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Genome-wide copy number analysis of single cells | Nature Protocols
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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 โผ3 d from flow cytometry to sequence-ready DNA libraries.
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sequence-ready dna libraries nature portfolio permissions reprints privacy policy body mass index sequence alignment/map format advertising cancer research somatic copy-number alteration social media single-cell genome sequencing institutional subscriptions read author information authors hbv-driven hepatocellular carcinoma childhood myelodysplastic syndromesโchallenge input-program-output labels dna cell-cycle analysis copy number variants nature 463 nature 461 nature 464 nature 467 nature 469 nature 472 nature author correspondence single-cell sequencing genome-wide association testing springerlink instant access copy number profiles high-resolution mapping copy-number alterations personalized copy number copy number estimation joint copy number copy number determination cancer development permissions breast cancer patients single-nucleus sequencing article initially published single nucleotide resolution technology development cold spring harbor change 25 february 2016 human genome genome-wide manner massively parallel sequencing single catastrophic event
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datePublished:2012-05-03T00:00:00Z
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headline:Genome-wide copy number analysis of single cells
description: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 รขยยผ3 d from flow cytometry to sequence-ready DNA libraries.
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