Chavda Rinal, Inchanalkar Mayuri, Gawde Jitendra, Mahimkar Manoj B
Mahimkar Lab, Cancer Research Institute Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, , Maharashtra, 410210, India.
Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India.
Sci Rep. 2025 Jul 2;15(1):23015. doi: 10.1038/s41598-025-08036-9.
Copy number alterations (CNAs) are imperative in determining the patient's prognostic and predictive status. Real-time polymerase chain reaction (PCR) is extensively used to validate the results of global genomic profiling methods. However, nCounter NanoString is yet to be thoroughly assessed and compared for copy number analysis. For the first time, we have comprehensively compared the aforementioned techniques in 119 oral cancer samples to evaluate 24 genes. Spearman's rank correlation and Cohen's Kappa score were calculated to identify concurrence. Kaplan-Meier curves with the Log-rank test were used to identify genes related to disease prognosis, including recurrence-free survival (RFS), disease-specific survival (DSS), and overall survival (OS). Spearman's rank correlation ranged from r = 0.188 to 0.517, and Cohen's kappa score showed a moderate to substantial agreement. Additionally, in real-time PCR, ISG15 was associated with a better prognosis for RFS, DSS and OS, along with ATM, CASP4, and CYB5A with poor RFS. However, in nCounter NanoString, ISG15 was associated with poor prognosis for RFS, DSS, and OS, while CDK11A showed poor prognosis for RFS. Real-time PCR remains a robust method to validate the genomic biomarkers. However, these observations should be rigorously validated by conducting additional, well-designed, independent studies.
拷贝数改变（CNAs）对于确定患者的预后和预测状态至关重要。实时聚合酶链反应（PCR）被广泛用于验证全基因组分析方法的结果。然而，nCounter NanoString在拷贝数分析方面尚未得到全面评估和比较。我们首次在119份口腔癌样本中全面比较了上述技术，以评估24个基因。计算斯皮尔曼等级相关性和科恩卡帕系数以确定一致性。使用带有对数秩检验的Kaplan-Meier曲线来确定与疾病预后相关的基因，包括无复发生存期（RFS）、疾病特异性生存期（DSS）和总生存期（OS）。斯皮尔曼等级相关性范围为r = 0.188至0.517，科恩卡帕系数显示出中度至高度一致性。此外，在实时PCR中，ISG15与RFS、DSS和OS的较好预后相关，而ATM、CASP4和CYB5A与较差的RFS相关。然而，在nCounter NanoString中，ISG15与RFS、DSS和OS的较差预后相关，而CDK11A与RFS的较差预后相关。实时PCR仍然是验证基因组生物标志物的可靠方法。然而，这些观察结果应通过进行额外的、设计良好的独立研究来严格验证。
