The key to a deeper understanding of cancer – single cell genomics


Three hundred years ago, the father of microbiology, Anton van Leeuwenhoek, observed single-celled organisms for the first time. Three hundred years later, advances in next-generation sequencing (NGS) and whole genome amplification (WGA) technologies now enable us to decode the genetic differences between single cells.

This ability has tremendous implications for the field of cancer research. Nowadays we are able to study all facets of tumor states and behaviors, looking into intratumor heterogeneity, clonal evolution in primary tumors, invasion in early stage cancers, epithelial–mesenchymal transition and metastatic dissemination. Academia has witnessed a rapid growth of “single cell genomics” research (see the graph below). REPLI-g technology appears in over 450 publications. We thought this would be a good time to look at the most cited reviews of single cell analysis and, at the same time, delve more deeply into the applications that shed light on the understanding of cancer.


Looking at single cell analysis, advances and future development, a key review for methodology is “Single cell analysis of cancer genomes” from Van Loo and Voet. This review covers the latest techniques for single cell isolation, whole genome and transcriptome amplification, and microarray and massively parallel sequencing analysis of amplification products. “The first five years of single-cell cancer genomics and beyond” from Navin looks at the extraordinary progress made in the development and application of single cell DNA and RNA sequencing methods for cancer research over the past 5 years. Wills and Mead discuss some recent advances in single cell genomics technologies and data modeling and investigate the implications for moving cancer research into the clinic in “Application of single cell genomics in cancer: promise and challenges.”

Turning to applications of single cell analysis in cancer research, Cheng-Zhong Zhang is definitely one of the pioneers in the field. Zhang et al.’s recent report in Nature, “Chromothripsis from DNA damage in micronuclei,” sheds light on a new approach to studying the molecular mechanism of this phenomenon at the single cell level. Chromothripsis is a catastrophic mutational event that results in massive rearrangements of one or more chromosomes. It helps to drive cancer development through oncogene amplification, tumor suppressor loss and DNA damage response impairment. This milestone paper describes a study on individual cells, which were selected based on live cell imaging and subjected to single cell whole genome sequencing. The approach, called “LookSeq,” allowed identification of the first molecular mechanism of chromothripsis. Whole genome amplification (WGA) with highly uniform genome coverage is a prerequisite for successful single cell sequencing. The superior performance of the REPLI-g Single Cell Kit in WGA was critical for this research.

A recent study from Yee and colleagues, “A novel approach for next-generation sequencing of circulating cells,” touched on one of the biggest topics in personalized medicine today, liquid biopsy. Enriching and characterizing circulating tumor cells (CTCs) from the blood provides a means for noninvasive detection of evolving tumor mutations. However, approaches suitable for solid tumors have proven limited for circulating tumor samples due to the low levels of input DNA. Furthermore, WGA methods are not always compatible with blood collection tube preservatives. In this study, the REPLI-g Single Cell Kit was successfully used for WGA when combined with a multiplex targeted resequencing approach. The results could stand as proof of concept for real-time monitoring of patient tumors using noninvasive liquid biopsies.

To read more selected applications of single cell technology for cancer research, check out our new mini review series! This series highlights state-of-the-art methods for single cell analysis and examples of how QIAGEN’s single cell technologies have provided solutions for experimental challenges faced by researchers. Download your copy 

Lily Xu Xuanyan

Lily Xu graduated from Leiden University, The Netherlands, after studying biochemistry and science-based business. With a background in both molecular genetics and the commercialization of new technologies, Lily joined QIAGEN in 2012. Since then, she has been involved in managing various parts of QIAGEN’s sample and assay portfolio. Lily's interests span several emerging fields, particularly single-cell analysis and microRNA biomarker discovery.

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