Although useful information has been obtained, there are serious limitations to this approach. Cross-species hybridization experiments utilizing rhesus samples with human oligonucleotide microarrays have also been attempted. One question which must be addressed is: given the close evolutionary relationship between rhesus macaque and humans, why not use available human oligonucleotide microarrays with rhesus macaque samples? Human oligonucleotide microarrays have been used with chimpanzee samples to obtain useful information. This is important because NHPs are required for the study of AIDS, stem cell biology, reproduction and neuroscience, but are expensive and in short supply. Gene expression profiling is expected to rapidly increase the information yield from experiments using nonhuman primates (NHPs). Affymetrix and Agilent used sequences obtained with this approach in the design of their rhesus macaque oligonucleotide microarrays. 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. 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. 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). This sequence information has been used to select probes for rhesus gene expression profiling. We cloned and sequenced the PCR products representing over 5,500 Macaca mulatta (rhesus monkey) orthologs of human genes. We designed primers to amplify genomic DNA, which included at least 300 bp of the terminal exon. We found the mean length of complete last exons to be approximately 1,400 bp, significantly longer than previous estimates. To accomplish this, we identified terminal exons of over 15,000 human genes by aligning mRNA sequences with genomic sequence. We have developed the algorithms and procedures necessary to quickly acquire sequence information from the 3' end of nonhuman primate orthologs of human genes. Sequence information from the 3' end of genes is the key resource needed to create oligonucleotide expression arrays. The utility of NHPs will be greatly increased by the application of genomics-based approaches such as gene expression profiling. Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans.
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