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Evolutionary sequence comparisons using high-density oligonucleotide arrays

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Abstract

We explored the utility of high-density oligonucleotide arrays (DMA chips) for obtaining sequence information from homologous genes in closely related species. Orthologues of the human BRCA1 exon 11, all approximately 3.4 kb in length and ranging from 98.2% to 83.5% nucleotide identity, were subjected to hybridization-based and conventional dideoxysequencing analysis. Retrospective guidelines for identifying high-fidelity hybridization-based sequence calls were formulated based upon dideoxysequencing results. Prospective application of these rules yielded base-calling with at least 98.8% accuracy over orthologous sequence tracts shown to have approximately 99% identity. For higher primate sequences with greater than 97% nucleotide identity, base-calling was made with at least 99.91 % accuracy covering a minimum of 97% of the sequence. Using a second-tier confirmatory hybridization chip strategy, shown in several cases to confirm the identity of predicted sequence changes, the complete sequence of the chimpanzee, gorilla and orangutan orthologues should be deducible solely through hybridization-based methodologies. Analysis of less highly conserved orthologues can still identify conserved nucleotide tracts of at least 15 nucleotides and can provide useful information for designing primers. DMA-chip based assays can be a valuable new technology for obtaining high-throughput cost-effective sequence information from related genomes.

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Authors and Affiliations

  1. National Human Genome Research Institute, Building 49/3A14, National Institutes of Health, Bethesda, Maryland, 20892, USA

    Joseph G. Hacia, Keith Edgemon, Michael R. Erdos, Christiane M. Robbins, Lawrence C. Brody & Francis S. Collins

  2. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, 20892, USA

    Wojciech Makalowski

  3. Affymetrix, 3380 Central Expressway, Santa Clara, California, 95051, USA

    Stephen P. A. Fodor

Authors
  1. Joseph G. Hacia
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  2. Wojciech Makalowski
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  3. Keith Edgemon
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  4. Michael R. Erdos
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  5. Christiane M. Robbins
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  6. Stephen P. A. Fodor
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  7. Lawrence C. Brody
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  8. Francis S. Collins
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Correspondence to Francis S. Collins.

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Hacia, J., Makalowski, W., Edgemon, K. et al. Evolutionary sequence comparisons using high-density oligonucleotide arrays. Nat Genet 18, 155–158 (1998). https://doi.org/10.1038/ng0298-155

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  • DOI: https://doi.org/10.1038/ng0298-155

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