Table3_Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing.XLSX

Background: Structural variations (SVs) are common genetic alterations in the human genome that could cause different phenotypes and diseases, including cancer. However, the detection of structural variations using the second-generation sequencing was limited by its short read length, which restrained our understanding of structural variations. Methods: In this study, we developed a 28-gene panel for long-read sequencing and employed it to Oxford Nanopore Technologies and Pacific Biosciences platforms. We analyzed structural variations in the 28 breast cancer-related genes through long-read genomic and transcriptomic sequencing of tumor, para-tumor, and blood samples in 19 breast cancer patients. Results: Our results showed that some somatic SVs were recurring among the selected genes, though the majority of them occurred in the non-exonic region. We found evidence supporting the existence of hotspot regions for SVs, which extended our previous understanding that they exist only for single nucleotide variations. Conclusion: In conclusion, we employed long-read genomic and transcriptomic sequencing to identify SVs from breast cancer patients and proved that this approach holds great potential in clinical application.背景：结构变异（Structural variations, SVs）是人类基因组中常见的遗传改变，可引发包括癌症在内的多种表型异常与疾病。然而，基于二代测序（second-generation sequencing）的结构变异检测受限于其短读长特性，这一局限制约了我们对结构变异的深入认知。 方法：本研究开发了一款面向长读长测序（long-read sequencing）的28基因面板（28-gene panel），并将其应用于牛津纳米孔科技公司（Oxford Nanopore Technologies）与太平洋生物科学公司（Pacific Biosciences）的测序平台。我们对19名乳腺癌患者的肿瘤、癌旁及血液样本进行长读长基因组与转录组测序，以此分析28个乳腺癌相关基因的结构变异情况。 结果：本研究结果显示，部分体细胞结构变异在选定基因中反复出现，不过其中绝大多数位于非外显子区域。我们找到了支持结构变异热点区域存在的证据，这拓展了此前仅认为单核苷酸变异（single nucleotide variations, SNVs）存在热点区域的认知。 结论：综上，本研究通过长读长基因组与转录组测序技术鉴定了乳腺癌患者的结构变异，证实该方法在临床应用中具有巨大潜力。