Here, we report the application of a long-read sequencer, PromethION, for analyzing human cancer genomes. We first conducted whole-genome sequencing on lung cancer cell lines. We found that it is possible to genotype known cancerous mutations, such as point mutations. We also found that long-read sequencing is particularly useful for precisely identifying and characterizing structural aberrations, such as large deletions, gene fusions, and other chromosomal rearrangements. In addition, we identified several medium-sized structural aberrations consisting of complex combinations of local duplications, inversions, and microdeletions. These complex mutations occurred even in key cancer-related genes, such as STK11, NF1, SMARCA4, and PTEN. The biological relevance of those mutations was further revealed by epigenome, transcriptome, and protein analyses of the affected signaling pathways. Such structural aberrations were also found in clinical lung adenocarcinoma specimens. Those structural aberrations were unlikely to be reliably detected by conventional short-read sequencing. Therefore, long-read sequencing may contribute to understanding the molecular etiology of patients for whom causative cancerous mutations remain unknown and therapeutic strategies are elusive.

中文翻译：

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非小细胞肺癌基因组的长读长测序。

在这里，我们报告了长读长测序仪 PromethION 在分析人类癌症基因组中的应用。我们首先对肺癌细胞系进行了全基因组测序。我们发现可以对已知的癌性突变进行基因分型，例如点突变。我们还发现，长读长测序对于精确识别和表征结构畸变特别有用，例如大缺失、基因融合和其他染色体重排。此外，我们确定了几个中等大小的结构畸变，包括局部重复、倒置和微缺失的复杂组合。这些复杂的突变甚至发生在关键的癌症相关基因中，例如STK11、NF1、SMARCA4和PTEN. 通过对受影响信号通路的表观基因组、转录组和蛋白质分析进一步揭示了这些突变的生物学相关性。在临床肺腺癌标本中也发现了这种结构畸变。传统的短读长测序不太可能可靠地检测到这些结构畸变。因此，长读长测序可能有助于了解致病性癌性突变仍然未知且治疗策略难以捉摸的患者的分子病因学。