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Nucleic Acids Research 2005 33(9):e84; doi:10.1093/nar/gni082
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Published online 24 May 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Methods Online

Sequence dependence of cross-hybridization on short oligo microarrays

Chunlei Wu, Roberto Carta1 and Li Zhang*

Department of Biostatistics and Applied Mathematics, The University of Texas M. D. Anderson Cancer Center 1515 Holcombe Blvd-447, Houston, TX 77030, USA 1Department of Statistic and Actuarial Sciences, University of Central Florida Orlando, FL 32816–2370, USA

*To whom correspondence should be addressed. Tel: +1 713 563 4298; Fax: +1 713 563 4243; Email: lzhangli{at}mdanderson.org

Received October 23, 2004. Revised February 12, 2005. Accepted May 2, 2005.

One of the critical problems in the short oligo microarray technology is how to deal with cross-hybridization that produces spurious data. Little is known about the details of cross-hybridization effect at molecular level. Here, we report a free energy analysis of cross-hybridization on short oligo microarrays using data from a spike-in study. Our analysis revealed that cross-hybridization on the arrays is mostly caused by oligo fragments with a run of 10–16 nt complementary to the probes. Mismatches were estimated to be energetically much more costly in cross-hybridization than that in gene-specific hybridization, implying that the sources of cross-hybridization must be very different between a PM–MM probe pair. Consequently, it is unreliable to use MM probe signal to track cross-hybridizing signal on a corresponding PM probe. Our results also showed that the oligo fragments tend to bind to the 5' ends of the probes, and are rarely seen at the 3' ends. These results are useful for microarray design and data analysis.


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