Purpose

Structural variants (SVs) may be an underestimated cause of hereditary cancer syndromes given the current limitations of short-read next-generation sequencing. Here we investigated the utility of long-read sequencing in resolving germline SVs in cancer susceptibility genes detected through short-read genome sequencing.

Methods

Known or suspected deleterious germline SVs were identified using Illumina genome sequencing across a cohort of 669 advanced cancer patients with paired tumor genome and transcriptome sequencing. Candidate SVs were subsequently assessed by Oxford Nanopore long-read sequencing.

Results

Nanopore sequencing confirmed eight simple pathogenic or likely pathogenic SVs, resolving three additional variants whose impact could not be fully elucidated through short-read sequencing. A recurrent sequencing artifact on chromosome 16p13 and one complex rearrangement on chromosome 5q35 were subsequently classified as likely benign, obviating the need for further clinical assessment. Variant configuration was further resolved in one case with a complex pathogenic rearrangement affecting TSC2.

Conclusion

Our findings demonstrate that long-read sequencing can improve the validation, resolution, and classification of germline SVs. This has important implications for return of results, cascade carrier testing, cancer screening, and prophylactic interventions.

中文翻译：

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使用长读长测序改进对遗传性癌症易感性的结构变异解释。

目的

鉴于目前短读长二代测序的局限性，结构变异 (SV) 可能是遗传性癌症综合征的一个被低估的原因。在这里，我们研究了长读长测序在解决通过短读长基因组测序检测到的癌症易感基因中的种系 SV 中的效用。

方法

使用 Illumina 基因组测序对一组 669 名晚期癌症患者进行了配对肿瘤基因组和转录组测序，鉴定了已知或疑似有害的种系 SV。随后通过牛津纳米孔长读长测序评估候选 SV。

结果

纳米孔测序证实了八种简单的致病或可能致病的 SV，解决了另外三种变异，其影响无法通过短读长测序完全阐明。染色体 16p13 上的反复测序伪影和染色体 5q35 上的一个复杂重排随后被归类为可能是良性的，无需进一步的临床评估。在一个影响TSC2的复杂致病性重排的情况下，变异配置得到了进一步解决。

结论

我们的研究结果表明，长读长测序可以提高种系 SV 的验证、分辨率和分类。这对返回结果、级联载体检测、癌症筛查和预防性干预具有重要意义。