| Representational oligonucleotide microarray analysis (ROMA) and comparison of binning and change-point methods of analysis: application to detection of del22q11.2 (DiGeorge) syndrome. | |
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MedLine Citation:
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PMID: 17694540 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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DiGeorge (del22q11.2) syndrome is estimated to occur in 1:4,000 births, is the most common contiguous-gene deletion syndrome in humans, and is caused by autosomal dominant deletions in the 22q11.2 DiGeorge syndrome critical region (DGCR). Multiple microarray methods have been developed recently for analyzing such copy number changes, but data analysis and accurate deletion detection remains challenging. Clinical use of these microarray methods would have many advantages, particularly when the possibility of a chromosomal disorder cannot be determined simply on the basis of history and physical examination data alone. We investigated the use of the microarray technique, representational oligonucleotide microarray analysis (ROMA), in the detection of del22q11.2 syndrome. Genomic DNA was isolated from three well-characterized cell lines with 22q11.2 DGCR deletions and from the blood of a patient suspected of having del22q11.2 syndrome, and analyzed using both the binning and change-point model algorithms. Though the 22q11.2 deletion was easily identified with either method, change-point models provide clearer identification of deleted regions, with the potential for fewer false-positive results. For circumstances in which a clear, a priori, copy-number change hypothesis is not present, such as in many clinical samples, change-point methods of analysis may be easier to interpret. |
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Authors:
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Christopher M Stanczak; Zugen Chen; Stanley F Nelson; Marc Suchard; Edward R B McCabe; Sean McGhee |
Publication Detail:
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Type: Comparative Study; Evaluation Studies; Journal Article; Research Support, N.I.H., Extramural |
Journal Detail:
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Title: Human mutation Volume: 29 ISSN: 1098-1004 ISO Abbreviation: Hum. Mutat. Publication Date: 2008 Jan |
Date Detail:
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Created Date: 2007-12-27 Completed Date: 2008-02-06 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9215429 Medline TA: Hum Mutat Country: United States |
Other Details:
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Languages: eng Pagination: 176-81 Citation Subset: IM |
Copyright Information:
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(c) 2007 Wiley-Liss, Inc. |
Affiliation:
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Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), Los Angeles, California 90095-1752, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms* Cell Line Chromosomes, Human, Pair 22 DNA / blood DiGeorge Syndrome / diagnosis* Gene Deletion Gene Dosage Humans Infant Male Oligonucleotide Array Sequence Analysis / methods* |
| Grant Support | |
ID/Acronym/Agency:
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R01 HD22563/HD/NICHD NIH HHS |
| Chemical | |
Reg. No./Substance:
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9007-49-2/DNA |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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