Microfabrication Leveraged Toward Single-Cell Genomics

November 11, 2013 | Researchers at the Bioengineering Department of the University of California, San Diego, have made progress in bringing single-cell genome sequencing to a level of precision on par with multi-cell approaches. Amplification bias - the tendency of DNA amplification by PCR to preferentially amplify certain regions of the genome, leaving other regions without enough copies to provide accurate reads - has traditionally thwarted attempts to perform genomic analyses like transcriptome, whole exome or whole genome sequencing on individual cells. For most current applications, this is not an issue, but when dealing with a heterogeneous population of cells, such as might be found in a tumor, stem cells, or the human nervous system, this limitation has made it difficult to gauge the frequency of rare variants within a cellular population. The San Diego lab created microwells on the level of just 12 nanoliters into which DNA from a single cell could be inserted; the tiny level of solution raises the concentration of DNA dramatically, dampening the amplification bias. Whole genome sequencing of a single E. coli cell using this method produced a much more complete genome than has previously been achieved with single cells. The lab has filed a patent on the technology. Nature Biotechnology