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ARS Home » Plains Area » Houston, Texas » Children's Nutrition Research Center » Research » Publications at this Location » Publication #224637
Title: Comparison between BAC and oligo array platforms in detecting submicroscopic genomic rearrangements

Author
item HIXSON, P - BAYLOR COLLEGE MED
item LARITSKY, E - BAYLOR COLLEGE MED
item WANG, X - BAYLOR COLLEGE MED
item JIANG, T - BAYLOR COLLEGE MED
item CHEUNG, S - BAYLOR COLLEGE MED
item Van Den Veyver, Ignatia
item CAI, W - BAYLOR COLLEGE MED

Submitted to: American Society of Human Genetics
Publication Type: Abstract Only
Publication Acceptance Date: 4/15/2006
Publication Date: 10/9/2006
Citation: Hixson, P., Laritsky, E., Wang, X., Jiang, T., Cheung, S., Van Den Veyver, I., Cai, W. 2006. Comparison between BAC and oligo array platforms in detecting submicroscopic genomic rearrangements [abstract]. American Society of Human Genetics, 2006 Annual Meeting, October 9-13, 2006, New Orleans, Louisiana. p. 239.

Interpretive Summary:

Technical Abstract: Array-based comparative genomic hybridization (array CGH) has emerged as a powerful diagnostic technique for high resolution analysis of the human genome. It is a specific, sensitive, and rapid technique enabling detection of genomic arrangements and copy number changes. A variety of array CGH platforms are currently available, both commercially and in academic institutions. The choice of platform may depend on the type of data sought; however, the price, reproducibility, and standardization are crucial factors that need to be considered. Our goal was to determine the ability of our in-house prepared BAC array to identify submicroscopic genomic rearrangements. We constructed a 39,000 human whole genome (HWG39K) BAC clone microarray from the RPCI-11 human library with a resolution of approximately 12 BACs/Mb using standard alkaline lysis method. This platform was used, in a masked fashion, to analyze genetic aberrations in five clinical samples showing abnormalities using a targeted array that has been clinically implemented. These samples were also examined using oligo-based platforms in an attempt to compare the performance of our BAC arrays with the oligo arrays. We were able to identify deletions on chromosomes 1 (1 patient), and 22 (2 patients), a deletion/duplication event on chromosome 8 (1 patient) and a duplication on chromosome 12 (1 patient). Our results were consistent with previous cytogenetic and FISH findings and were comparable to those obtained by different oligo array platforms available commercially. The negative rate of detection for our BAC array platform ranges from 0 to 12.4% using 2.5 SD units as the cutoff level. Therefore, this platform provides us with an alternative to characterizing submicroscopic genomic rearrangements on a whole human genome array in a single experiment at an affordable cost.