Ginkgo

Ginkgo constructs single-cell copy-number profiles from mapped sequencing reads and derives phylogenetic trees to analyze copy-number variation and cellular relationships.

Key Features:

• Single-cell CNV analysis: Performs analysis of single-cell copy-number variations (CNVs).
• Copy-number profile construction: Automatically constructs detailed copy-number profiles from mapped sequencing reads.
• Phylogenetic reconstruction: Generates phylogenetic trees from CNV profiles to elucidate relationships among individual cells.
• Validation: Reproduces results from five published single-cell CNV studies as part of method validation.
• Amplification-method comparison: Compares degenerate oligonucleotide-primed PCR (DOP-PCR), multiple displacement amplification (MDA), and whole-genome amplification (WGA), identifying DOP-PCR as the most consistent for CNV analysis.

Scientific Applications:

• Single-cell CNV profiling: Profiles copy-number variation at single-cell resolution for studies of genomic variation.
• Cellular phylogenetics: Reconstructs phylogenetic relationships among individual cells using CNV data to study clonal architecture.
• Method benchmarking: Assesses and compares single-cell amplification techniques (DOP-PCR, MDA, WGA) for CNV analysis consistency.
• Heterogeneity and evolution: Analyzes cellular genomic heterogeneity and evolutionary relationships among cells.

Methodology:

Constructs copy-number profiles from mapped sequencing reads, generates phylogenetic trees from CNV profiles, and conducts comparative analyses of DOP-PCR, MDA, and WGA.