Rare or de novo structural variation, primarily in the form of copy number variants, is detected in 5%–10% of autism spectrum disorder (ASD) families. While complex structural variants involving duplications can generally be detected using microarray or short-read genome sequencing (GS), these methods frequently fail to characterize breakpoints at nucleotide resolution, requiring additional molecular methods for validation and fine-mapping. Here, we use Oxford Nanopore Technologies PromethION long-read GS to characterize complex genomic rearrangements (CGRs) involving large duplications that segregate with ASD in five families. In total, we investigated 13 CGR carriers and were able to resolve all breakpoint junctions at nucleotide resolution. While all breakpoints were identified, the precise genomic architecture of one rearrangement remained unresolved with three different potential structures. The findings in two families include potential fusion genes formed through duplication rearrangements, involving IL1RAPL1–DMD and SUPT16H–CHD8. In two of the families originating from the same geographical region, an identical rearrangement involving ANK2 was identified, which likely represents a founder variant. In addition, we analyze methylation status directly from the long-read data, allowing us to assess the activity of rearranged genes and regulatory regions. Investigation of methylation across the CGRs reveals aberrant methylation status in carriers across a rearrangement affecting the CREBBP locus. In aggregate, our results demonstrate the utility of nanopore sequencing to pinpoint CGRs associated with ASD in five unrelated families, and highlight the importance of a gene-centric description of disease-associated complex chromosomal rearrangements.

中文翻译：

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使用长读长基因组测序解决自闭症谱系障碍中的复杂重复变异


罕见或新发结构变异，主要以拷贝数变异的形式，在 5%-10% 的自闭症谱系障碍 （ASD） 家庭中检测到。虽然通常可以使用微阵列或短读长基因组测序 （GS） 来检测涉及重复的复杂结构变异，但这些方法通常无法以核苷酸分辨率表征断点，需要额外的分子方法进行验证和精细定位。在这里，我们使用 Oxford Nanopore Technologies PromethION 长读长 GS 来表征复杂的基因组重排 （CGR），涉及与 ASD 分离的大量重复，这些重复与 ASD 分离在五个家族中。我们总共研究了 13 个 CGR 载体，并能够以核苷酸分辨率解析所有断点连接。虽然确定了所有断点，但一种重排的精确基因组结构仍未解析，具有三种不同的潜在结构。两个家族的研究结果包括通过重复重排形成的潜在融合基因，涉及 IL1RAPL1-DMD 和 SUPT16H-CHD8。在源自同一地理区域的两个家族中，鉴定出涉及 ANK2 的相同重排，这可能代表创始人变异。此外，我们直接从长读长数据中分析甲基化状态，使我们能够评估重排基因和调控区域的活性。对 CGR 甲基化的研究揭示了影响 CREBBP 基因座的重排中载体的异常甲基化状态。 总的来说，我们的结果证明了纳米孔测序在五个不相关的家族中精确定位与 ASD 相关的 CGR 的效用，并强调了以基因为中心的疾病相关复杂染色体重排描述的重要性。