CanGEM
 
Sunday, December 17, 2017
Logged in as guest | Register
Login: Password:
Buffart et al.: Across array comparative genomic hybridization: A strategy to reduce reference channel hybridizations.
CG-EXP-47

Buffart TE, Israeli D, Tijssen M, Vosse SJ, Mršić A, Meijer GA, Ylstra B.
Array comparative genomic hybridization (array CGH) is widely used for studying chromosomal copy number aberrations (CNAs) on a genome-wide and high-resolution scale in heritable disorders and cancers. The aim of this study was to test if the separate channels of dual channel arrays can be interchanged (across array) to either make array CGH more sensitive and cost effective and/or to generate profiles of CNAs and copy number variations (CNVs). Therefore the BT474 breast cancer cell line was compared with a mix of normal reference DNAs hybridized on different arrays and days and DNA copy number profiles were evaluated. Quality was assessed, using regular dual channel array CGH as a standard, using four quality measures, i.e., the median absolute deviation value of chromosome 2, the amplitude of the ERBB2 gene amplification, a deletion on chromosome 9, and the deflection on chromosome 8. The quality of the across array CGH profiles matched or even surpassed the quality of regular dual channel array CGH. In addition, this across array approach was tested for genomic DNA derived from formalin-fixed paraffin-embedded tumors tissue samples, resulting in high-quality copy number profiles, comparable to regular dual channel arrays. Finally, we demonstrated this approach to obtain both CNA and CNV profiles. In summary, across array CGH avoids redundant hybridizations of the same reference material in every experiment either allowing hybridization of two test samples on one array or producing both CNA and CNV profiles simultaneously. (c) 2008 Wiley-Liss, Inc.
Integrative Genomics Viewer
Gene calls
Gene frequencies
The links above can be used to open data in IGV.
This requires that http requests are turned on in IGV preferences.
Contents
[+] Series: aaCGH 105KCG-SER-268
Data Files

2008-08-11 15:36:19 by Ilari Scheinin
2008-08-11 15:36:39 by Ilari Scheinin

Add experiment to dataset
GUID: {40349530-1A27-40FC-983B-A15D836CA0FB}