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

Eliot Spindel, Mark A. Pauley, Yibing Jia, Courtney Gravett, Shaun L. Thompson, Nicholas F. Boyle, Sergio Ojeda, Robert B. Norgren

    Research output: Contribution to journalArticle

    23 Citations (Scopus)

    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. Conclusions: This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3′ end of NBP 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.

    Original languageEnglish (US)
    Article number160
    JournalBMC Genomics
    Volume6
    DOIs
    StatePublished - Nov 15 2005

    Fingerprint

    Primates
    Papio hamadryas
    Oligonucleotide Array Sequence Analysis
    Macaca mulatta
    Cercopithecus aethiops
    Exons
    Macaca fascicularis
    Genes
    Gene Expression Profiling
    DNA
    Genomics
    Biomedical Research
    Polymerase Chain Reaction
    Messenger RNA

    ASJC Scopus subject areas

    • Medicine(all)
    • Biotechnology
    • Genetics

    Cite this

    Leveraging human genomic information to identify nonhuman primate sequences for expression array development. / Spindel, Eliot; Pauley, Mark A.; Jia, Yibing; Gravett, Courtney; Thompson, Shaun L.; Boyle, Nicholas F.; Ojeda, Sergio; Norgren, Robert B.

    In: BMC Genomics, Vol. 6, 160, 15.11.2005.

    Research output: Contribution to journalArticle

    Spindel, Eliot ; Pauley, Mark A. ; Jia, Yibing ; Gravett, Courtney ; Thompson, Shaun L. ; Boyle, Nicholas F. ; Ojeda, Sergio ; Norgren, Robert B. / Leveraging human genomic information to identify nonhuman primate sequences for expression array development. In: BMC Genomics. 2005 ; Vol. 6.
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    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. Conclusions: This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3′ end of NBP 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.",
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    AU - Gravett, Courtney

    AU - Thompson, Shaun L.

    AU - Boyle, Nicholas F.

    AU - Ojeda, Sergio

    AU - Norgren, Robert B.

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