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BMC Genomics. 2010 Apr 16;11:244. doi: 10.1186/1471-2164-11-244.

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.

Author information

  • 1Rosetta Inpharmatics LLC, Merck & Co., Inc., Seattle, Washington 98109, USA. castle@uni-mainz.de

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.

PMID:
20398377
[PubMed - indexed for MEDLINE]
PMCID:
PMC2867831
Free PMC Article

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