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Abstract：
Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina\'s TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.
摘要：
拷贝数改变(CNA)在肿瘤起始和进展中是显著的。识别这些畸变对于靶向治疗和个性化癌症诊断至关重要。下一代测序（NGS）方法在可扩展性和成本效益方面具有优势，超越了传统实验室方法中与参考组件和探针能力相关的限制。这项回顾性研究评估了50个FFPE肿瘤样本中的CNA(乳腺癌，卵巢癌,胰腺癌,黑色素瘤，和前列腺癌）使用Illumina的TruSight肿瘤学500（TSO500）和AffymetrixOncoscan分子反演探针（OS-MIP）（ThermoFisherScientific，沃尔瑟姆,MA,美国）。使用NxClinical6.2软件的NGS分析证明了CNA检测的高灵敏度和特异性（100％），与OS-MIP相比，具有完全一致率。所有54个已知的CNA均由NGS鉴定，收益最普遍(63%)。在MYC中观察到显著的CNA(18%)，TP53（12%），BRAF（8%），PIK3CA,EGFR,和FGFR1(6%)基因。诊断参数表现出很高的准确性，包括积极的预测值，负预测值，和整体诊断准确性。这项研究强调了NxClinical作为使用NGSTSO500识别临床相关基因改变的可靠软件，为基于CNA分析的个性化癌症治疗策略提供了有价值的见解。
