Interactive analysis and 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:10.1038/nmeth.3578

Interactive analysis and 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

Research output: Contribution to journal › Review article › peer-review

Abstract

We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.

Original language	English (US)
Pages (from-to)	1058-1060
Number of pages	3
Journal	Nature Methods
Volume	12
Issue number	11
DOIs	https://doi.org/10.1038/nmeth.3578
State	Published - Nov 1 2015
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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title = "Interactive analysis and assessment of single-cell copy-number variations",

abstract = "We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.",

author = "Tyler Garvin and Robert Aboukhalil and Jude Kendall and Timour Baslan and Atwal, {Gurinder S.} and James Hicks and Michael Wigler and Schatz, {Michael C.}",

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AU - Aboukhalil, Robert

AU - Kendall, Jude

AU - Baslan, Timour

AU - Atwal, Gurinder S.

AU - Hicks, James

AU - Wigler, Michael

AU - Schatz, Michael C.

PY - 2015/11/1

Y1 - 2015/11/1

N2 - We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.

AB - We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.

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

Abstract

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