title: Enhancer chip: detecting human copy number variations in regulatory elements.
abstract: Critical functional properties are embedded in the non-coding portion of the human genome. Recent successful studies have shown that variations in distant-acting gene enhancer sequences can contribute to disease. In fact, various disorders, such as thalassaemias, preaxial polydactyly or susceptibility to Hirschsprung's disease, may be the result of rearrangements of enhancer elements. We have analyzed the distribution of enhancer loci in the genome and compared their localization to that of previously described copy-number variations (CNVs). These data suggest a negative selection of copy number variable enhancers. To identify CNVs covering enhancer elements, we have developed a simple and cost-effective test. Here we describe the gene selection, design strategy and experimental validation of a customized oligonucleotide Array-Based Comparative Genomic Hybridization (aCGH), designated Enhancer Chip. It has been designed to investigate CNVs, allowing the analysis of all the genome with a 300 Kb resolution and specific disease regions (telomeres, centromeres and selected disease loci) at a tenfold higher resolution. Moreover, this is the first aCGH able to test over 1,250 enhancers, in order to investigate their potential pathogenic role. Validation experiments have demonstrated that Enhancer Chip efficiently detects duplications and deletions covering enhancer loci, demonstrating that it is a powerful instrument to detect and characterize copy number variable enhancers.
authors.affiliation: Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Savarese
authors.forename: Giulio
authors.initials: G
authors.lastname: Piluso
authors.forename: Daniela
authors.initials: D
authors.lastname: Orteschi
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Di Fruscio
authors.forename: Manuela
authors.initials: M
authors.lastname: Dionisi
authors.forename: Francesca del Vecchio
authors.initials: Fdel V
authors.lastname: Blanco
authors.forename: Annalaura
authors.initials: A
authors.lastname: Torella
authors.forename: Teresa
authors.initials: T
authors.lastname: Giugliano
authors.forename: Michele
authors.initials: M
authors.lastname: Iacomino
authors.forename: Marcella
authors.initials: M
authors.lastname: Zollino
authors.forename: Giovanni
authors.initials: G
authors.lastname: Neri
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Nigro
mesh_terms: D055028:Comparative Genomic Hybridization; D019295:Computational Biology / Q000379:methods*; D056915:DNA Copy Number Variations / Q000235:genetics*; D005260:Female; D006801:Humans; D008297:Male; D060888:Real-Time Polymerase Chain Reaction; D050436:Regulatory Elements, Transcriptional / Q000235:genetics