title: DNA quality assessment for array CGH by isothermal whole genome amplification.
abstract: BACKGROUND
  Array Comparative Genomic Hybridization (array CGH) is increasingly applied on DNA obtained from formalin-fixed paraffin-embedded (FFPE) tissue, but in a proportion of cases this type of DNA is unsuitable. Due to the high experimental costs of array CGH and unreliable methods for DNA quality testing, better prediction methods are needed. The aim of this study was to accurately determine the quality of FFPE DNA input in order to predict quality of array CGH outcome.
  
  
  METHODS
  DNA quality was assessed by isothermal amplification and compared to array CGH quality on 59 FFPE gastric cancer samples, one FFPE colorectal cancer sample, two FFPE normal uvula samples, one fresh frozen and six FFPE HNSCC samples. Gastric cancer DNA was also quality tested by beta-globin PCR.
  
  
  RESULTS
  Accurate prediction of DNA quality using the isothermal amplification was observed in the colorectal carcinoma, HNSCC and uvula samples. In gastric cancer samples, the isothermal amplification was a more accurate method for selecting good quality DNA for array CGH compared to using PCR product lengths. The isothermal amplification product was used for array CGH and compared to the results achieved using non-amplified DNA in four of the samples. DNAs before and after amplification yielded the same segmentation patterns of chromosomal copy number changes for both the fresh DNA sample and the FFPE samples.
  
  
  CONCLUSIONS
  The efficiency of isothermal DNA amplification is a reliable predictor for array CGH quality. The amplification product itself can be used for array CGH, even starting with FFPE derived DNA samples.
authors.affiliation: Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
authors.forename: Tineke E
authors.initials: TE
authors.lastname: Buffart
authors.forename: Marianne
authors.initials: M
authors.lastname: Tijssen
authors.forename: Thijs
authors.initials: T
authors.lastname: Krugers
authors.forename: Beatriz
authors.initials: B
authors.lastname: Carvalho
authors.forename: Serge J
authors.initials: SJ
authors.lastname: Smeets
authors.forename: Ruud H
authors.initials: RH
authors.lastname: Brakenhoff
authors.forename: Heike
authors.initials: H
authors.lastname: Grabsch
authors.forename: Gerrit A
authors.initials: GA
authors.lastname: Meijer
authors.forename: Henry B
authors.initials: HB
authors.lastname: Sadowski
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
mesh_terms: D004247:DNA / Q000032:analysis*; D015894:Genome, Human; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016612:Paraffin Embedding; D016707:Tissue Fixation
chemical_list: D004247:DNA