Accurate detection of D4Z4 repeats, methylation and allele haplotype in facioscapulohumeral muscular dystrophy 1 using nanopore long-read adaptive sampling sequencing: a pilot study.

IF 3.7 2区 医学 Q2 GENETICS & HEREDITY
Mingtao Huang, Qinxin Zhang, Sihui Wu, Yixuan Liang, Yan Wang, Zhengfeng Xu, Ping Hu
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引用次数: 0

Abstract

Background: Facioscapulohumeral muscular dystrophy 1 (FSHD1) is one of the most common autosomal dominant neuromuscular diseases. Genetic diagnosis of FSHD1 remains a challenge because of the long length and repetitive nature of D4Z4 repeats. Long-read sequencing is an effective method for detecting FSHD1, but sequencing depth remains a limitation.

Methods: We developed a long-read library adaptive sampling (LRL-AS) method based on Oxford Nanopore Technologies (ONT) sequencing to comprehensively detect FSHD1. Two patients were sequenced by adaptive sampling, followed by analyses of D4Z4 repeat units (RUs), methylation and haplotype.

Results: Compared with whole-genome sequencing, our LRL-AS method shows significant improvements in both sequencing depth and read length. LRL-AS can identify D4Z4 RUs contraction with accuracy comparable to optical genome mapping in both 4q35 and 10q26 regions. We also calculated methylation levels in the double homeobox 4 (DUX4) gene region. With the benefit of higher sequencing depth, allele-specific methylation can be calculated with greater precision. We also observed that, at different sequencing depths, ONT sequencing data consistently provide stable calculations of methylation levels. More importantly, we demonstrated that data from adaptive sampling can be effectively used to construct the haplotype of the pathogenic allele using single-nucleotide polymorphisms.

Conclusion: Our LRL-AS method is a comprehensive approach for FSHD1 detection, improving the accuracy of D4Z4 RUs and methylation detection while enabling allele-specific haplotype construction. It holds promising potential for clinical application.

利用纳米孔长读自适应采样测序准确检测面肩肱肌营养不良1的D4Z4重复序列、甲基化和等位基因单倍型:一项初步研究
背景:面肩肱骨肌营养不良1型(FSHD1)是最常见的常染色体显性神经肌肉疾病之一。由于D4Z4重复序列的长长度和重复性质,FSHD1的遗传诊断仍然是一个挑战。长读测序是检测FSHD1的有效方法,但测序深度仍受限制。方法:建立基于Oxford Nanopore Technologies (ONT)测序的长读文库自适应采样(LRL-AS)方法,全面检测FSHD1。采用适应性取样法对2例患者进行测序,随后进行D4Z4重复单位(RUs)、甲基化和单倍型分析。结果:与全基因组测序相比,我们的lrr - as方法在测序深度和读取长度上都有显著提高。lrr - as可以在4q35和10q26区域识别D4Z4 RUs收缩,其精度与光学基因组定位相当。我们还计算了双同源盒4 (DUX4)基因区域的甲基化水平。随着测序深度的增加,可以更精确地计算等位基因特异性甲基化。我们还观察到,在不同的测序深度,ONT测序数据一致地提供稳定的甲基化水平计算。更重要的是,我们证明了适应性采样的数据可以有效地利用单核苷酸多态性构建致病等位基因的单倍型。结论:我们的LRL-AS方法是一种检测FSHD1的综合方法,提高了D4Z4 RUs和甲基化检测的准确性,同时实现了等位基因特异性单倍型的构建。具有良好的临床应用潜力。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Medical Genetics
Journal of Medical Genetics 医学-遗传学
CiteScore
7.60
自引率
2.50%
发文量
92
审稿时长
4-8 weeks
期刊介绍: Journal of Medical Genetics is a leading international peer-reviewed journal covering original research in human genetics, including reviews of and opinion on the latest developments. Articles cover the molecular basis of human disease including germline cancer genetics, clinical manifestations of genetic disorders, applications of molecular genetics to medical practice and the systematic evaluation of such applications worldwide.
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