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Enhancer Chip: Detecting Human Copy Number Variations in Regulatory Elements
- Source :
- PLoS ONE; Vol 7, PLoS ONE, PLoS ONE, Vol 7, Iss 12, p e52264 (2012)
- Publication Year :
- 2012
- Publisher :
- Public Library of Science, 2012.
-
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.""
- Subjects :
- Male
DNA Copy Number Variations
lcsh:Medicine
Biology
Real-Time Polymerase Chain Reaction
Genome
Molecular Genetics
03 medical and health sciences
Negative selection
Chromosomal Disorders
0302 clinical medicine
Genome Analysis Tools
Genetics
Humans
Gene Regulation
Copy-number variation
Regulatory Elements, Transcriptional
Gene Networks
lcsh:Science
Enhancer
Trait Locus Analysis
Gene
030304 developmental biology
Clinical Genetics
0303 health sciences
Comparative Genomic Hybridization
Multidisciplinary
lcsh:R
Computational Biology
Chromosomal Deletions and Duplications
Human Genetics
Genomics
Thalassaemias
Genetics of Disease
Medicine
lcsh:Q
Human genome
Female
030217 neurology & neurosurgery
Comparative genomic hybridization
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 7
- Issue :
- 12
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....e7b8262129376e0d32fdf4ee424cc184
- Full Text :
- https://doi.org/10.1371/journal.pone.0052264