Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders
Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders
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DOI：
10.1016/j.xhgg.2021.100023
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发表时间：
2021-04-08
期刊：
影响因子：
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通讯作者：
Cooper, Gregory M.
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文献类型：
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作者：
Hiatt, Susan M.;Lawlor, James M. J.;Cooper, Gregory M.
外显子组和基因组测序已被证明是诊断神经发育障碍（NDD）的有效工具，但大部分NDD不能归因于目前可检测到的遗传变异。这可能至少部分是由于许多遗传变异难以或不可能通过典型的短读段测序方法检测的事实。在这里，我们描述了使用Pacific Biosciences环状共有序列测序（CCS）读数的基因组分析，其既长（>10 kb）又准确（> 99%bp准确度）。我们使用CCS对六个先证者父母三人组进行了NDD，尽管进行了广泛的测试，包括基因组测序和短读段，但这些NDD无法解释。我们在每个三人组中识别了变体并创建了从头组装，全局指标表明这些数据集比短读数据提供的数据集更准确和全面。在一名先证者中，我们发现了一种可能的致病性（LP），从头L1介导的CDKL 5插入，导致外显子3重复，从而导致移码。在第二个先证者中，我们鉴定了多个大的从头结构变异，包括影响DGKB和MLLT3的插入易位，我们显示其破坏MLLT3转录水平。我们认为这种广泛的结构变异可能是致病的。变异检测的广度和质量，再加上在六个不明原因的NDD先证者中的两个中发现临床和研究兴趣的变异，支持长读基因组测序可以大大提高罕见疾病遗传发现率的假设。
Exome and genome sequencing have proven to be effective tools for the diagnosis of neurodevelopmental disorders (NDDs), but large fractions of NDDs cannot be attributed to currently detectable genetic variation. This is likely, at least in part, a result of the fact that many genetic variants are difficult or impossible to detect through typical short-read sequencing approaches. Here, we describe a genomic analysis using Pacific Biosciences circular consensus sequencing (CCS) reads, which are both long (>10 kb) and accurate (>99% bp accuracy). We used CCS on six proband-parent trios with NDDs that were unexplained despite extensive testing, including genome sequencing with short reads. We identified variants and created de novo assemblies in each trio, with global metrics indicating these datasets are more accurate and comprehensive than those provided by short-read data. In one proband, we identified a likely pathogenic (LP), de novo L1-mediated insertion in CDKL5 that results in duplication of exon 3, leading to a frameshift. In a second proband, we identified multiple large de novo structural variants, including insertion-translocations affecting DGKB and MLLT3, which we show disrupt MLLT3 transcript levels. We consider this extensive structural variation likely pathogenic. The breadth and quality of variant detection, coupled to finding variants of clinical and research interest in two of six probands with unexplained NDDs, support the hypothesis that long-read genome sequencing can substantially improve rare disease genetic discovery rates.