title: Performance assessment of copy number microarray platforms using a spike-in experiment.
abstract: BACKGROUND
  Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice.
  
  
  RESULTS
  We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.
  
  
  BACKGROUND
  The data is available from http://rafalab.jhsph.edu/cnvcomp/.
  
  
  BACKGROUND
  pevsner@jhmi.edu; fspencer@jhmi.edu; rafa@jhu.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Eitan
authors.initials: E
authors.lastname: Halper-Stromberg
authors.forename: Laurence
authors.initials: L
authors.lastname: Frelin
authors.forename: Ingo
authors.initials: I
authors.lastname: Ruczinski
authors.forename: Robert
authors.initials: R
authors.lastname: Scharpf
authors.forename: Chunfa
authors.initials: C
authors.lastname: Jie
authors.forename: Benilton
authors.initials: B
authors.lastname: Carvalho
authors.forename: Haiping
authors.initials: H
authors.lastname: Hao
authors.forename: Kurt
authors.initials: K
authors.lastname: Hetrick
authors.forename: Anne
authors.initials: A
authors.lastname: Jedlicka
authors.forename: Amanda
authors.initials: A
authors.lastname: Dziedzic
authors.forename: Kim
authors.initials: K
authors.lastname: Doheny
authors.forename: Alan F
authors.initials: AF
authors.lastname: Scott
authors.forename: Steve
authors.initials: S
authors.lastname: Baylin
authors.forename: Jonathan
authors.initials: J
authors.lastname: Pevsner
authors.forename: Forrest
authors.initials: F
authors.lastname: Spencer
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
mesh_terms: D000465:Algorithms; D056915:DNA Copy Number Variations; D005260:Female; D006801:Humans; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity