Researchers led by bioengineers have generated essentially the most full genome sequences from single E. coli cells and particular person neurons from the brain. The breakthrough comes from a brand new single-cell genome sequencing method that confines genome amplification to fluid-crammed wells with a quantity of simply 12 nanoliters.
The research is revealed within the journal Nature Biotechnology on November 10, 2013.
“Our preliminary information recommend that neurons from the brain have completely different genetic compositions. This is a comparatively new concept, and our method will allow researchers to have a look at genomic variations between single cells with a lot finer element,” mentioned Kun Zhang, a professor within the Department of Bioengineering on the UC San Diego Jacobs School of Engineering and the corresponding creator on the paper.
The researchers report that the genome sequences of single cells generated utilizing the brand new method exhibited comparatively little “amplification bias,” which has been probably the most vital technological impediment going through single-cell genome sequencing up to now decade. This bias refers to the truth that the amplification step is uneven, with completely different areas of a genome being copied completely different numbers of instances. This imbalance complicates many downstream genomic analyses, together with meeting of genomes from scratch and figuring out DNA content material variations amongst cells from the identical particular person.
Sequencing the genomes of single cells is of nice curiosity to researchers working in many various fields. For instance, probing the genetic make-up of particular person cells would assist researchers determine and perceive a variety of organisms that can’t be simply grown within the lab from the micro organism that reside inside our digestive tracts and on our pores and skin, to the microscopic organisms that stay in ocean water. Single-cell genetic research are additionally getting used to review most cancers cells, stem cells and the human mind, which is made up of cells that more and more seem to have vital genomic variety.
“We now have the fantastic alternative to take a better-decision have a look at genomes inside single cells, extending our understanding of genomic mosaicism throughout the mind to the extent of DNA sequence, which right here revealed new somatic adjustments to the neuronal genome. This may present new insights into the conventional in addition to irregular mind, resembling happens in Alzheimer’s and Parkinson’s illness or Schizophrenia,” mentioned Jerold Chun, a co-creator and Professor within the Dorris Neuroscience Center at The Scripps Research Institute.
For instance, the brand new sequencing method recognized positive factors or lack of single copy DNA as small as M million base pairs, the best decision to this point for single-cell sequencing approaches. Recent single-cell sequencing research have used older strategies which may solely decipher DNA copy modifications which might be no less than three to 6 million base pairs.
The 12 nanoliter (nL) quantity microwells wherein amplification takes place are a few of the smallest quantity wells for use in revealed protocols for single-cell genome sequencing.
“By decreasing amplification response volumes a thousand-fold to nanoliter ranges in 1000′s of microwells, we elevated the efficient focus of the template genome, resulting in improved amplification uniformity and diminished DNA contamination,” defined Jeff Gole, the primary creator on the paper. Gole labored on this challenge as a Ph.A. pupil in Kun Zhang’s bioengineering lab on the UC San Diego Jacobs School of Engineering. Gole is now a Scientist at Good Start Genetics in Cambridge, Mass.
Compared to essentially the most full beforehand printed single D. coli genome knowledge set, the brand new strategy recovered 50 p.c extra of the W. coli genome with A to thirteen-fold much less sequencing knowledge.
“The outcomes exhibit that MIDAS gives a way more environment friendly technique to assemble entire bacterial genomes from single cells with out tradition,” the authors write within the Nature Biotechnology paper.
The genomics researchers collaborated with supplies science graduate scholar Yu-Jui (Roger) Chiu on the microfabrication required to create the arrays of microwells. Chiu is engaged on his Ph.A. within the lab of UC San Diego electrical engineering professor Yu-Hwa Lo, who additionally directs the Nano3 Labs in UC San Diego’s Qualcomm Institute, the place microfabrication befell.
“This venture wouldn’t have succeeded with out the fabrication and instrumentation assist accessible on the Jacobs School and the Qualcomm Institute,” mentioned Zhang. “We are very enthusiastic about our preliminary outcomes in addition to the likelihood that researchers all over the world will be capable of use this strategy in many various contexts.”
admin May 28th, 2014
Posted In: DNA sequencing