Solid phase selection of differentially expressed genes

• US 6,265,163 B1
• Filed: 08/06/1998
• Issued: 07/24/2001
• Est. Priority Date: 01/09/1998
• Status: Expired due to Term

• Current Assignee: Solexa Incorporated (Illumina Incorporated)
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Brenner, Sydney, DuBridge, Robert B., Albrecht, Glenn
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/130,546
• Time in Patent Office: 1,083 Days
• Field of Search: 435/5, 435/6, 536/24.31, 536/24.32, 536/25.32
• US Class Current: 435/6.12
• CPC Class Codes: C12N 15/1096 cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target

Abstract

The invention provides a method and materials for monitoring and isolating differentially expressed genes. In accordance with the method of the invention, differently labeled populations of DNAs from sources to be compared are competitively hybridized with reference DNA cloned on solid phase supports, e.g. microparticles, to provide a differential expression library which, in the preferred embodiment, may be manipulated by fluorescence-activated cell sorting (FACS). Monitoring the relative signal intensity of the different fluoresent labels on the microparticles permits quantitative analysis of expression levels relative to the reference DNA. Populations of microparticles having relative signal intensities of interest can be isolated by FACS and the attached DNAs identified by sequencing, such as with massively parallel signature sequencing (MPSS), or with conventional DNA sequencing protocols.

Claims

1. A method of analyzing relative gene expression in a plurality of different cells or tissues, the method comprising the steps of:

providing a reference DNA population of DNA sequences attached to septerate solid phase supports in clonal subpopulations;

providing a population of polynucleotides of expressed genes from each of the plurality of different cells or tissues, the polynucleotides of expressed genes from different cells or tissues having a different light-generating label and the polynucleotides of expressed genes from the same cells or tissues having the same light-generating label; and

competitively hybridizing the populations of polynucleotides of expressed genes from each of the plurality of different cells or tissues with the reference DNA population to form duplexes between the DNA sequences of the reference DNA population and polynucleotides of each of the different cells or tissues such that polynucleotides from the same gene of the different cells or tissues hybeidize with the same complementary sequence of the reference DNA population and such that such polynucleotides are present in duplexes on each of the solid phase supports in ratios directly related to the relative expression of their corresponding genes in the different cells or tissues; and

sorting each solid phase support according to a relative optical signal generated by the light-generating labels of the duplexes attached thereto.

2. The method of claim 1 wherein said reference DNA population is derived from said expressed genes of said plurality of different cells or tissues being analyzed.

3. The method of claim 2 wherein said different light-generating labels are different fluorescent labels.

4. The method of claim 3 wherein said population of polynucleotides of expressed genes are populations of cDNAs.

5. The method of claim 4 further comprising the steps of:

accumulating in a seperate vessel each said solid phase support having said relative optical signal with a value within one or more predetermined ranges of values corresponding to a difference in gene expression among said plurality of different cells or tissues; and

identifying said polynucleotides on each of said solid supports by determining a nucleotide sequence of a portion of each of said polynucleotides.

6. The method of claim 5 wherein said relative optical signal is a ratio of fluorescence intensities and wherein said plurality of different cells or tissues is two.

7. The method of claim 6 wherein said portion of said polynucleotides is a sequence of at least ten nucleotides.

8. The method of claim 6 wherein said step of identifying includes simultaneous sequencing of at least ten thousand of said polynucleotides by massively parallel signature sequencing.

9. A method of isolating polynucleotides derived from genes differentially expressed in a plurality of different cells or tissues, the method comprising the steps of:

providing a reference DNA population of DNA sequences attached to separate microparticles in clonal subpopulations;

providing a population of polynucleotides derived from genes expressed in each of the plurality of different cells or tissues, each polynucleotide having a light-generating label capable of generating an optical signal indicative of the cells or tissues from which it is derived;

competitively hybridizing the populations of polynucleotides of genes expressed in each of the plurality of different cells or tissues with the reference DNA population to form duplexes between the DNA sequences of the reference DNA population and polynucleotides from each of the different cells or tissues such that polynucleotides from the same gene of the different cells or tissues hybridize with the same complementary sequence of the reference DNA population and such that such polynucleotides are present in dupleses on each of the microparticles in ratios directly related to the relative expression of their corresponding genes in the different cells or tissues; and

isolating polynucleotides corresponding to genes differentially expressed in the different cells or tissues by sorting microparticles in accordance with the optical signals generated by the populations of polynucleotides hybridized thereto.

10. The method of claim 9 wherein said reference DNA population is derived from genes expressed in the plurality of different cells or tissues being analyzed.

11. The method of claim 10 wherein said plurality of different cells or tissues is two and wherein said optical signal is a fluorescent signal.

12. The method of claim 11 wherein said populations of polynucleotides are labeled with different fluorescent labels.

13. The method of claim 12 wherein said populations of polynucleotides are populations of cDNAs.

14. The method of claim 13 wherein said step of isolating includes sorting said microparticles in accordance with the ratio of fluorescence intensities generated by said populations of cDNAs hybridized thereto.

15. The method of claim 14 wherein said step of isolating includes sorting said microparticle with a fluorescence-activated cell sorter.

16. The method of claim 15 further including the step of identifying said isolated cDNAs by determining a nucleotide sequence of a portion of each said isolated cDNA.