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Ultra-accurate Genome Sequencing and Haplotyping of Single Human Cells

Wai Keung Chu, Peter Edge, Ho Suk Lee, Vikas Bansal, Vineet Bafna, Xiaohua Huang, Kun Zhang
doi: https://doi.org/10.1101/135384
Wai Keung Chu
aDepartment of Bioengineering, University of San Diego, CA 92093
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Peter Edge
bDepartment of Computer Science and Engineering, University of San Diego, CA 92093
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Ho Suk Lee
cDepartment of Electrical and Computer Engineering, University of San Diego, CA 92093
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Vikas Bansal
bDepartment of Computer Science and Engineering, University of San Diego, CA 92093
dDepartment of Pediatrics, University of San Diego, CA 92093
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Vineet Bafna
bDepartment of Computer Science and Engineering, University of San Diego, CA 92093
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  • For correspondence: x2huang@ucsd.edu vbafna@cs.ucsd.edu kzhang@eng.ucsd.edu
Xiaohua Huang
aDepartment of Bioengineering, University of San Diego, CA 92093
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  • For correspondence: x2huang@ucsd.edu vbafna@cs.ucsd.edu kzhang@eng.ucsd.edu
Kun Zhang
aDepartment of Bioengineering, University of San Diego, CA 92093
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  • For correspondence: x2huang@ucsd.edu vbafna@cs.ucsd.edu kzhang@eng.ucsd.edu
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Abstract

Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (Single-Stranded Sequencing using micrOfluidic Reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10−8 and average 500kb long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 08, 2017.
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Ultra-accurate Genome Sequencing and Haplotyping of Single Human Cells
Wai Keung Chu, Peter Edge, Ho Suk Lee, Vikas Bansal, Vineet Bafna, Xiaohua Huang, Kun Zhang
bioRxiv 135384; doi: https://doi.org/10.1101/135384
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Ultra-accurate Genome Sequencing and Haplotyping of Single Human Cells
Wai Keung Chu, Peter Edge, Ho Suk Lee, Vikas Bansal, Vineet Bafna, Xiaohua Huang, Kun Zhang
bioRxiv 135384; doi: https://doi.org/10.1101/135384

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