title: Optimizing sparse sequencing of single cells for highly multiplex copy number profiling.
abstract: Genome-wide analysis at the level of single cells has recently emerged as a powerful tool to dissect genome heterogeneity in cancer, neurobiology, and development. To be truly transformative, single-cell approaches must affordably accommodate large numbers of single cells. This is feasible in the case of copy number variation (CNV), because CNV determination requires only sparse sequence coverage. We have used a combination of bioinformatic and molecular approaches to optimize single-cell DNA amplification and library preparation for highly multiplexed sequencing, yielding a method that can produce genome-wide CNV profiles of up to a hundred individual cells on a single lane of an Illumina HiSeq instrument. We apply the method to human cancer cell lines and biopsied cancer tissue, thereby illustrating its efficiency, reproducibility, and power to reveal underlying genetic heterogeneity and clonal phylogeny. The capacity of the method to facilitate the rapid profiling of hundreds to thousands of single-cell genomes represents a key step in making single-cell profiling an easily accessible tool for studying cell lineage.
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11790, USA;
authors: Timour
authors: T
authors: Baslan
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Jude
authors: J
authors: Kendall
authors: Sigma-Aldrich Research Technology, Saint Louis, Missouri 63103, USA;
authors: Brian
authors: B
authors: Ward
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Hilary
authors: H
authors: Cox
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Anthony
authors: A
authors: Leotta
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Linda
authors: L
authors: Rodgers
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Michael
authors: M
authors: Riggs
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Sean
authors: S
authors: D'Italia
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Guoli
authors: G
authors: Sun
authors: Phillips Research North America, Biomedical Informatics, Briarcliff Manor, New York 10510, USA;
authors: Mao
authors: M
authors: Yong
authors: Division of Hematology/Oncology, Department of Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio 44106, USA;
authors: Kristy
authors: K
authors: Miskimen
authors: Department of Pathology, University Hospitals Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA;
authors: Hannah
authors: H
authors: Gilmore
authors: Clinic for Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School, 30625 Hannover, Germany;
authors: Michael
authors: M
authors: Saborowski
authors: Phillips Research North America, Biomedical Informatics, Briarcliff Manor, New York 10510, USA;
authors: Nevenka
authors: N
authors: Dimitrova
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Alexander
authors: A
authors: Krasnitz
authors: Division of Hematology/Oncology, Department of Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio 44106, USA; Seidman Cancer Center, University Hospitals of Case Western, Cleveland, Ohio 44106, USA.
authors: Lyndsay
authors: L
authors: Harris
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: Michael
authors: M
authors: Wigler
authors: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
authors: James
authors: J
authors: Hicks
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations; D004273:DNA, Neoplasm / Q000235:genetics*; D015894:Genome, Human; D006801:Humans; D008969:Molecular Sequence Data; D060885:Multiplex Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D004273:DNA, Neoplasm