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

Baslan, T., Kendall, J., Ward, B., Cox, H., Leotta, A., Rodgers, L., Riggs, M., D'Italia, S., Sun, G., Yong, M., Miskimen, K., Gilmore, H., Saborowski, M., Dimitrova, N., Krasnitz, A., Harris, L., Wigler, M., Hicks, J. (May 2015) Optimizing sparse sequencing of single cells for highly multiplex copy number profiling. Genome Research, 25 (5). pp. 714-724. ISSN 1088-9051

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.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > copy number variants Investigative techniques and equipment > assays > next generation sequencing Investigative techniques and equipment > assays > Single cell sequencing
CSHL Authors:	Baslan, Timour Cox, Hilary D'Italia, Sean Hicks, James B. Kendall, Jude T. Krasnitz, Alexander Leotta, Anthony Riggs, Michael Rodgers, Linda Sun, Guoli Wigler, Michael H.
Communities:	CSHL Cancer Center Program > Cancer Genetics CSHL labs > Hicks lab CSHL labs > Krasnitz lab CSHL labs > Wigler lab CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User:	Matt Covey
Date:	May 2015
Date Deposited:	16 Apr 2015 14:43
Last Modified:	04 Nov 2015 15:56
PMCID:	PMC4417119
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/31333

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