| 引用本文: | 李燕,李垚垚.新一代测序的拷贝数变异检测算法研究与设计[J].生物信息学,2015,13(3):186-191. |
| LI Yan,LI Yaoyao.An algorithm for detecting copy number alteration from next generation sequencing of human genome[J].Chinese Journal of Bioinformatics,2015,13(3):186-191. |
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| 摘要: |
| 基于不同的测序技术,基因拷贝数变异的检测方法有多种,但时间复杂度较高,而新一代测序技术的发展为基因拷贝数变异检测的研究开辟了新领域。通过仿真实验、置换检验设计出一种新的基于新一代测序的拷贝数变异检测算法。不同于其它算法,本算法无需参考样本,通过直接研究比对后的序列以及reads与拷贝数的关系,来研究检测拷贝数变异,实验结果表明在时间复杂度上能提高50%以上的运算速度,这对今后拷贝数与疾病的研究具有重要意义。 |
| 关键词: 新一代测序 拷贝数变异 仿真 置换检验 |
| DOI：10.3969/j.issn.1672-5565.2015.03.07 |
| 分类号:TP301.6 |
| 基金项目:黑龙江省教育厅科学技术研究项目(12541565)。 |
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| An algorithm for detecting copy number alteration from next generation sequencing of human genome |
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LI Yan, LI Yaoyao
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(Harbin Medical University Daqing campus, Daqing Heilongjiang 163319,China)
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| Abstract: |
| Based on different sequencing technologies, the detection methods of gene copy number variation are available. However, with the development of new generation sequencing technology, a new field for researchingcopy number variations has been opened up.Through the simulation experiment and the replacement test, this paper designs a new copy number variation detection algorithm based on the new generation of sequencing. Unlike other algorithms, our algorithm doesn’t need thereference samples, butuses the mapped datafrom next generation sequencing platforms and the relationship between reads and gene copy number to detect gene copy number variations in the genome. The experimental results show that the performance in time complexity can be improved by more than 50%, indicating the important significance for the further study of gene copy number and disease in the future. |
| Key words: Next generation sequencing Copy number variations Simulation Permutation test |
