Method and apparatus for determining gene expression levels

• US 6,816,790 B2
• Filed: 02/13/2003
• Issued: 11/09/2004
• Est. Priority Date: 12/31/2002
• Status: Expired due to Fees

• Current Assignee: Pendragon Networks LLC (Pendrell Corporation)
• Original Assignee: International Business Machines Corporation
• Inventors: Tu, Yuhai, Held, Glenn Allen, Grinstein, Geoffrey
• Primary Examiner(s): Barlow, John
• Assistant Examiner(s): LE, JOHN H
• Application Number:
  US10/365,891
• Publication Number:
  US 20040128082A1
• Time in Patent Office: 635 Days
• Field of Search: 702/19, 702/20, 702/22, 702/23, 702/27, 435/6, 435/7.92, 435/69.1, 435/91.2, 435/973
• US Class Current: 702/23
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation

Abstract

Techniques for analyzing gene expression levels are provided. In one aspect of the invention, the technique provides a method for determining a concentration level of a target nucleic acid, the target nucleic acid comprising at least one target oligonucleotide. The method determines (i) a measure of affinity value of the target oligonucleotide with a probe oligonucleotide; and (ii) a hybridization intensity value for the target oligonucleotide and the probe oligonucleotide at a probe spot. The measure of affinity value and the hybridization intensity value are used to determine the concentration level of the target nucleic acid.

Claims

1. A method for determining a concentration level of a target nucleic acid, the target nucleic acid comprising at least one target oligonucleotide, the method comprising the steps of:

determining a measure of affinity value of the target oligonucleotide with a probe oligonucleotide;

determining a hybridization intensity value for the target oligonucleotide and the probe oligonucleotide at a probe spot; and

using the measure of affinity value and the hybridization intensity value to determine the concentration level of the target nucleic acid.

2. The method of claim 1, wherein the measure of affinity value comprises a free energy of hybridization of the target oligonucleotide with the probe oligonucleotide.

3. The method of claim 1, wherein the measure of affinity value comprises a net rate of hybridization of the target oligonucleotide with the probe oligonucleotide.

4. The method of claim 1, wherein the method is carried out for a plurality of probe spots.

5. The method of claim 4, wherein the plurality of probe spots are attached to a microarray.

6. The method of claim 1, wherein the hybridization intensity value is determined using fluorescence.

7. The method of claim 1, comprising a plurality of measure of affinity values, hybridization intensity values and concentration levels of the target nucleic acid.

8. The method of claim 7, further comprising the step of comparing the plurality of hybridization intensity values to determine an overall hybridization intensity value.

9. The method of claim 1, comprising a plurality of probe oligonucleotides.

10. The method of claim 9, further comprising the steps of:

obtaining an observed hybridization intensity value for the probe oligonucleotide at the probe spot;

using the observed hybridization intensity value to determine a concentration level of the target nucleic acid;

performing the steps of obtaining and using for the plurality of probe oligonucleotides to obtain a plurality of concentration levels of the target nucleic acid; and

comparing the plurality of concentration levels of the target nucleic acid to determine an overall concentration level of the target nucleic acid.

11. The method of claim 10, wherein the using step further comprises the step of removing probe spots with statistically outlying observed hybridization intensity values.

12. The method of claim 1, wherein the step of determining the measure of affinity value of the target oligonucleotide with a probe oligonucleotide further comprises the step of correlating observed hybridization intensity values at known target nucleic acid concentrations with probe oligonucleotide sequences.

13. The method of claim 1, wherein the measure of affinity value is calculated on the basis of the physical principles of hybridization.

14. A method for predicting a concentration level of a target nucleic acid, the target nucleic acid comprising at least one target oligonucleotide, the method comprising the steps of:

determining a measure of affinity value of the target oligonucleotide with a probe oligonucleotide at a probe spot;

obtaining an observed hybridization intensity value;

determining an expected hybridization intensity value; and

comparing the measure of affinity value, the observed hybridization intensity value and the expected hybridization intensity value for a plurality of probe spots to determine a unique predicted target nucleic acid concentration.

15. The method of claim 14, wherein the obtaining step further comprises the step of removing probe spots from the plurality of probe spots having statistically outlying observed hybridization intensity values.

16. An apparatus for determining a concentration level of a target nucleic acid, the target nucleic acid comprising at least one target oligonucleotide, the apparatus comprising:

a memory; and

at least one processor, coupled to the memory, operative to;

determine a measure of affinity value of the target oligonucleotide with a probe oligonucleotide;

determine a hybridization intensity value for the target oligonucleotide and the probe oligonucleotide at a probe spot; and

use the measure of affinity value and the hybridization intensity value to determine the concentration level of the target nucleic acid.

17. An article of manufacture for determining a concentration level of a target nucleic acid, the target nucleic acid comprising at least one target oligonucleotide, comprising a machine readable medium containing one or more programs which when executed implement the steps of:

determining a measure of affinity value of the target oligonucleotide with a probe oligonucleotide;

determining a hybridization intensity value for the target oligonucleotide and the probe oligonucleotide at a probe spot; and

using the measure of affinity value and the hybridization intensity value to determine the concentration level of the target nucleic acid.