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

We present an open-source web platform, Ginkgo (http://qb.cshl.edu/ginkgo), for the analysis and assessment 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 validate Gi...

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Detalles Bibliográficos
Autores principales: Garvin, Tyler, Aboukhalil, Robert, Kendall, Jude, Baslan, Timour, Atwal, Gurinder S., Hicks, James, Wigler, Michael, Schatz, Michael C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2015
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775251/
https://www.ncbi.nlm.nih.gov/pubmed/26344043
http://dx.doi.org/10.1038/nmeth.3578
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author Garvin, Tyler
Aboukhalil, Robert
Kendall, Jude
Baslan, Timour
Atwal, Gurinder S.
Hicks, James
Wigler, Michael
Schatz, Michael C.
author_facet Garvin, Tyler
Aboukhalil, Robert
Kendall, Jude
Baslan, Timour
Atwal, Gurinder S.
Hicks, James
Wigler, Michael
Schatz, Michael C.
author_sort Garvin, Tyler
collection PubMed
description We present an open-source web platform, Ginkgo (http://qb.cshl.edu/ginkgo), for the analysis and assessment 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 validate Ginkgo by reproducing the results of five major studies and examine the characteristics of three commonly used single-cell amplification techniques to conclude degenerate oligonucleotide-primed PCR to be the most consistent for CNV analysis.
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spelling pubmed-47752512016-05-01 Interactive analysis and assessment of single-cell copy-number variations Garvin, Tyler Aboukhalil, Robert Kendall, Jude Baslan, Timour Atwal, Gurinder S. Hicks, James Wigler, Michael Schatz, Michael C. Nat Methods Article We present an open-source web platform, Ginkgo (http://qb.cshl.edu/ginkgo), for the analysis and assessment 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 validate Ginkgo by reproducing the results of five major studies and examine the characteristics of three commonly used single-cell amplification techniques to conclude degenerate oligonucleotide-primed PCR to be the most consistent for CNV analysis. 2015-09-07 2015-11 /pmc/articles/PMC4775251/ /pubmed/26344043 http://dx.doi.org/10.1038/nmeth.3578 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Garvin, Tyler
Aboukhalil, Robert
Kendall, Jude
Baslan, Timour
Atwal, Gurinder S.
Hicks, James
Wigler, Michael
Schatz, Michael C.
Interactive analysis and assessment of single-cell copy-number variations
title Interactive analysis and assessment of single-cell copy-number variations
title_full Interactive analysis and assessment of single-cell copy-number variations
title_fullStr Interactive analysis and assessment of single-cell copy-number variations
title_full_unstemmed Interactive analysis and assessment of single-cell copy-number variations
title_short Interactive analysis and assessment of single-cell copy-number variations
title_sort interactive analysis and assessment of single-cell copy-number variations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775251/
https://www.ncbi.nlm.nih.gov/pubmed/26344043
http://dx.doi.org/10.1038/nmeth.3578
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