This article is part of the Research Topic Single Cell Analysis


Front. Oncol., 27 January 2014 |

Current challenges in the bioinformatics of single cell genomics

imageLuwen Ning1, imageGeng Liu2, imageGuibo Li2, imageYong Hou2, imageYin Tong1 and imageJiankui He1*
  • 1Department of Biology, South University of Science and Technology of China, Shenzhen, China
  • 2BGI-Shenzhen, Shenzhen, China

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.

Keywords: single cell analysis, RNA sequencing, DNA sequencing, SNP, CNV

Citation: Ning L, Liu G, Li G, Hou Y, Tong Y and He J (2014) Current challenges in the bioinformatics of single cell genomics. Front. Oncol. 4:7. doi: 10.3389/fonc.2014.00007

Received: 30 October 2013; Paper pending published: 22 December 2013;
Accepted: 12 January 2014; Published online: 27 January 2014.

Edited by:

Tomer Kalisky, Bar-Ilan University, Israel

Reviewed by:

Myriam Alcalay, Istituto Europeo di Oncologia, Italy
Luisa Lanfrancone, European Institute of Oncology, Italy

Copyright: © 2014 Ning, Liu, Li, Hou, Tong and He. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Jiankui He, Department of Biology, South University of Science and Technology of China, No 1088, Xueyuan Road, Xili, Nanshan District, Shenzhen, Guangdong 518055, China e-mail: