title: Detection limits of DNA copy number alterations in heterogeneous cell populations.
abstract: BACKGROUND
  Array Comparative Genomic Hybridization (aCGH) is a widely used technique to assess chromosomal copy number alterations. Chromosomal content, however, is often not uniform throughout cell populations. Here we evaluated to what extent aCGH can detect DNA copy number alterations in heterogeneous cell populations. A systematic evaluation is currently lacking, despite its importance in diagnostics and research. The detection limits reported are a compound of analytical software and laboratory techniques and do not account for the number of probes in relation to sample homogeneity.
  
  
  METHODS
  Detection limits were explored with DNA isolated from a patient with intellectual disability (ID) and from tumor cell line BT474. Both were diluted with increasing amounts of normal DNA to simulate different levels of cellularity. Samples were hybridized on microarrays containing 180,880 oligonucleotides evenly distributed over the genome (spacing ~17 kb).
  
  
  RESULTS
  Single copy number alterations, represented by down to 249 probes (4 Mb) and present in 10 % of a cell population, could be detected. Alterations encompassing as few as 14 probes (~238 Kb) could also be detected, but for this a 35 % mosaic level was required.
  
  
  CONCLUSIONS
  DNA copy number alterations can be detected in cell populations containing 10 % abnormal cells. Detection of sub-megabase alterations requires a higher percentage of abnormal cells or microarrays with a higher probe density.
authors.affiliation: Department of Pathology, VU University Medical Center, MB, Amsterdam, The Netherlands.
authors.forename: Oscar
authors.initials: O
authors.lastname: Krijgsman
authors.forename: Daniëlle
authors.initials: D
authors.lastname: Israeli
authors.forename: Hendrik F
authors.initials: HF
authors.lastname: van Essen
authors.forename: Paul P
authors.initials: PP
authors.lastname: Eijk
authors.forename: Michel L M
authors.initials: ML
authors.lastname: Berens
authors.forename: Clemens H M
authors.initials: CH
authors.lastname: Mellink
authors.forename: Aggie W
authors.initials: AW
authors.lastname: Nieuwint
authors.forename: Marjan M
authors.initials: MM
authors.lastname: Weiss
authors.forename: Renske D M
authors.initials: RD
authors.lastname: Steenbergen
authors.forename: Gerrit A
authors.initials: GA
authors.lastname: Meijer
authors.forename: Bauke
authors.initials: B
authors.lastname: Ylstra
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000473:pathology; D045744:Cell Line, Tumor; D002869:Chromosome Aberrations; D055028:Comparative Genomic Hybridization / Q000379:methods*; D004247:DNA / Q000032:analysis / Q000235:genetics; D056915:DNA Copy Number Variations / Q000235:genetics*; D005260:Female; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008607:Intellectual Disability / Q000235:genetics; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D004247:DNA