Genome-wide copy number analysis of single cells

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)

URL: http://www.ncbi.nlm.nih.gov/pubmed/22555242
DOI: 10.1038/nprot.2012.039

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 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
CSHL Cancer Center Program > Cancer Genetics
Depositing User: Matt Covey
Date: 3 May 2012
Date Deposited: 01 Feb 2013 14:23
Last Modified: 26 Dec 2018 16:25
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26895

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving