Interactive analysis and assessment of single-cell copy-number variations.
basic_science · Level V
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- Record sourced from PubMed, PMID 26344043.
- Also identified by DOI 10.1038/nmeth.3578 and PMC identifier 4775251.
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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.
Medical subject headings
- Computational Biology
- DNA Copy Number Variations
- Genome, Human
- Oligonucleotides