title: DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Rosetta Inpharmatics LLC, Merck & Co., Inc., Seattle, Washington 98109, USA. castle@uni-mainz.de
authors.forename: John C
authors.initials: JC
authors.lastname: Castle
authors.forename: Matthew
authors.initials: M
authors.lastname: Biery
authors.forename: Heather
authors.initials: H
authors.lastname: Bouzek
authors.forename: Tao
authors.initials: T
authors.lastname: Xie
authors.forename: Ronghua
authors.initials: R
authors.lastname: Chen
authors.forename: Kira
authors.initials: K
authors.lastname: Misura
authors.forename: Stuart
authors.initials: S
authors.lastname: Jackson
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Armour
authors.forename: Jason M
authors.initials: JM
authors.lastname: Johnson
authors.forename: Carol A
authors.initials: CA
authors.lastname: Rohl
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Raymond
mesh_terms: D000818:Animals; D002276:Carcinoid Tumor / Q000235:genetics*; D045744:Cell Line, Tumor; D056915:DNA Copy Number Variations; D005260:Female; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008297:Male; D051379:Mice; D008928:Mitochondria / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D016615:Telomere
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