高通量基因测序相位问题的校正研究.docVIP

高通量基因测序相位问题的校正研究 　　摘 要:边合成边测序的高通量基因测序技术存在一个相位问题,即碱基合成的先后顺序会出现“超前”和“延迟”。针对此问题,结合Markov过程的方法提出一种回归分析,在建立有关相位“超前”与“延迟”问题的荧光强度数据基础上,构造出相位校正矩阵,解决高通量基因测序中的相位问题。实验结果表明,采用提出的相位校正方法,达到对碱基合成时出现的相位“超前”和“延迟”问题的校正。 　　 　　关键词:高通量;测序;相位校正;Markov过程 　　中图分类号: TP751 　　文献标志码:A 　　 　　Phase emendation of high-throughput genome sequencing 　　 　　YE Bing-gang??1, WANG De-peng??2, LI Jing-xiang??2, ZHOU Yan??2, WU Xiao-ming??1 　　 　　( 　　1. School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Guangdong 510006, China??;?? 　　2. Shenzhen BGI, Shenzhen Guangdong 518083, China 　　 　　) 　　Abstract: 　　The phase problem exists in the high-throughput genome sequencing, one of sequencing by synthesize. It shows exceeding or delaying, and comes out in the order of bases synthesizing. Combining with Markov process, a method of regression analysis was provided. Based on the constructed data of fluorescence intensity, which correlated with phase exceeding and delaying questions, a phase emendation matrix was set up to resolve the phase problem. The experiment result shows the method can eliminate the questions of phase exceeding or delaying. 　　 　　The high-throughput genome sequencing has a phase problem, i.e. exceeding or delaying, which appears in the order of bases synthesizing. Combined with Markov process, a method of regression analysis was proposed. Based on the constructed data of fluorescence intensity, being correlated with phase exceeding and delaying questions, a phase emendation matrix was set up to resolve the phase problem. The experimental result shows the method can eliminate the phase exceeding or delaying. 　　 　　Key words: 　　high-throughput; sequencing; phase emendation; Markov process 　　 　　0 引言 　　 　　在电泳荧光测序方法中,存在因荧光基团电泳迁移率不同而导致的碱基相对错位问题[1-3]。高通量基因测序作为新一代的测序技术[4-7],不存在电泳迁移率有关的碱基相对错位问题,但对于采用边合成边测序方法[8]的高通量基因测序来说,碱基合成的先后顺序会出现“超前”或“延迟”的问题,如图1所示。正常的合成顺序如图1(a)的三条DNA待测链所示,而图1(b)和(c)出现了“超前”和“延迟”的合成的问题。这些都可以类比为相位超前或延迟问题,需要用数学方法来校正所得到的碱基簇荧光强度,