Methodology article

In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip^® technology

Dmitry N Grigoryev¹, Shwu-Fan Ma¹, Brett A Simon², Rafael A Irizarry³, Shui Q Ye¹ and Joe GN Garcia^1*

• * Corresponding author: Joe GN Garcia drgarcia@jhmi.edu

Author Affiliations

¹ Center for Translational Respiratory Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, 5501 Hopkins Bayview Circle, JHAAC/4A.24, Baltimore, MD 21224, USA

² Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, 600 North Wolfe Street, Tower 711, Baltimore, MD 21287, USA

³ Department of Biostatistics, Johns Hopkins University,615 N. Wolfe Street, E3035, Baltimore, MD 21205, USA

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BMC Genomics 2005, 6:62 doi:10.1186/1471-2164-6-62

Published: 4 May 2005

Abstract

Background

Genomic approaches in large animal models (canine, ovine etc) are challenging due to insufficient genomic information for these species and the lack of availability of corresponding microarray platforms. To address this problem, we speculated that conserved interspecies genetic sequences can be experimentally detected by cross-species hybridization. The Affymetrix platform probe redundancy offers flexibility in selecting individual probes with high sequence similarities between related species for gene expression analysis.

Results

Gene expression profiles of 40 canine samples were generated using the human HG-U133A GeneChip (U133A). Due to interspecies genetic differences, only 14 ± 2% of canine transcripts were detected by U133A probe sets whereas profiling of 40 human samples detected 49 ± 6% of human transcripts. However, when these probe sets were deconstructed into individual probes and examined performance of each probe, we found that 47% of human probes were able to find their targets in canine tissues and generate a detectable hybridization signal. Therefore, we restricted gene expression analysis to these probes and observed the 60% increase in the number of identified canine transcripts. These results were validated by comparison of transcripts identified by our restricted analysis of cross-species hybridization with transcripts identified by hybridization of total lung canine mRNA to new Affymetrix Canine GeneChip^®.

Conclusion

The experimental identification and restriction of gene expression analysis to probes with detectable hybridization signal drastically increases transcript detection of canine-human hybridization suggesting the possibility of broad utilization of cross-hybridizations of related species using GeneChip technology.