title: Detection of Copy Number Alterations Using Single Cell Sequencing.
abstract: Detection of genomic changes at single cell resolution is important for characterizing genetic heterogeneity and evolution in normal tissues, cancers, and microbial populations. Traditional methods for assessing genetic heterogeneity have been limited by low resolution, low sensitivity, and/or low specificity. Single cell sequencing has emerged as a powerful tool for detecting genetic heterogeneity with high resolution, high sensitivity and, when appropriately analyzed, high specificity. Here we provide a protocol for the isolation, whole genome amplification, sequencing, and analysis of single cells. Our approach allows for the reliable identification of megabase-scale copy number variants in single cells. However, aspects of this protocol can also be applied to investigate other types of genetic alterations in single cells.
authors.affiliation: Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology; Howard Hughes Medical Institute; Division of Health Sciences and Technology, Harvard Medical School; kknouse@mit.edu.
authors.forename: Kristin A
authors.initials: KA
authors.lastname: Knouse
authors.affiliation: The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology.
authors.forename: Jie
authors.initials: J
authors.lastname: Wu
authors.affiliation: BioMicro Center, Department of Biology, Massachusetts Institute of Technology.
authors.forename: Austin
authors.initials: A
authors.lastname: Hendricks
mesh_terms: D056915:DNA Copy Number Variations; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008390:Markov Chains; D009369:Neoplasms / Q000235:genetics; D012680:Sensitivity and Specificity; D059010:Single-Cell Analysis / Q000379:methods*