Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing.
Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing.
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DOI：
10.1002/humu.23223
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发表时间：
2017-07
期刊：
影响因子：
3.9
通讯作者：
Anvar SY
中科院分区：
文献类型：
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作者：
Borràs DM;Vossen RHAM;Liem M;Buermans HPJ;Dauwerse H;van Heusden D;Gansevoort RT;den Dunnen JT;Janssen B;Peters DJM;Losekoot M;Anvar SY
常染色体显性遗传性多囊肾病（ADPKD）的遗传学诊断具有挑战性，因为等位基因异质性、高GC含量以及PKD1基因与6个假基因的同源性。短读的下一代测序方法，如全基因组测序和全外显子组测序，通常无法可靠地表征复杂区域，如PKD1。然而，长读单分子测序已被证明是一种替代策略，可以克服PKD 1的复杂性，并区分PKD 1的同源区域及其假基因。在这项研究中，我们提出了使用长读段测序来表征19例ADPKD患者队列的复杂区域的分辨率增加的能力。我们的方法在鉴定PKD 1致病性变体方面具有高灵敏度，诊断了94.7%的患者。我们表明，通过直接长读序，在一次测试中可靠地筛查ADPKD患者，而不干扰PKD1同源序列，通常由PKD1假基因的残留扩增引入，现在是可能的。该策略可以在诊断中实施，并且非常适合于测序和解析具有临床相关性的复杂基因组区域。
A genetic diagnosis of autosomal‐dominant polycystic kidney disease (ADPKD) is challenging due to allelic heterogeneity, high GC content, and homology of the PKD1 gene with six pseudogenes. Short‐read next‐generation sequencing approaches, such as whole‐genome sequencing and whole‐exome sequencing, often fail at reliably characterizing complex regions such as PKD1. However, long‐read single‐molecule sequencing has been shown to be an alternative strategy that could overcome PKD1 complexities and discriminate between homologous regions of PKD1 and its pseudogenes. In this study, we present the increased power of resolution for complex regions using long‐read sequencing to characterize a cohort of 19 patients with ADPKD. Our approach provided high sensitivity in identifying PKD1 pathogenic variants, diagnosing 94.7% of the patients. We show that reliable screening of ADPKD patients in a single test without interference of PKD1 homologous sequences, commonly introduced by residual amplification of PKD1 pseudogenes, by direct long‐read sequencing is now possible. This strategy can be implemented in diagnostics and is highly suitable to sequence and resolve complex genomic regions that are of clinical relevance.