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Interactive analysis and quality assessment of single-cell copy-number variations

Tyler Garvin, Robert Aboukhalil, Jude Kendall, Timour Baslan, Gurinder S. Atwal, James Hicks, Michael Wigler, Michael C. Schatz
doi: https://doi.org/10.1101/011346
Tyler Garvin
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
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Robert Aboukhalil
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
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Jude Kendall
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
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Timour Baslan
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
2Department of Molecular and Cellular Biology (MCB, Stony Brook University, Stony Brook, New York, 11790.
3Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, 10065 (Current affiliation)
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Gurinder S. Atwal
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
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James Hicks
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
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Michael Wigler
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
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Michael C. Schatz
1Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor NY, 11724
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  • For correspondence: mschatz@cshl.edu
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Abstract

We present an open-source visual-analytics web platform, Ginkgo (http://qb.cshl.edu/ginkgo), for the interactive analysis and quality assessment of single-cell copy-number alterations. Ginkgo automatically constructs copy-number profiles of individual cells from mapped reads, as well as constructing phylogenetic trees of related cells. We validate Ginkgo by reproducing the results of five major studies and examine the data characteristics of three commonly used single-cell amplification techniques to conclude DOP-PCR to be the most consistent for CNV analysis.

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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 March 06, 2015.
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Interactive analysis and quality assessment of single-cell copy-number variations
Tyler Garvin, Robert Aboukhalil, Jude Kendall, Timour Baslan, Gurinder S. Atwal, James Hicks, Michael Wigler, Michael C. Schatz
bioRxiv 011346; doi: https://doi.org/10.1101/011346
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Interactive analysis and quality assessment of single-cell copy-number variations
Tyler Garvin, Robert Aboukhalil, Jude Kendall, Timour Baslan, Gurinder S. Atwal, James Hicks, Michael Wigler, Michael C. Schatz
bioRxiv 011346; doi: https://doi.org/10.1101/011346

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