Method of comparing nucleic acid sequences

• US 6,551,784 B2
• Filed: 05/09/2001
• Issued: 04/22/2003
• Est. Priority Date: 06/07/1989
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Solas, Dennis W., Dower, William J., Fodor, Stephen P. A.
• Primary Examiner(s): ZITOMER, STEPHANIE W
• Application Number:
  US09/851,312
• Publication Number:
  US 20020102567A1
• Time in Patent Office: 713 Days
• Field of Search: 435/6, 435/283.1, 435/287.1, 435/288.3, 435/288.7, 536/23.1, 536/24.3
• US Class Current: 506/9
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00434 Liquid crystal masks
• CPC Class Codes: B01J 2219/00436 Maskless processes
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00475 Sheets
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B82Y 10/00 : Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07H 19/10 : with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07K 1/042 : characterised by the nature of the carrier
• CPC Class Codes: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C07K 17/06 : attached to the carrier via a bridging agent
• CPC Class Codes: C07K 17/14 : Peptides being immobilised on, or in, an inorganic carrier
• CPC Class Codes: C12Q 2600/158 : Expression markers
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 15/1433 : using image recognition
• CPC Class Codes: G03F 7/00 : Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printing surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor using photoresist structures for special production processes, see the relevant places, e.g. B44C, H01L, e.g. H01L21/00, H05K
• CPC Class Codes: G03F 7/265 : Selective reaction with inorganic or organometallic reagents after image-wise exposure, e.g. silylation
• CPC Class Codes: G03F 7/38 : Treatment before imagewise removal, e.g. prebaking G03F7/265 takes precedence
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules

Abstract

The present invention provides methods for comparing and identifying differences in nucleic acid sequences using a plurality of sequence specific recognition reagents (i.e., probes comprising a nucleic acid complementary to a nucleic acid sequence in collections to be compared) bound to a solid surface.

Claims

1. A method for identifying differences in at least one gene from a diseased cell compared to a normal cell comprising:

a) providing a plurality of probes bound to a solid surface, at least some of said plurality of probes comprising a nucleic acid sequence complementary to a nucleic acid sequence in said cells to be compared;

b) contacting the probes with a first collection of labeled nucleic acids obtained from a diseased cell having a first label, and at least a second collection of labeled nucleic acids obtained from a normal cell having a second label;

wherein said first and second labels are distinguishable from each other and wherein said labeled nucleic acids in said first and second collections bind to said probes; and

c)detecting the binding for each of the first and at least second labeled nucleic acids to the probes;

thereby identifying differences if any in said nucleic acid sequences in said at least one gene from a diseased cell compared to a normal cell.

2. The method as recited in claim 1 wherein the labeled nucleic acids are labeled with labels of first and second fluorescent reporters.

3. The method as recited in claim 2 wherein said first and second fluorescent reporters are different colors of fluorescent reporters.

4. The method as recited in claim 3 wherein said colors are red and green.

5. The method as recited in claim 3 wherein said probes are provided by synthesis of RNA or DNA on the solid surface.

6. The method of claim 1 wherein the first and second labeled nucleic acids are DNA.

7. The method of claim 1 wherein the first and second labeled nucleic acids are cDNA.

8. The method of claim 1 wherein the first and second labeled nucleic acids comprise human DNA.

9. The method of claim 1 wherein the first and second labeled nucleic acids are greater than about 25 nucleotides in complexity.

10. The method of claim 1 wherein the solid surface is glass.

11. The method of claim 1 wherein the first and second labels are fluorescent labels.

12. The method of claim 1 wherein the first labeled nucleic acids comprise mRNA or cDNA from a test cell and the second labeled nucleic acids comprise mRNA or cDNA from a reference cell.

13. The method of claim 1 wherein the first labeled nucleic acids are from a test genome and the second labeled nucleic acids are from a normal reference genome.

14. The method of claim 1 wherein the first labeled nucleic acids are from a tumor.

15. The method of claim 1 wherein the plurality of probes includes more than 100 probes per square centimeter bound to said solid surface.

16. The method of claim 1 wherein the plurality of probes includes more than 1000 probes per square centimeter bound to said solid surface.

17. The method of claim 1 wherein the plurality of probes includes more than 10,000 probes per square centimeter bound to said solid surface.

18. The method of claim 1, wherein said plurality of probes represents all known mutations of at least one given gene.

19. The method of claim 1 wherein said labeled nucleic acids obtained from a diseased cell and said labeled nucleic acids obtained from a normal cell are each obtained from total cDNA.

20. A method for identifying differences in at least one gene from a diseased cell compared to a normal cell comprising:

a) providing a plurality of probes comprising all known mutations of at least one given gene bound to a solid surface, at least some of said plurality comprising a nucleic acid sequence complementary to a nucleic acid sequence in said cells to be compared;

b) contacting the probes with a first collection of labeled nucleic acids obtained from total cDNA from a diseased cell having a first label, and at least a second collection of labeled nucleic acids obtained from total cDNA from a normal cell having a second label;

wherein said first and second labels are distinguishable from each other and wherein said labeled nucleic acids in said first and second collections bind to said probes;

c) detecting the binding for each of the first and at least second labeled nucleic acids to the probes;

thereby identifying differences if any in said nucleic acid sequences in said at least one gene from a diseased cell compared to a normal cell.