Genomic analysis of single cells
Recent technological attention has focused on the development of high-throughput methods for cell and genomic analysis. However, there are instances where genomic analysis is required at the single cell level such as in the case of circulating cancer cells. Existing technology does not support genomic analysis and sequencing of single cells. The EU-funded CELL-O-MATIC (High throughput systematic single cell genomics using micro/nano-fluidic chips for extracting, pre-analysing, selecting and preparing sequence-ready DNA) initiative set out to overcome bottlenecks associated with isolating cells out of a heterogeneous population, extracting the genomic material and preparing it for sequencing. In this context, researchers developed a lab-on-chip device for preparing DNA from individual cells as a readily usable sample for a sequencing instrument. Initially they established and optimised a fast, simple protocol for extraction and amplification of minute amounts of DNA from single cells as well as a microfluidic fractionation protocol. This led to separating cancer cells from white blood cells with an efficiency of over 90 %. The prototype instrument additionally offered epi-fluorescence and bright field microscopy in a strictly regulated environment to allow trapping of single cells, DNA extraction and amplification of the genetic material. The approach was successfully tested towards the analysis of mega-base lengths of DNA extracted from single cells. Mapping data showed an average of 98 % of reads mapped to the genome, and is in par with existing devices. Overall, the activities of the CELL-O-MATIC approach provided state-of-the-art next generation whole genome sequencing and demonstrated the optical mapping of genomic DNA extracted from a single cell. Importantly, these lab-on-chip devices could be produced by scalable industrial processes. Considering that genomic analysis of circulating tumour cells has a strong prognostic value, the CELL-O-MATIC approach is a step forward towards effective personalised cancer management.
Keywords
Genomic analysis, cancer, sequencing, CELL-O-MATIC, microfluidic fractionation