Current challenges in the bioinformatics of single cell genomics.
Current challenges in the bioinformatics of single cell genomics.
复制标题
单细胞基因组学生物信息学的当前挑战。
DOI：
10.3389/fonc.2014.00007
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发表时间：
2014
影响因子：
4.7
通讯作者：
He J
中科院分区：
文献类型：
--
作者：
Ning L;Liu G;Li G;Hou Y;Tong Y;He J
单细胞基因组学是一个快速发展的领域，近年来出现了许多新技术。然而，很少有针对单细胞基因组学分析的生物信息学工具可用。单细胞DNA/RNA测序数据通常具有低基因组覆盖率和高扩增偏倚，这给生物信息学分析带来了挑战。目前许多为大细胞测序开发的生物信息学工具不能很好地处理单细胞测序数据。在这里，我们总结了当前单细胞基因组DNA测序和单细胞转录组生物信息学分析面临的挑战。这些挑战包括呼叫拷贝数变异，识别肿瘤样本中的突变基因，重建细胞系，恢复低丰度转录本，以及提高转录本定量分析的准确性。单细胞基因组学生物信息学分析的发展将促进该技术在基础生物学和医学研究中的应用。
Single cell genomics is a rapidly growing field with many new techniques emerging in the past few years. However, few bioinformatics tools specific for single cell genomics analysis are available. Single cell DNA/RNA sequencing data usually have low genome coverage and high amplification bias, which makes bioinformatics analysis challenging. Many current bioinformatics tools developed for bulk cell sequencing do not work well with single cell sequencing data. Here, we summarize current challenges in the bioinformatics analysis of single cell genomic DNA sequencing and single cell transcriptomes. These challenges include calling copy number variations, identifying mutated genes in tumor samples, reconstructing cell lineages, recovering low abundant transcripts, and improving the accuracy of quantitative analysis of transcripts. Development in single cell genomics bioinformatics analysis will promote the application of this technology to basic biology and medical research.