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

• US 8,288,521 B2
• Filed: 03/25/2011
• Issued: 10/16/2012
• 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:
  US13/072,442
• Publication Number:
  US 20110177975A1
• Time in Patent Office: 571 Days
• Field of Search: None
• US Class Current: 536/24.3
• 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 kit for identifying one or more of a plurality of sequences differing by single-base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences comprising:

a ligase;

a collection of oligonucleotide probe sets, each set characterized by (a) a first oligonucleotide probe comprising a target-specific portion and (b) a second oligonucleotide probe comprising a target-specific portion and a further portion, wherein the further portion comprises a nucleic acid sequence of greater than sixteen nucleotides that differs for each different target-specific portion, and wherein the nucleic acid sequence of a complement to one further portion differs from the nucleic acid sequence of a complement to another further portion in the collection by at least 25%, when aligned to each other.

2. The kit according to claim 1 further comprising

a solid support and

a collection of capture oligonucleotides immobilized at particular sites on the solid support, wherein the capture oligonucleotides have nucleotide sequences complementary to the further portions and, wherein the solid support and the capture oligonucleotides form an addressable array.

3. The kit according to claim 2, 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.

4. The kit according to claim 2, wherein the solid support is in a form selected from the group consisting of beads, spheres, plates, strands, slides, discs, membranes, films, and composites thereof.

5. The kit according to claim 4, wherein the solid support comprises a plurality of beads, wherein each bead comprises one or more types of capture oligonucleotides from the collection of capture oligonucleotides.

6. The kit according to claim 4, wherein the solid support comprises a plurality of spheres, wherein each sphere comprises one or more types of capture oligonucleotides from the collection of capture oligonucleotides.

7. The kit according to claim 2, wherein the solid support has an array of positions with a plurality of capture oligonucleotides attached to the array of positions.

8. The kit of claim 2, wherein the solid support comprises a high-density array of capture oligonucleotides immobilized thereto.

9. The kit according to claim 2, wherein the collection of capture oligonucleotides comprises at least 25 different capture oligonucleotides.

10. The kit according to claim 9, wherein the collection of capture oligonucleotides comprises at least 1000 different capture oligonucleotides.

11. The kit according to claim 9, wherein the collection of capture oligonucleotides comprises 25 to 1200 different capture oligonucleotides.

12. The kit according to claim 1 further comprising:

amplification primers suitable for amplification of the target nucleotide sequences and

a polymerase.

13. The kit according to claim 2, wherein each capture oligonucleotide in the collection of capture oligonucleotides comprises a nucleotide sequence of greater than sixteen nucleotides.

14. The kit according to claim 13, wherein each capture oligonucleotide in the collection comprises a nucleotide sequence of 24 nucleotides or less.

15. The kit according to claim 1, wherein the collection of oligonucleotide probe sets comprises at least 25 different oligonucleotide probe sets.

16. The kit according to claim 15, wherein the collection of oligonucleotide probe sets comprises at least 1000 different oligonucleotide probe sets.

17. The kit according to claim 15, wherein the collection of oligonucleotide probe sets comprises 25 to 1200 different oligonucleotide probe sets.

18. A kit for identifying one or more of a plurality of target nucleotide sequences in a sample comprising:

a ligase;

a plurality of oligonucleotide probe sets, each set characterized by (a) a first oligonucleotide probe, having a target-specific portion and an address-specific portion and (b) a second oligonucleotide probe, having a target-specific portion; and

a collection of capture oligonucleotides wherein each type of capture oligonucleotide in the collection comprises a nucleotide sequence complementary to an address-specific portion, wherein the address-specific portion is comprised of a nucleotide sequence which is distinct from that of the target-specific portions, and wherein each type of capture oligonucleotide in the collection hybridizes to its complement under uniform hybridization conditions but differs by at least 25% in nucleotide sequence, when aligned to another type of capture oligonucleotide in the collection.

19. The kit according to claim 18 further comprising:

amplification primers suitable for amplification of the target nucleotide sequences and

a polymerase.

20. The kit according to claim 18, wherein the address-specific portion of the first oligonucleotide probe comprises a nucleotide sequence of greater than sixteen nucleotides.

21. The kit according to claim 18, wherein each capture oligonucleotide in the collection of capture oligonucleotides comprises a nucleotide sequence of greater than sixteen nucleotides.

22. The kit according to claim 21, wherein each capture oligonucleotide in the collection of capture oligonucleotides comprises a nucleotide sequence of 24 nucleotides or less.

23. The kit according to claim 18 further comprising:

a solid support, wherein capture oligonucleotides of the collection are immobilized at particular sites on the solid support.

24. The kit according to claim 23, wherein the collection of capture oligonucleotides and the solid support form an addressable array.

25. The kit according to claim 23, wherein the solid support comprises a plurality of beads, wherein each bead comprises one or more types of capture oligonucleotides from the collection.

26. The kit according to claim 23, wherein the solid support comprises a plurality of spheres, wherein each sphere comprises one or more types of capture oligonucleotides from the collection.

27. The kit according to claim 18, wherein the plurality of oligonucleotide probe sets comprises at least 25 different oligonucleotide probe sets.

28. The kit according to claim 27, wherein the plurality of oligonucleotide probe sets comprises at least 1000 different oligonucleotide probe sets.

29. The kit according to claim 27, wherein the plurality of oligonucleotide probe sets comprises 25 to 1200 different oligonucleotide probe sets.

30. The kit according to claim 18, wherein the collection of capture oligonucleotides comprises at least 25 different capture oligonucleotides.

31. The kit according to claim 30, wherein the collection of capture oligonucleotides comprises at least 1000 different capture oligonucleotides.

32. The kit according to claim 30, wherein the collection of capture oligonucleotides comprises 25 to 1200 different capture oligonucleotides.