚期黑色素瘤；2份来自胃肠道间质瘤患者）的变异调用格式（VCF）文件，这些样本先前已由每个参与机构（共5个）采用标准化内部分析流程进行分析，然后上传到Navify突变分析器（nMP）系统（美国加利福尼亚州普莱森顿的罗氏测序解决方案公司），用于对DNA和RNA分子改变进行自动分析和解读，nMP系统进行分子谱分析和临床解读，并与参与机构分析的标准流程数据进行比较。
总体而言，所有VCF文件均成功由nMP系统提交并解读。自动分析系统与标准流程系统之间的一致性协议率为89.6%。具体而言，nMP系统获得的DNA和RNA分子谱分别在48例患者中的44例（91.7%）和12例中的11例（91.7%）与采用标准化方法获得的分子谱相匹配。此外，nMP系统在7例中的6例（85.7%）中检测到野生型变异。
nMP系统是一个有效、易于管理且对解读实体瘤患者诊断常规样本的NGS数据具有临床实用价值的系统。
