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

Garvin, T., Aboukhalil, R., Kendall, J., Baslan, T., Atwal, G. S., Hicks, J., Wigler, M., Schatz, M. C. (2015) Interactive analysis and assessment of single-cell copy-number variations. Nat Methods, 12. pp. 1058-1060. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

URL: http://www.ncbi.nlm.nih.gov/pubmed/26344043
DOI: 10.1038/nmeth.3578

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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > computational biology
bioinformatics > genomics and proteomics > computers > computer software
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > copy number variants
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL labs > Atwal lab
CSHL labs > Hicks lab
CSHL labs > Schatz lab
CSHL labs > Wigler lab
Depositing User: Matt Covey
Date Deposited: 11 Sep 2015 14:43
Last Modified: 07 Sep 2017 15:14
Related URLs:
Dataset ID:
URI: http://repository.cshl.edu/id/eprint/31762

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