Interactive analysis and assessment of single-cell copy-number variations.
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.
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Tyler
T
Garvin
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Robert
R
Aboukhalil
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Jude
J
Kendall
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.|Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York, USA.
Timour
T
Baslan
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Gurinder S
GS
Atwal
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
James
J
Hicks
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Michael
M
Wigler
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
Michael C
MC
Schatz
D000465:Algorithms; D000818:Animals; D001331:Automation; D016000:Cluster Analysis; D019295:Computational Biology; D056915:DNA Copy Number Variations; D004330:Drosophila; D005260:Female; D018628:Gene Dosage; D016678:Genome; D015894:Genome, Human; D006801:Humans; D020407:Internet; D008175:Lung Neoplasms / Q000175:diagnosis / Q000235:genetics; D008297:Male; D051379:Mice; D009841:Oligonucleotides / Q000235:genetics*; D002679:Pan troglodytes; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D051381:Rats; D015203:Reproducibility of Results; D012730:Sex Chromosomes; D055752:Small Cell Lung Carcinoma / Q000175:diagnosis / Q000235:genetics; D012984:Software
D009841:Oligonucleotides