Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Methodology article

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

John C Castle12*, Matthew Biery13, Heather Bouzek14, Tao Xie15, Ronghua Chen16, Kira Misura17, Stuart Jackson16, Christopher D Armour13, Jason M Johnson16, Carol A Rohl16 and Christopher K Raymond13*

Author Affiliations

1 Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co., Inc., Seattle, Washington 98109, USA

2 Institute for Translational Oncology and Immunology (TrOn), Mainz, Germany

3 NuGEN Technologies, Inc., Seattle, Washington, USA

4 University of Washington, Seattle, Washington, USA

5 Pfizer, Inc., San Diego, California, USA

6 Merck Research Laboratories, Boston, Massachusetts, USA

7 Amgen, Inc., Seattle, Washington, USA

For all author emails, please log on.

BMC Genomics 2010, 11:244  doi:10.1186/1471-2164-11-244

Published: 16 April 2010

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.