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Universal arrays

  • US 20050074787A1
  • Filed: 12/08/2003
  • Published: 04/07/2005
  • Est. Priority Date: 03/26/1999
  • Status: Abandoned Application
First Claim
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1. A method of genotyping a nucleic acid sample at one or more loci, comprising the steps of:

  • (a) combining a nucleic acid sample comprising a nucleic acid molecule with one or more locus-specific tagged oligonucleotides under conditions suitable for hybridization of the nucleic acid molecule in the nucleic acid sample to one or more locus-specific tagged oligonucleotides, wherein each locus-specific tagged oligonucleotide comprises (a) a nucleotide sequence capable of hybridizing to a complementary sequence in an oligonucleotide tag and (b) a nucleotide sequence complementary to the nucleic acid molecule in the nucleic acid sample which terminates one nucleotide 5′

    of a nucleotide locus to be queried in the nucleic acid molecule in the nucleic acid sample, thereby creating an amplification product-locus-specific tagged oligonucleotide complex;

    (b) subjecting the complex to a single base extension reaction in the presence of two or more labeled ddNTPs, wherein the reaction results in the addition of a labeled ddNTP to the locus-specific tagged oligonucleotide, and wherein each type of ddNTP has a label that can be distinguished from the label of the other three types of ddNTPs;

    (c) contacting the complex with an oligonucleotide array comprising one or more oligonucleotide tags fixed to a solid substrate under suitable hybridization conditions, wherein each oligonucleotide tag comprises a unique arbitrary sequence complementary and of sufficient length to hybridize to a complementary sequence in a locus-specific tagged oligonucleotide, whereby the complex hybridizes to a specific oligonucleotide tag on the array; and

    assaying the array to determine the labeled ddNTPs present in the complex hybridized to one or more oligonucleotide tags, thereby determining the genotype of the queried nucleotide locus.

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