title: Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities.
abstract: Microdeletions and microduplications, not visible by routine chromosome analysis, are a major cause of human malformation and mental retardation. Novel high-resolution, whole-genome technologies can improve the diagnostic detection rate of these small chromosomal abnormalities. Array-based comparative genomic hybridization allows such a high-resolution screening by hybridizing differentially labeled test and reference DNAs to arrays consisting of thousands of genomic clones. In this study, we tested the diagnostic capacity of this technology using approximately 3,500 flourescent in situ hybridization-verified clones selected to cover the genome with an average of 1 clone per megabase (Mb). The sensitivity and specificity of the technology were tested in normal-versus-normal control experiments and through the screening of patients with known microdeletion syndromes. Subsequently, a series of 20 cytogenetically normal patients with mental retardation and dysmorphisms suggestive of a chromosomal abnormality were analyzed. In this series, three microdeletions and two microduplications were identified and validated. Two of these genomic changes were identified also in one of the parents, indicating that these are large-scale genomic polymorphisms. Deletions and duplications as small as 1 Mb could be reliably detected by our approach. The percentage of false-positive results was reduced to a minimum by use of a dye-swap-replicate analysis, all but eliminating the need for laborious validation experiments and facilitating implementation in a routine diagnostic setting. This high-resolution assay will facilitate the identification of novel genes involved in human mental retardation and/or malformation syndromes and will provide insight into the flexibility and plasticity of the human genome.
authors: Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands.
authors: Lisenka E L M
authors: LE
authors: Vissers
authors: Bert B A
authors: BB
authors: de Vries
authors: Kazutoyo
authors: K
authors: Osoegawa
authors: Irene M
authors: IM
authors: Janssen
authors: Ton
authors: T
authors: Feuth
authors: Chik On
authors: CO
authors: Choy
authors: Huub
authors: H
authors: Straatman
authors: Walter
authors: W
authors: van der Vliet
authors: Erik H L P G
authors: EH
authors: Huys
authors: Anke
authors: A
authors: van Rijk
authors: Dominique
authors: D
authors: Smeets
authors: Conny M A
authors: CM
authors: van Ravenswaaij-Arts
authors: Nine V
authors: NV
authors: Knoers
authors: Ineke
authors: I
authors: van der Burgt
authors: Pieter J
authors: PJ
authors: de Jong
authors: Han G
authors: HG
authors: Brunner
authors: Ad Geurts
authors: AG
authors: van Kessel
authors: Eric F P M
authors: EF
authors: Schoenmakers
authors: Joris A
authors: JA
authors: Veltman
mesh_terms: D002869:Chromosome Aberrations; D015894:Genome, Human; D006801:Humans; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008607:Intellectual Disability / Q000235:genetics*; D011110:Polymorphism, Genetic; D012680:Sensitivity and Specificity