Chip-based species identification and phenotypic characterization of microorganisms

• US 6,924,094 B1
• Filed: 11/28/2000
• Issued: 08/02/2005
• Est. Priority Date: 02/08/1996
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Mack, David, Chee, Mark S., Berno, Anthony J., Gingeras, Thomas R., Ghandour, Ghassan, Wang, Ching, Stryer, Lubert
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US09/724,938
• Time in Patent Office: 1,708 Days
• Field of Search: 435/5, 435/6, 435/91.2, 436/94
• US Class Current: 435/5
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C40B 80/00 Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers
• CPC Class Codes: G01N 33/54386 Analytical elements
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

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.

Claims

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.

12. The method of claim 1 wherein the probes of the array are 19, 20, 21, 22, 23, 24, 25 or 30 bases in length and exhibit perfect complementarity to said reference DNA or RNA sequence.

2. A method of identifying the presence of a nucleic acid polymorphism in a patient sample, comprising the steps of:

(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.

3. The method of claim 2, wherein the nucleic acid reference sequence is a sequence or subsequence of mitochondrial DNA.

4. The method of claim 2, wherein the nucleic acid reference sequence comprises an HIV gene or subsequence thereof.

5. The method of claim 2, wherein the nucleic acid reference sequence comprises a gene associated with a heritable disease or subsequence thereof.

6. The method of claim 5, wherein the heritable disease is cystic fibrosis.

7. The method of claim 2, wherein the nucleic acid sequence is a least a subsequence of p53.

8. The method of claim 2, wherein the nucleic acid sequence is at least a subsequence of MSH.

9. The method of claim 2 wherein the nucleic acid sequence is at least a subsequence of MLH1.

10. The method of claim 2, wherein the nucleic acid sequence is at least a subsequence of BRCA-1.

11. The method of claim 2 wherein the probes of the array are 19, 20, 21, 22, 23, 24, 25 or 30 bases in length and exhibit perfect complementarity to said reference sequence.