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Open Access Research article

Leveraging human genomic information to identify nonhuman primate sequences for expression array development

Eliot R Spindel1, Mark A Pauley2, Yibing Jia1, Courtney Gravett1, Shaun L Thompson3, Nicholas F Boyle3, Sergio R Ojeda1 and Robert B Norgren3*

Author Affiliations

1 Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA

2 College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, 68182 USA

3 Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA

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BMC Genomics 2005, 6:160  doi:10.1186/1471-2164-6-160

Published: 15 November 2005

Abstract

Background

Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans. The utility of NHPs will be greatly increased by the application of genomics-based approaches such as gene expression profiling. Sequence information from the 3' end of genes is the key resource needed to create oligonucleotide expression arrays.

Results

We have developed the algorithms and procedures necessary to quickly acquire sequence information from the 3' end of nonhuman primate orthologs of human genes. To accomplish this, we identified terminal exons of over 15,000 human genes by aligning mRNA sequences with genomic sequence. We found the mean length of complete last exons to be approximately 1,400 bp, significantly longer than previous estimates. We designed primers to amplify genomic DNA, which included at least 300 bp of the terminal exon. We cloned and sequenced the PCR products representing over 5,500 Macaca mulatta (rhesus monkey) orthologs of human genes. This sequence information has been used to select probes for rhesus gene expression profiling. We have also tested 10 sets of primers with genomic DNA from Macaca fascicularis (Cynomolgus monkey), Papio hamadryas (Baboon), and Chlorocebus aethiops (African green monkey, vervet). The results indicate that the primers developed for this study will be useful for acquiring sequence from the 3' end of genes for other nonhuman primate species.

Conclusion

This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3' end of NHP orthologs and that this sequence can then be used to generate NHP oligonucleotide microarrays. Affymetrix and Agilent used sequences obtained with this approach in the design of their rhesus macaque oligonucleotide microarrays.