Strategies for gene expression analysis

• US 7,897,750 B2
• Filed: 11/26/2008
• Issued: 03/01/2011
• Est. Priority Date: 07/19/2002
• Status: Expired due to Fees

• Current Assignee: Altheadx, Inc.
• Original Assignee: Althea Technologies Inc. (Ajinomoto Co., Inc.)
• Inventors: Monforte, Joseph
• Primary Examiner(s): Kim; Young J
• Application Number:
  US12/315,115
• Publication Number:
  US 20090149346A1
• Time in Patent Office: 825 Days
• Field of Search: None
• US Class Current: 536/24.33
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The invention provides methods for screening compound or chemical libraries by analyzing expressed RNA samples from biological samples treated with members of a compound library in a high throughput format.

Claims

1. A hybridization system comprising:

(a) an array comprising at least 500 nucleic acid samples that each comprise a plurality of different nucleic acids, wherein each nucleic acid sample is deposited at a single unique location on the array, wherein each nucleic acid sample is produced from a biological sample that has been contacted with at least one member of a compound library prior to producing the nucleic acid sample, and wherein the plurality of different nucleic acids in each nucleic acid sample comprises subsequences of at least two different genes in the biological sample; and

,

(b) a plurality of solution-based, defined sequence probes wherein each comprises a subsequence of a different gene in the biological sample, and wherein each probe is capable of generating a different detectable signal.

2. The hybridization system of claim 1, wherein the at least 500 nucleic acid samples are selected from:

(i) total cellular RNA or a subset thereof derived from the biological sample;

(ii) mRNA isolated from the biological sample;

(iii) cDNA produced from (i) or (ii); and

(iv) nucleic acids amplified from (i), (ii), or (iii).

3. The hybridization system of claim 1 wherein the plurality of defined sequence probes comprises a set of genes comprising disease-related targets.

4. The hybridization system of claim 1, wherein the array comprises a two-dimensional solid-phase surface.

5. The hybridization system of claim 1, wherein the array comprises a plurality of solid-phase surfaces.

6. The hybridization system of claim 5, wherein the plurality of solid-phase surfaces are selected from the group consisting of:

beads, spheres, and optical fibers.

7. The hybridization system of claim 6, wherein the array comprises a solid-phase surface comprising a material selected from the group consisting of:

glass, coated glass, silicon, porous silicon, nylon, ceramic, and plastic.