Sequencing of human genomes with nanopore technology
Sequencing of human genomes with nanopore technology
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DOI：
10.1038/s41467-019-09637-5
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发表时间：
2019-04-23
影响因子：
16.6
通讯作者：
Donnelly, Peter
中科院分区：
文献类型：
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作者：
Bowden, Rory;Davies, Robert W.;Donnelly, Peter
全基因组测序 (WGS) 正在临床医学中广泛应用于诊断领域并为治疗选择提供信息。在这里，我们通过对参考样本 NA12878 和患有共济失调全血细胞减少综合征和严重免疫失调的个体的基因组进行测序，评估了 Oxford Nanopore Technologies (ONT) MinION 长读长测序仪用于常规 WGS 的潜力。我们开发并应用一种新颖的无参考面板分析方法来推断并利用相位信息，从而将单核苷酸变异（SNV）调用性能从其他适度水平提高。在临床样本中，我们识别并直接对 SAMD9L (OMIM #159550) 中的两个非同义 de novo 变异进行阶段分析，推断它们位于相同的父本单倍型上。虽然 ONT 数据的共识 SNV 调用错误率仍然远高于短读方法的错误率，但我们证明了分析创新的实质性好处。纳米孔测序必须继续对碱基识别和 SNV 识别方法进行持续改进，以使其成为临床 WGS 的主要方法。
Whole-genome sequencing (WGS) is becoming widely used in clinical medicine in diagnostic contexts and to inform treatment choice. Here we evaluate the potential of the Oxford Nanopore Technologies (ONT) MinION long-read sequencer for routine WGS by sequencing the reference sample NA12878 and the genome of an individual with ataxia-pancytopenia syndrome and severe immune dysregulation. We develop and apply a novel reference panel-free analytical method to infer and then exploit phase information which improves single-nucleotide variant (SNV) calling performance from otherwise modest levels. In the clinical sample, we identify and directly phase two non-synonymous de novo variants in SAMD9L, (OMIM #159550) inferring that they lie on the same paternal haplotype. Whilst consensus SNV-calling error rates from ONT data remain substantially higher than those from short-read methods, we demonstrate the substantial benefits of analytical innovation. Ongoing improvements to base-calling and SNV-calling methodology must continue for nanopore sequencing to establish itself as a primary method for clinical WGS.