低深度测序在检测单细胞染色体微小变异中的应用探索

生物技术通报 ›› 2016, Vol. 32 ›› Issue (12): 58-64.

低深度测序在检测单细胞染色体微小变异中的应用探索

陈大洋¹,甄贺富²,刘萍²,邱咏²,谢林²,刘弘泰¹,陈芳²

1. 中国科学院大学华大教育中心，深圳 518083；
2. 深圳华大基因研究院，深圳 518083

收稿日期:2016-04-16 出版日期:2016-12-25 发布日期:2016-12-07
作者简介:陈大洋，男，硕士研究生，研究方向：胚胎筛查；E-mail：chendayang@genomics.cn
基金资助:
深圳市未来产业专项资金（CXZZ20140808170655268）

Application of Low-coverage Whole Genome Sequencing in Detecting Chromosome Micro Variations of Single Cell

CHEN Da-yang¹,ZHEN He-fu²,LIU Ping²,QIU Yong²,XIE Lin²,LIU Hong-tai¹,CHEN Fang²

1. BGI Education Center，University of Chinese Academy of Sciences，Shenzhen 518083；
2. Beijing Genomics Institute，Shenzhen 518083

Received:2016-04-16 Published:2016-12-25 Online:2016-12-07

摘要/Abstract

摘要： 旨在探讨低深度测序在检测单细胞染色体微小变异中的应用。以经过比较基因组杂交（array CGH，aCGH）检测的5例阳性细胞系为研究对象，从中分离的单细胞分别用两种单细胞扩增试剂盒进行扩增，采用Hiseq2000测序平台进行全基因组测序，然后进行生物信息学分析，将检测结果与已被aCGH证实的结果进行比较。结果显示，5个单细胞的全基因组扩增成功，通过低深度测序均获得明确的检测结果。在用GenomePlex? Single Cell WGA Kit试剂盒的处理中检出区域与aCGH检测区域均有80%以上的重叠，1个样本检出了8 Mb（Megabase）左右的假阳性；在用PicoPLEX? WGA Kit试剂盒处理时检出信号与aCGH区域也有80%以上的重叠且无假阳性信号产生。证实在数据量为0.1 X左右时可以检出单细胞染色体上7 Mb以上的拷贝数变异。

关键词: 单细胞, 低深度, 染色体变异, 扩增

Abstract: The paper aims to study the application of low-coverage whole genome sequencing in detecting chromosome micro variations of single cell. Using 5 cell lines with positive signal and validated by aCGH as research object，the complete genome of single cell amplified by two commercial kits was sequenced by Hiseq2000；then，comparing the results by bioinformatics with those validated by aCGH. Results showed that in preliminary tests，the whole genome amplification（WGA）was successful in the 5 single cells. Following the low-coverage whole genome sequencing，they all showed the expected karyotype. While using the GenomePlex? Single Cell WGA Kit，the overlapping rate of the detection results and aCGH results was more than 80%，but there was 1 false positive signal of about 8 Mb（Megabase）in 1 sample. While using PicoPLEX? WGA Kit，the overlapping rate of the detection results and aCGH results also was more than 80%，and there was no false positive signal in detection results. The results confirmed that the method would detect the copy number variations larger than 7 Mb via the low-coverage whole genome sequencing（0.1 X）.

Key words: single cell, low-coverage, chromosome variations, amplification

中图分类号:

10.13560/j.cnki.biotech.bull.1985.2016.12.011

陈大洋,甄贺富,刘萍,邱咏,谢林,刘弘泰,陈芳. 低深度测序在检测单细胞染色体微小变异中的应用探索[J]. 生物技术通报, 2016, 32(12): 58-64.

CHEN Da-yang,ZHEN He-fu,LIU Ping,QIU Yong,XIE Lin,LIU Hong-tai,CHEN Fang. Application of Low-coverage Whole Genome Sequencing in Detecting Chromosome Micro Variations of Single Cell[J]. Biotechnology Bulletin, 2016, 32(12): 58-64.

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