Single-Cell Genome Sequencing
Single-Cell Genome Sequencing
A novel strategy and approach that allows for whole genome amplification of many single cells in parallel in an unbiased manner. In addition, a low input sequencing library construction technique allows DNA from the whole genome amplification be sequenced
San Diego, CA, United States
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Background

Sequencing the genomes of single cells is of great interest to researchers working in many different fields. Existing whole genome amplification techniques for single cells amplify genomes in an extremely biased manner. Small regions of the genome are amplified greatly, whereas most of the genome is amplified very little. Therefore, a large amount of sequencing effort is required to resolve any of the genome. Downstream applications, such as de novo assembly or copy number variation calling, are thus extremely difficult and inaccurate.


Technology Description

UCSD researchers have developed a novel strategy and approach that allows for whole genome amplification of many single cells in parallel in an unbiased manner. In addition, a low input sequencing library construction technique allows DNA from the whole genome amplification be sequenced directly.

The Massively Parallel Single Cell Amplification and Sequencing with Microwell Displacement (MIDAS) sequencing approach amplify hundreds (or more) of cells simultaneously in nanoliter volumes. By reducing amplification reaction volumes 1000-fold to nanoliter levels in thousands of microwells, the effective concentration of the template genome is increased, leading to improved amplification uniformity and reduced DNA contamination. It have been demonstrated that MIDAS can identify 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. 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 sequencing data.


Advantages

Most of the genome is amplified to a similar degree by this technology. Therefore, relatively little sequencing effort is necessary for downstream analysis. De novo assembly can be accomplished and copy number variations can be called with a much greater accuracy.


Applications

  • De novo assembly of unculturable bacteria in the human gut
  • De novo assembly of unculturable bacteria in heterogeneous environments such as sea water
  • Copy number variation calling on single neurons
  • Copy number variation calling on single cancerous cells or circulating tumor cells
  • Human haplotyping 

 

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