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Genome Res. 2015 May;25(5):714-24. doi: 10.1101/gr.188060.114. Epub 2015 Apr 9.

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling.

Author information

1
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;
2
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
3
Sigma-Aldrich Research Technology, Saint Louis, Missouri 63103, USA;
4
Phillips Research North America, Biomedical Informatics, Briarcliff Manor, New York 10510, USA;
5
Division of Hematology/Oncology, Department of Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio 44106, USA;
6
Department of Pathology, University Hospitals Case Medical Center and Case Western Reserve University, Cleveland, Ohio 44106, USA;
7
Clinic for Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School, 30625 Hannover, Germany;
8
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.

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.

PMID:
25858951
PMCID:
PMC4417119
DOI:
10.1101/gr.188060.114
[Indexed for MEDLINE]
Free PMC Article

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