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Single-cell genome sequencing gets better
Date:11/10/2013

o being used to study cancer cells, stem cells and the human brain, which is made up of cells that increasingly appear to have significant genomic diversity.

"We now have the wonderful opportunity to take a higher-resolution look at genomes within single cells, extending our understanding of genomic mosaicism within the brain to the level of DNA sequence, which here revealed new somatic changes to the neuronal genome. This could provide new insights into the normal as well as abnormal brain, such as occurs in Alzheimer's and Parkinson's disease or Schizophrenia," said Jerold Chun, a co-author and Professor in the Dorris Neuroscience Center at The Scripps Research Institute.

For example, the new sequencing approach identified gains or loss of single copy DNA as small as 1 million base pairs, the highest resolution to date for single-cell sequencing approaches. Recent single-cell sequencing studies have used older techniques which can only decipher DNA copy changes that are at least three to six million base pairs.

Amplification in Nano-Scale Wells

The 12 nanoliter (nL) volume microwells in which amplification takes place are some of the smallest volume wells to be used in published protocols for single-cell genome sequencing.

"By reducing amplification reaction volumes 1000-fold to nanoliter levels in thousands of microwells, we increased the effective concentration of the template genome, leading to improved amplification uniformity and reduced DNA contamination," explained Jeff Gole, the first author on the paper. Gole worked on this project as a Ph.D. student in Kun Zhang's bioengineering lab at the UC San Diego Jacobs School of Engineering. Gole is now a Scientist at Good Start Genetics in Cambridge, Mass.

Compared to the most complete previously published single E. coli genome data set, the new approach recovered 50 percent more of the E. coli genome with 3 to 13-fold less sequenci
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Contact: Daniel Kane
dbkane@ucsd.edu
858-534-3262
University of California - San Diego
Source:Eurekalert  

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