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

Nat Methods. 2015 Nov;12(11):1058-60. doi: 10.1038/nmeth.3578. Epub 2015 Sep 7.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Animals
  • Automation
  • Cluster Analysis
  • Computational Biology*
  • DNA Copy Number Variations*
  • Drosophila
  • Female
  • Gene Dosage
  • Genome
  • Genome, Human*
  • Humans
  • Internet
  • Lung Neoplasms / diagnosis
  • Lung Neoplasms / genetics
  • Male
  • Mice
  • Oligonucleotides / genetics*
  • Pan troglodytes
  • Phylogeny
  • Polymerase Chain Reaction
  • Rats
  • Reproducibility of Results
  • Sex Chromosomes
  • Small Cell Lung Carcinoma / diagnosis
  • Small Cell Lung Carcinoma / genetics
  • Software

Substances

  • Oligonucleotides