Chip-based species identification and phenotypic characterization of microorganisms
First Claim
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1. A method for assigning a first organism to a particular group or species, comprising:
- (a) providing an array of oligonucleotides at known locations on a substrate, said array comprising probes complementary to at least one reference DNA or RNA sequence;
(b) obtaining a first hybridization pattern for said first organism by hybridizing a target nucleic acid sequence from the first organism to the array;
(c) comparing the first hybridization pattern to a plurality of reference hybridization patterns to identify the reference hybridization pattern that most closely matches the first hybridization pattern, wherein each reference hybridization pattern is from an organism of known group or species, and (d) identifying the group or species of the first organism.
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Abstract
This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the Mycobacterium tubercluosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.
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Citations
12 Claims
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1. A method for assigning a first organism to a particular group or species, comprising:
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(a) providing an array of oligonucleotides at known locations on a substrate, said array comprising probes complementary to at least one reference DNA or RNA sequence;
(b) obtaining a first hybridization pattern for said first organism by hybridizing a target nucleic acid sequence from the first organism to the array;
(c) comparing the first hybridization pattern to a plurality of reference hybridization patterns to identify the reference hybridization pattern that most closely matches the first hybridization pattern, wherein each reference hybridization pattern is from an organism of known group or species, and (d) identifying the group or species of the first organism. - View Dependent Claims (12)
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2. A method of identifying the presence of a nucleic acid polymorphism in a patient sample, comprising the steps of:
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(a) obtaining a first hybridization pattern for the patient sample by hybridizing a target nucleic acid sequence from the patient sample to an array comprising a plurality of probes that are complementary to at least one nucleic acid reference sequence;
(b) comparing the first hybridization pattern obtained for said target nucleic acid sequence from the patient sample and a corresponding second hybridization pattern obtained for a target nucleic acid sequence from a wild type sample to identify at least one difference in hybridization intensity of a reference probe between the first and second hybridization patterns;
(c) deriving a hybridization intensity ratio from the at the least one difference in (b); and
(d) identifying the presence of a polymorphism at a base position within the reference probe if the ratio in (c) is greater than or equal to an assigned value. - View Dependent Claims (3, 4, 5, 6, 7, 8, 9, 10, 11)
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Specification