Baslan, T., Kendall, J. T., Rodgers, L., Cox, H., Riggs, M., Stepansky, A., Troge, J. E., Ravi, K., Esposito, D., Lakshmi, B., Wigler, M., Navin, N. E., Hicks, J. B. (May 2012) Genome-wide copy number analysis of single cells. Nat Protoc, 7 (6). pp. 1024-41. ISSN 1750-2799 (Electronic)1750-2799 (Linking)
Abstract
Copy number variation (CNV) is increasingly recognized as an important contributor to phenotypic variation in health and disease. Most methods for determining CNV rely on admixtures of cells in which information regarding genetic heterogeneity is lost. Here we present a protocol that allows for the genome-wide copy number analysis of single nuclei isolated from mixed populations of cells. Single-nucleus sequencing (SNS), combines flow sorting of single nuclei on the basis of DNA content and whole-genome amplification (WGA); this is followed by next-generation sequencing to quantize genomic intervals in a genome-wide manner. Multiplexing of single cells is discussed. In addition, we outline informatic approaches that correct for biases inherent in the WGA procedure and allow for accurate determination of copy number profiles. All together, the protocol takes approximately 3 d from flow cytometry to sequence-ready DNA libraries.
| Item Type: | Paper |
|---|---|
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > copy number variants bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes |
| CSHL Authors: | |
| Communities: | CSHL Cancer Center Program > Cancer Genetics CSHL Cancer Center Shared Resources > DNA Sequencing Service CSHL Cancer Center Shared Resources > Flow Cytometry Service CSHL Cancer Center Shared Resources > Instrumentation Service CSHL labs > Hicks lab CSHL labs > Wigler lab |
| Depositing User: | Matt Covey |
| Date: | 3 May 2012 |
| Date Deposited: | 01 Feb 2013 14:23 |
| Last Modified: | 19 Jul 2021 20:17 |
| PMCID: | PMC5069701 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/26895 |
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