Transcriptomics

Dataset Information

3

Benign Copy Number Changes in Clinical Cytogenetic Diagnostics by Array CGH


ABSTRACT: A database of apparently benign copy number variants (bCNVs) detected by a Spectral Genomics Inc./PerkinElmer BAC array platform has been maintained through the University of Utah Comparative Genomic Hybridization laboratory since 2005. The target population for this database represents 1275 patients with abnormal phenotypes, primarily children referred for developmental delay and mental retardation. These bCNVs are independent of any identified copy number abnormality detected. The most common 35 bCNVs observed and their frequencies are reported here, and a subset of ten of the patients studied was evaluated on a new oligonucleotide CNV array set designed by Agilent Technologies. There was a 76% concordance of calls detected by both array platforms in the same patients; the discordant regions may be due to differences in reference DNAs, or false positive/negative results on either array. The higher resolution of the Agilent oligonucleotide array compared to the BAC array allowed for further characterization to determine precise breakpoints of the observed CNVs, in addition to documenting additional CNVs of smaller sizes. As expected, observed CNVs and their frequencies were generally consistent with those of other previously published and available databases, including the Database of Genomic Variants (http://projects.tcag.ca/variation/). The availability of these data should assist other clinical laboratories in the evaluation of CNVs of unknown clinical significance. The Cytogenetics Laboratory at the University of Utah has been using aCGH to evaluate DNA derived from blood of patients with developmental delay, mental retardation and “syndromic” or dysmorphic phenotypes since 2005. From this database, we were able to determine which clones represented sequences which were frequently deleted or duplicated in our patient population. We identified our most common CNV regions and then selected DNAs from ten patients who exhibited copy number changes of those common regions for further study with the Agilent CNV microarray set. Normal male or female DNA from Promega was used as a sex-mismatched control. In addition to the ten clinical specimens, two self-self experiments for two patient samples were analyzed to estimate a false positive rate and to fine tune the parameters used for data analysis. A replicate hybridization was performed on one patient to determine reproducibility.

ORGANISM(S): Homo sapiens  

SUBMITTER: Garrick Peters   Laurakay Bruhn  Peter Tsang  Arthur R Brothman  Christopher M Hopkins  Anya Tsalenko  Pinar Bayrak-Toydemir  Dione K Bailey  Heidi Whitby  Sheri Mitchell  Emily Aston 

PROVIDER: E-GEOD-11815 | ArrayExpress | 2008-08-31

SECONDARY ACCESSION(S): GSE11815PRJNA105905

REPOSITORIES: GEO, ArrayExpress

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Publications

Benign copy number changes in clinical cytogenetic diagnostics by array CGH.

Whitby H H   Tsalenko A A   Aston E E   Tsang P P   Mitchell S S   Bayrak-Toydemir P P   Hopkins C C   Peters G G   Bailey D K DK   Bruhn L L   Brothman A R AR  

Cytogenetic and genome research 20080101 1-4


A database of apparently benign copy number variants (bCNVs) detected by a Spectral Genomics Inc./PerkinElmer BAC array platform has been maintained through the University of Utah Comparative Genomic Hybridization laboratory since 2005. The target population for this database represents 1,275 patients with abnormal phenotypes, primarily children referred for developmental delay and mental retardation. These bCNVs are independent of any identified copy number abnormality detected. The most common  ...[more]

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