EVOLUTIONARY SEQUENCE COMPARISONS USING HIGH-DENSITY OLIGONUCLEOTIDE ARRAYS

We explored the utility of high-density oligonucleotide arrays (DNA ch ips) for obtaining sequence information from homologous genes in close ly related species. Orthologues of the human BRCA1 exon 11, all approx imately 3.4 kb in length and ranging from 98.2% to 83.5% nucleotide id entity, were subjected to hybridization-based and conventional dideoxy sequencing analysis. Retrospective guidelines for identifying high-fid elity hybridization-based sequence calls were formulated based upon di deoxysequencing results. Prospective application of these rules yielde d base-calling with at least 98.8% accuracy over orthologous sequence tracts shown to have approximately 99% identity. For higher primate se quences with greater than 97% nucleotide identity, base-calling was ma de with at least 99.91% accuracy covering a minimum of 97% of the sequ ence. Using a second-tier confirmatory hybridization chip strategy, sh own in several cases to confirm the identity of predicted sequence cha nges, the complete sequence of the chimpanzee. gorilla and orangutan o rthologues should be deducible solely through hybridization-based meth odologies. Analysis of less highly conserved orthologues can still ide ntify conserved nucleotide tracts of at least 15 nucleotides and can p rovide useful information for designing primers. DNA-chip based assays can be a valuable new technology for obtaining high-throughput cost-e ffective sequence information from related genomes.