DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-12

AUTHORS

John C Castle, Matthew Biery, Heather Bouzek, Tao Xie, Ronghua Chen, Kira Misura, Stuart Jackson, Christopher D Armour, Jason M Johnson, Carol A Rohl, Christopher K Raymond

ABSTRACT

BACKGROUND: DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. RESULTS: We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. CONCLUSION: The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads. More... »

PAGES

244

Journal

TITLE

BMC Genomics

ISSUE

1

VOLUME

11

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-11-244

    DOI

    http://dx.doi.org/10.1186/1471-2164-11-244

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1000146260

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20398377


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