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.
Subscribe to Journal
Get full journal access for 1 year
only $17.42 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Li, W.-H. Molecular evolution. (Sinauer Associates, Sunderland, Massachusetts, 1997).
Tagle, D.A. et al. Embyonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus) nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203, 439–455 (1988).
Chee, M.S. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610–614 (1996).
Drmanac, R. et al. DNA sequence determination by hybridization: a strategy for efficient large-scale sequencing. Science 260, 1649–1652 (1993).
Fodor, S.P.A. et al. Light-directed spatially addressable parallel chemical synthesis. Science 251, 767–773 (1991).
Cronin, M.T. et al Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum. Mut. 7, 244–255 (1996).
Kozal, M.J. et al. Extensive polymorphisms observed in HIV-1 clade B protease gene using high density oligonucleotide arrays. Nature Med. 2, 753–759 (1996).
Yershov, G. et al. DNA analysis and diagnostics on oligonucleotide microchips. Proc. Natal. Acad. Sci. USA 93, 4913–4918 (1996).
Hacia, J.G. et al. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nature Genet. 14, 441–447 (1996).
Lockhart, D. et al. Monitoring gene expression using high density oligonucleotide arrays. Nature Biotech. 14, 1675–1680 (1996).
Shoemaker, D.D. et al Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genet. 14, 450–456 (1996).
Milner, N. et al. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nature Biotech. 15, 537–541 (1997).
Miki, Y. et al A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266, 66–71 (1994).
McConkey, E.H. & Goodman, M. A human genome evolution project is needed. Trends in Genet. 13, 350–351 (1997).
Kruglyak, L. The use of a genetic map of biallelic markers in linkage studies. Nature Genet. 17, 21–24 (1997).
Hoheisel, J.D. Sequence-independent and linear variation of oligonucleotide DNA binding stabilities. Nucleic Acids Res. 24, 430–432 (1996).
Broude, N.E. Enhanced sequencing by hybridization. Proc. Natl. Acad. Sci. USA 91, 3072–3076 (1994).
Szabo, C.I. et al. Human, canine, and murine BRCA1 genes: sequence comparison among species. Hum. Mol. Genet. 5, 1289–1298 (1996).
Huang, X. On global sequence alignment. Comput Appl. Biosci. 10, 227–235 (1994).
About this article
Cite this article
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
Discrimination of a single nucleotide polymorphism in the haptoglobin promoter region, rs5472, using a competitive fluorophore-labeled probe hybridization assay following loop-mediated isothermal amplification
Bioscience, Biotechnology, and Biochemistry (2021)
Journal of Neural Transmission (2018)
Behavioral Effects and Pharmacokinetics of (±)-3,4-Methylenedioxymethamphetamine (MDMA, Ecstasy) after Intragastric Administration to Baboons
Journal of Pharmacology and Experimental Therapeutics (2013)
Biochemical Pharmacology (2012)
Genetics Research International (2011)