Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays

• US 9,234,241 B2
• Filed: 12/09/2013
• Issued: 01/12/2016
• Est. Priority Date: 02/09/1996
• Status: Expired due to Fees

• Current Assignee: Cornell Research Foundation Incorporated (Cornell University)
• Original Assignee: Cornell Research Foundation Incorporated (Cornell University)
• Inventors: Barany, Francis, Barany, George, Hammer, Robert P., Kempe, Maria, Blok, Herman, Zirvi, Monib
• Primary Examiner(s): Martinell, James
• Application Number:
  US14/101,067
• Publication Number:
  US 20140100135A1
• Time in Patent Office: 764 Days
• Field of Search: None
• US Class Current: 1/1
• 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 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• 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 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00729 Peptide nucleic acids [PNA]
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 : for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• 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 2561/125 : Ligase Detection Reaction [LDR]
• CPC Class Codes: C12Q 2565/501 : being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/514 : characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C12Q 2600/156 : Polymorphic or mutational markers
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries

Abstract

The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.

Claims

1. A method comprising:

providing a collection of oligonucleotides wherein each type of oligonucleotide is greater than 16 nucleotides and differs in nucleotide sequence, when aligned to another type of oligonucleotide in the collection, by at least 25%;

providing a sample comprising a plurality of composite oligonucleotides, each composite oligonucleotide comprising (i) a zip-code portion, and (ii) one or more further nucleotide sequences;

contacting the sample comprising the plurality of composite oligonucleotides with the collection of oligonucleotides under conditions effective to hybridize the zip-code portion of each composite oligonucleotide to its complementary oligonucleotide in the collection; and

detecting the one or more of the plurality of composite oligonucleotides hybridized to their complementary oligonucleotides in the collection.

2. The method according to claim 1, wherein each oligonucleotide in the collection comprises 20-25 nucleotides.

3. The method of according to claim 1, wherein the collection of oligonucleotides is coupled to a solid support.

4. The method according to claim 3, wherein said detecting is carried out on the solid support.

5. The method according to claim 1, wherein the zip-code portions of the composite oligonucleotides hybridize to their complementary oligonucleotides in the collection under stringent hybridization conditions.

6. The method according to claim 1, wherein the collection contains at least 25 types of oligonucleotides.

7. The method according to claim 1, wherein the collection contains at least 1000 types of oligonucleotides.

8. The method according to claim 1, wherein the one or more further nucleotide sequences of the composite oligonucleotide comprises an amplification product, or complement thereof, of one or more cellular target nucleic acid sequences.

9. A method comprising:

providing a solid support having an array of positions, wherein composite oligonucleotides are coupled to the solid support at the array of positions, each of said composite oligonucleotides characterized by having a target-specific portion and a zip code portion, wherein the zip code portion of each of the composite oligonucleotides comprises a nucleotide sequence of greater than sixteen nucleotides that differs for each different target-specific portion, wherein the nucleotide sequence of one zip code portion differs from the nucleotide sequence of another zip code portion, when aligned to each other, by at least 25% of the nucleotides; and

detecting one or more labels coupled to at least one of the composite oligonucleotides, thereby facilitating identification of the composite oligonucleotide and its zip code portion.

10. The method of claim 9, wherein said detecting is carried out in an imager.

11. The method of claim 10, wherein the imager is a fluorescence imager and the detectable label is a fluorescent label suitable for detection by the fluorescence imager.

12. The method of claim 9, wherein the composite oligonucleotides are coupled to beads.

13. The method of claim 9, wherein different composite oligonucleotides are coupled to the solid support at different array positions.

14. The method of claim 9, wherein the solid support having an array of positions comprises a high-density array of composite oligonucleotides immobilized thereto.

15. The method of claim 9, wherein the solid support is made from a material selected from the group consisting of plastic, ceramic, metal, resin, gel, glass, silicon, and composites thereof.

16. The method of claim 9, wherein the solid support is in a form selected from the group consisting of slides, discs, membranes, films, and composites thereof.

17. The method of claim 9, wherein the target nucleotide sequence in the sample comprises an amplification product, or complement thereof, of one or more cellular target nucleic acid sequences.

18. The method of claim 9, wherein the zip-code portion of the composite oligonucleotide comprises a nucleotide sequence of 24 nucleotides or less.

19. An apparatus comprising:

a solid support having an array of positions;

composite oligonucleotides coupled to the solid support at the array of positions, each of said composite oligonucleotides characterized by having a target-specific portion and a zip code portion, wherein the zip code portion of each of the composite oligonucleotides comprises a nucleotide sequence of greater than sixteen nucleotides, wherein the nucleotide sequence of one zip code portion differs from the nucleotide sequence of another zip code portion, when aligned to each other, by at least 25% of the nucleotides; and

one or more detectable labels coupled to at least one of the composite oligonucleotides.

20. The apparatus of claim 19 further comprising:

an imager for detecting or quantifying at least one of the detectable labels at at least one of the array positions on the solid support.

21. The apparatus of claim 19, wherein the composite oligonucleotides are coupled to beads.

22. The apparatus of claim 19, wherein the solid support having an array of positions comprises a high-density array of composite oligonucleotides immobilized thereto.

23. The apparatus of claim 19, wherein the target nucleotide sequence in the sample comprises an amplification product, or complement thereof, of one or more cellular target nucleic acid sequences.