Skip Navigation


Bioinformatics Advance Access originally published online on November 11, 2004
Bioinformatics 2005 21(7):1138-1145; doi:10.1093/bioinformatics/bti133
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/7/1138    most recent
bti133v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (14)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Bilke, S.
Right arrow Articles by Khan, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bilke, S.
Right arrow Articles by Khan, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press 2004.

Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays

Sven Bilke *,{dagger}, Qing-Rong Chen {dagger}, Craig C. Whiteford and Javed Khan

Oncogenomics Section, Pediatric Oncology Branch, Advanced Technology Center, National Cancer Institute 8717 Grovemont Circle, Gaithersburg, MD 20877, USA

*To whom correspondence should be addressed.

Motivation: The accumulation of genomic alterations is an important process in tumor formation and progression. Comparative genomic hybridization performed on cDNA arrays (cDNA aCGH) is a common method to investigate the genomic alterations on a genome-wide scale. However, when detecting low-level DNA copy number changes this technology requires the use of noise reduction strategies due to a low signal to noise ratio.

Results: Currently a running average smoothing filter is the most frequently used noise reduction strategy. We analyzed this strategy theoretically and experimentally and found that it is not sensitive to very low level genomic alterations. The presence of systematic errors in the data is one of the main reasons for this failure. We developed a novel algorithm which efficiently reduces systematic noise and allows for the detection of low-level genomic alterations. The algorithm is based on comparison of the biological relevant data to data from so-called self–self hybridizations, additional experiments which contain no biological information but contain systematic errors. We find that with our algorithm the effective resolution for ±1 DNA copy number changes is about 2 Mb. For copy number changes larger than three the effective resolution is on the level of single genes.

Contact: bilkes{at}mail.nih.gov


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
H.-I H. Chen, F.-H. Hsu, Y. Jiang, M.-H. Tsai, P.-C. Yang, P. S. Meltzer, E. Y. Chuang, and Y. Chen
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization
Bioinformatics, August 15, 2008; 24(16): 1749 - 1756.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
P. L. Rosa, E. Viara, P. Hupe, G. Pierron, S. Liva, P. Neuvial, I. Brito, S. Lair, N. Servant, N. Robine, et al.
VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles
Bioinformatics, September 1, 2006; 22(17): 2066 - 2073.
[Abstract] [Full Text] [PDF]

Home page
 JCOHome page
S. Bilke, Q.-R. Chen, F. Westerman, M. Schwab, D. Catchpoole, and J. Khan
Inferring a Tumor Progression Model for Neuroblastoma From Genomic Data
J. Clin. Oncol., October 10, 2005; 23(29): 7322 - 7331.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.