Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing.
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DOI：
10.1186/1471-2105-12-5
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发表时间：
2011-01-05
影响因子：
3
通讯作者：
Ulivi G
中科院分区：
文献类型：
--
作者：
Prosperi MC;Prosperi L;Bruselles A;Abbate I;Rozera G;Vincenti D;Solmone MC;Capobianchi MR;Ulivi G
下一代测序（NGS）为高通量基因组学提供了独特的机会，并有可能在许多领域取代Sanger测序，包括从头测序、重测序、元基因组学和感染性病原体（如病毒准种）的表征。尽管针对NGS数据已经开发和完善了用于全基因组组装和基因组变异分析的方法和软件，但利用NGS数据重建病毒准种仍然是一个挑战。这一应用将有助于分析与免疫反应和抗逆转录病毒治疗暴露有关的宿主内进化途径。本文介绍了一组基于NGS重测序实验的准种组合分析公式和一种准种重建算法。我们要求测序片段与参考基因组对齐，并将参考基因组划分为一组滑动窗口（扩增子）。重建算法是基于多项分布的组合，旨在最大限度地减少虚假变体的重建，称为硅重组。重建算法被应用于无错误的模拟数据，并重建了高比例的真实变异，即使在低遗传多样性的情况下，获得硅重组的机会很高。来自乙型肝炎病毒感染患者的经验NGS数据的结果证实了它能够表征不同患者的不同病毒变体。组合分析描述了在给定扩增子分配和种群多样性的情况下重建准种的困难。该重构算法在考虑模拟数据和真实数据的情况下，即使存在序列误差，也具有良好的性能。
Next-generation sequencing (NGS) offers a unique opportunity for high-throughput genomics and has potential to replace Sanger sequencing in many fields, including de-novo sequencing, re-sequencing, meta-genomics, and characterisation of infectious pathogens, such as viral quasispecies. Although methodologies and software for whole genome assembly and genome variation analysis have been developed and refined for NGS data, reconstructing a viral quasispecies using NGS data remains a challenge. This application would be useful for analysing intra-host evolutionary pathways in relation to immune responses and antiretroviral therapy exposures. Here we introduce a set of formulae for the combinatorial analysis of a quasispecies, given a NGS re-sequencing experiment and an algorithm for quasispecies reconstruction. We require that sequenced fragments are aligned against a reference genome, and that the reference genome is partitioned into a set of sliding windows (amplicons). The reconstruction algorithm is based on combinations of multinomial distributions and is designed to minimise the reconstruction of false variants, called in-silico recombinants. The reconstruction algorithm was applied to error-free simulated data and reconstructed a high percentage of true variants, even at a low genetic diversity, where the chance to obtain in-silico recombinants is high. Results on empirical NGS data from patients infected with hepatitis B virus, confirmed its ability to characterise different viral variants from distinct patients. The combinatorial analysis provided a description of the difficulty to reconstruct a quasispecies, given a determined amplicon partition and a measure of population diversity. The reconstruction algorithm showed good performance both considering simulated data and real data, even in presence of sequencing errors.
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影响因子：
12.3
作者：
Huse SM;Huber JA;Morrison HG;Sogin ML;Welch DM
通讯作者：
Welch DM
影响因子：
14.9
作者：
Philippe, Nicolas;Boureux, Anthony;Rivals, Eric
通讯作者：
Rivals, Eric
DOI：
10.1073/pnas.0801523105
发表时间：
2008-09-02
影响因子：
11.1
作者：
Campbell, Peter J.;Pleasance, Erin D.;Stratton, Michael R.
通讯作者：
Stratton, Michael R.
影响因子：
14.9
作者：
Parameswaran P;Jalili R;Tao L;Shokralla S;Gharizadeh B;Ronaghi M;Fire AZ
通讯作者：
Fire AZ
影响因子：
4.3
作者：
Chen K;Pachter L
通讯作者：
Pachter L