Lynch syndrome is a hereditary disease characterized by an increased risk of colorectal and other cancers. Germline variants in the mismatch repair (MMR) genes are responsible for this disease. Previously, we screened the MMR genes in colorectal cancer patients who fulfilled modified Amsterdam II criteria, and multiplex ligation-dependent probe amplification (MPLA) identified 11 structural variants (SVs) of MLH1 and MSH2 in 17 patients. In this study, we have tested the efficacy of long read-sequencing coupled with target enrichment for the determination of SVs and their breakpoints. DNA was captured by array probes designed to hybridize with target regions including four MMR genes and then sequenced using MinION, a nanopore sequencing platform. Approximately, 1000-fold coverage was obtained in the target regions compared with other regions. Application of this system to four test cases among the 17 patients correctly mapped the breakpoints. In addition, we newly found a deletion across an 84 kb region of MSH2 in a case without the pathogenic single nucleotide variants. These data suggest that long read-sequencing combined with hybridization-based enrichment is an efficient method to identify both SVs and their breakpoints. This strategy might replace MLPA for the screening of SVs in hereditary diseases.

林奇综合征是一种遗传性疾病，其特征是患结直肠癌和其他癌症的风险增加。错配修复 (MMR) 基因中的种系变异是导致这种疾病的原因。此前，我们筛选了符合改良阿姆斯特丹 II 标准的结直肠癌患者的 MMR 基因，并且多重连接依赖性探针扩增 (MPLA) 鉴定了MLH1和MSH2的 11 个结构变异 (SV)在 17 名患者中。在这项研究中，我们测试了长读序列结合目标富集确定 SV 及其断点的功效。DNA 被设计用于与包括四个 MMR 基因在内的目标区域杂交的阵列探针捕获，然后使用纳米孔测序平台 MinION 进行测序。与其他区域相比，在目标区域中获得了大约 1000 倍的覆盖率。将该系统应用于 17 名患者中的 4 个测试用例，正确映射了断点。此外，我们在MSH2的 84 kb 区域中新发现了一个缺失。在没有致病性单核苷酸变异的情况下。这些数据表明，长读序列结合基于杂交的富集是识别 SV 及其断点的有效方法。这种策略可能会取代 MLPA 来筛查遗传性疾病中的 SV。