Optimizing sparse sequencing of single cells for highly multiplex copy number profiling
Open Access
- 9 April 2015
- journal article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 25 (5), 714-724
- https://doi.org/10.1101/gr.188060.114
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.Keywords
Funding Information
- National Cancer Institute Cancer Center Shared (CA045508)
- Department of the Army (W81XWH-11-1-0747)
- Breast Cancer Research Fund
- American Cancer Society
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