18. HIGH-THROUGHPUT SINGLE CELL GENOMICS ON A MICROFLUIDIC DEVICE

Department: Bioengineering
Faculty Advisor(s): Xiaohua Huang | Kun Zhang

Primary Student
Name: Wai Keung Chu
Email: wkchu@ucsd.edu
Phone: 858-822-4702
Grad Year: 2014

Student Collaborators
Hosuk Lee, hosuki78@gmail.com

Abstract
Conventional human genome studies are limited by the inability to study the homologous copies of the chromosomes individually. The capability to isolate and amplify homologous copies of each chromosome from a single mammalian cell is enabled by reducing reaction volumes to the nano-liter scale in microfluidic devices. Microfluidic polydimethylsiloxane (PDMS) channel with integrated pneumatic valves allowed for an even distribution of chromosomes from a single mouse cell in serial 1-nl chambers. Multiple Displacement Amplification (MDA) in 4-nl reaction chambers effectively produced sufficient DNA for sequencing, and the quantity of product from single-cell amplification was comparable to that from standard 20ul volumes. qPCR results of genome amplification confirmed no environmental contamination. Quality DNA fragments can be separated by size and then sequenced by a high-throughput sequencing-by-synthesis method. The sequencing data is not biased and maps to every mouse chromosome. Confining single cells and their contents in compartments near their intrinsic volumes can minimize the dilution effect and increase processing efficiency. The potential application of our approach includes single-cell genomics and personal haplotyping.

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