Cytosine Variant Calling with High-throughput Nanopore Sequencing
Cytosine Variant Calling with High-throughput Nanopore Sequencing
复制标题
通过高通量纳米孔测序进行胞嘧啶变异体识别
DOI：
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发表时间：
2016
期刊：
影响因子：
--
通讯作者：
B. Paten
中科院分区：
文献类型：
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作者：
Arthur C. Rand;Miten Jain;Jordan M. Eizenga;Audrey Musselman;Hugh E. Olsen;M. Akeson;B. Paten
DNA 的化学修饰可调节细胞状态和功能。 Oxford Nanopore MinION 是一款便携式单分子 DNA 测序仪，可以对基因组 DNA 的长片段进行测序。在这里，我们展示了 MinION 可用于检测和绘制两种化学修饰胞嘧啶：5-甲基胞嘧啶和 5-羟甲基胞嘧啶。我们提出了一种概率方法，可以扩展核苷酸字母表以包括含有化学修饰的碱基。我们对合成 DNA 的结果表明，在三向比较中单个胞嘧啶碱基修饰的分类准确度高达 95%，在双向比较中分类准确度高达 98%。意义声明 基于纳米孔的测序技术可以从未扩增的基因组 DNA 中产生长读数，从而有可能对细胞中发生的化学修饰和非规范 DNA 核苷酸进行表征。随着纳米孔测序仪吞吐量的提高，同时检测胞嘧啶的多个表观遗传修饰将成为这些设备的重要功能。在这里，我们提出了一个统计模型，允许 Oxford Nanopore Technologies MinION 使用标准 DNA 制备和测序技术检测胞嘧啶的化学修饰。我们的方法基于使用变阶隐马尔可夫模型对 DNA k-mers 产生的离子电流进行建模，其中发射根据正态分布的分层狄利克雷过程混合进行分布。该方法提供了扩展核苷酸字母表以允许修饰碱基的变体调用的原则性方法。
Chemical modifications to DNA regulate cellular state and function. The Oxford Nanopore MinION is a portable single-molecule DNA sequencer that can sequence long fragments of genomic DNA. Here we show that the MinION can be used to detect and map two chemical modifications cytosine, 5-methylcytosine and 5-hydroxymethylcytosine. We present a probabilistic method that enables expansion of the nucleotide alphabet to include bases containing chemical modifications. Our results on synthetic DNA show that individual cytosine base modifications can be classified with accuracy up to 95% in a three-way comparison and 98% in a two-way comparison. Statement of Significance Nanopore-based sequencing technology can produce long reads from unamplified genomic DNA, potentially allowing the characterization of chemical modifications and non-canonical DNA nucleotides as they occur in the cell. As the throughput of nanopore sequencers improves, simultaneous detection of multiple epigenetic modifications to cytosines will become an important capability of these devices. Here we present a statistical model that allows the Oxford Nanopore Technologies MinION to be used for detecting chemical modifications to cytosine using standard DNA preparation and sequencing techniques. Our method is based on modeling the ionic current due to DNA k-mers with a variable-order hidden Markov model where the emissions are distributed according to a hierarchical Dirichlet process mixture of normal distributions. This method provides a principled way to expand the nucleotide alphabet to allow for variant calling of modified bases.
影响因子：
3.4
作者：
Timp, Winston;Comer, Jeffrey;Aksimentiev, Aleksei
通讯作者：
Aksimentiev, Aleksei