Microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method

• US 20060240443A1
• Filed: 04/20/2005
• Published: 10/26/2006
• Est. Priority Date: 04/20/2005
• Status: Abandoned Application

• Current Assignee: CombiMatrix Corporation
• Original Assignee: CombiMatrix Corporation
• Inventors: Lodes, Michael J., McShea, Andy, Suciu, Dominic
• Application Number:
  US11/110,630
• Publication Number:
  US 20060240443A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation

Abstract

There is disclosed a microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method. Specifically, there is disclosed a method using a microarray device wherein a plurality of hybridized structures is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged targets and a plurality of detection sequences. The detection sequences of each hybridized structure is extended using an extension-ligation solution and an extension-ligation condition. After extension, ligation of the extended sequence occurs to a probe if the terminal nucleotide of a probe is complementary to the hybridized tagged targets. Non-bound material is removed by using a washing solution and a washing method. The target nucleotide and the target sequence of the tagged targets is determined by which probe is ligated to the detection sequences.

Claims

1. A microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method comprising:

(a) providing a microarray having a plurality of probes;

(b) forming a plurality of hybridized structures on the microarray, wherein each hybridized structure is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged targets and a plurality of detection sequences, wherein each hybridized structure comprises one tagged target hybridized to one probe and to one detection sequence;

(c) extending each hybridized structure using an extension-ligation solution;

(d) ligating each hybridized structure having a terminal nucleotide that is complementary to a target nucleotide using the extension-ligation solution;

(e) removing non-bound material by washing the microarray using a wash solution; and

(f) identifying the target nucleotide and a hybridized sequence from the hybridized structures having ligation.

2. The method of claim 1, wherein the plurality of probes is selected from the group consisting of probe DNA, probe RNA, and combinations thereof.

3. The method of claim 1, wherein the plurality of probes is attached to the microarray by a spacer.

4. The method of claim 1, wherein the plurality of tagged targets is selected from the group consisting of tagged target DNA, tagged target RNA, and combinations thereof.

5. The method of claim 3, wherein the tagged target DNA is cDNA.

6. The method of claim 3, wherein the tagged target RNA is mRNA.

7. The method of claim 1, wherein the plurality of tagged targets is first amplified.

8. The method of claim 1, wherein the plurality of detection sequences is selected from the group consisting of a detection sequence DNA, a detection sequence RNA, and combinations thereof.

9. The method of claim 1, wherein the plurality of detection sequences has a fluorescent tag.

10. The method of claim 1, wherein the plurality of tagged targets and the plurality of probes have less than approximately five internal mismatches when hybridized, and the plurality of tagged targets and the plurality of detection sequences have less than approximately five internal mismatches when hybridized.

11. The method of claim 1, wherein the hybridizing solution comprises a plurality of tagged targets and a plurality of detection sequences in a buffer solution comprising a 1×

T4 ligase buffer, and the hybridizing condition comprises approximately 45°

C. for approximately one hour.

12. The method of claim 1, wherein the extension-ligation solution comprises a formulation comprising water, buffer, triphosphate mix, polymerase, and ligase.

13. The method of claim 12, wherein the polymerase is selected from the group consisting of DNA polymerase and RNA polymerase, and combinations thereof.

14. The method of claim 12, wherein the polymerase is selected from the group consisting of Taq polymerase Stoffel fragment, a reverse transcriptase, E. coli DNA polymerase, Klenow fragment polymerase, T7 RNA polymerase, T3 RNA polymerase, viral replicase, and SP6 RNA polymerase, and combinations thereof.

15. The method of claim 12, wherein the buffer is selected from the group consisting of T4 DNA ligase buffer and T4 RNA ligase buffer, and combinations thereof.

16. The method of claim 12, wherein the ligase is selected from the group consisting of E. coli DNA ligase, T4 DNA ligase, and T4 RNA ligase, and combinations thereof.

17. The method of claim 12, wherein the triphosphate mix is selected from the group consisting of dNTP and rNTP.

18. A microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method comprising:

(a) providing a microarray having a plurality of probe DNA;

(b) forming a plurality of hybridized structure DNA on the microarray, wherein each hybridized structure DNA is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged target DNA and a plurality of detection sequence DNA, wherein each hybridized structure DNA comprises one tagged target DNA hybridized to one probe DNA and to one detection sequence DNA;

(c) extending each hybridized structure DNA using an extension-ligation solution;

(d) ligating each hybridized structure DNA having a terminal nucleotide DNA that is complementary to a target nucleotide DNA using the extension-ligation solution;

(e) removing non-bound material by washing the microarray using a wash solution; and

(f) identifying the target nucleotide DNA and a hybridized sequence DNA from the hybridized structures having ligation.

19. The method of claim 18, wherein the plurality of probe DNA is attached to the microarray by a spacer.

20. The method of claim 18, wherein the tagged target DNA is a cDNA.

21. The method of claim 18, wherein the tagged target DNA is first amplified.

22. The method of claim 21, wherein the amplification is by PCR.

23. The method of claim 18, wherein the plurality of detection sequence DNA has a fluorescent tag.

24. The method of claim 18, wherein the plurality of tagged target DNA and the plurality of probe DNA have less than five internal mismatches when hybridized, and the plurality of tagged target DNA and the plurality of detection sequence DNA have less than approximately five internal mismatches when hybridized.

25. The method of claim 18, the hybridizing solution comprises a plurality of tagged target DNA and a plurality of detection sequence DNA in a buffer solution comprising a 1×

T4 ligase buffer, and the hybridizing condition comprises approximately 45°

C. for approximately one hour.

26. The method of claim 18, wherein the extension-ligation solution comprises a formulation comprising water, buffer, dNTP, polymerase, and ligase.

27. The method of claim 26, wherein the polymerase is a DNA polymerase.

28. The method of claim 27, wherein the DNA polymerase is selected from the group consisting of Taq polymerase Stoffel fragment, a reverse transcriptase, E. coli polymerase, and Klenow fragment polymerase, and combinations thereof.

29. The method of claim 26, wherein the buffer comprises E. coli ligase buffer, and the ligase comprises E. coli ligase.

30. The method of claim 34, wherein the buffer comprises T4 ligase buffer and the ligase comprises T4 DNA ligase.

31. The method of claim 18, wherein the plurality of probe DNA comprises a plurality of match probe DNA and a plurality of mismatch probe DNA, and the plurality of hybridized structure DNA comprises a plurality of match structures and a plurality of mismatch structures.

32. The method of claim 18, wherein the plurality of probe DNA comprises a plurality of set probes, and the plurality of hybridized structure DNA comprises a plurality of set structures.

33. The method of claim 18, wherein the plurality of probe DNA comprises a plurality of consecutive sequence probes, and the plurality of hybridized structure DNA comprises a plurality of consecutive sequence structures.

34. The method of claim 18, wherein the plurality of probe DNA comprises a plurality of gene expression probes, and the plurality of hybridized structure DNA comprises a plurality of gene expression structures.

35. A microarray-based single nucleotide polymorphism, sequencing, and gene expression assay method comprising:

(a) providing a microarray having a plurality of probe DNA;

(b) forming a plurality of hybridized structure DNA/RNA on the microarray, wherein each hybridized structure DNA/RNA is formed by contacting the microarray under a hybridizing condition to a hybridizing solution comprising a plurality of tagged target RNA and a plurality of detection sequence DNA, wherein each hybridized structure DNA/RNA comprises one tagged target RNA hybridized to one probe DNA and to one detection sequence DNA;

(c) extending each hybridized structure DNA/RNA using an extension-ligation solution and an extension-ligation condition;

(d) ligating each hybridized structure DNA/RNA having a terminal nucleotide DNA that is complementary to a target nucleotide RNA using the extension-ligation solution and the extension-ligation condition;

(e) removing non-bound material by washing the microarray using a wash solution and a wash method; and

(f) identifying the target nucleotide RNA and a hybridized sequence RNA from the hybridized structures having ligation.

36. The method of claim 35, wherein the plurality of probes is attached to the microarray by a spacer.

37. The method of claim 35, wherein the tagged target RNA is a mRNA.

38. The method of claim 35, wherein the plurality of detection sequence DNA has a fluorescent tag.

39. The method of claim 35, wherein the plurality of tagged target RNA and the plurality of probe DNA have less than five internal mismatches when hybridized, and the plurality of tagged target RNA and the plurality of detection sequence DNA have less than approximately five internal mismatches when hybridized.

40. The method of claim 35, the hybridizing solution comprises a plurality of tagged target RNA and a plurality of detection sequence DNA in a buffer solution comprising a 1×

T4 ligase buffer, and the hybridizing condition comprises approximately 45°

C. for approximately one hour.

41. The method of claim 35, wherein the extension-ligation solution comprises water, buffer, dNTP, polymerase.

42. The method of claim 41, wherein the polymerase is a reverse transcriptase.

43. The method of claim 41, wherein the buffer comprises E. coli ligase buffer, and the ligase comprises E. Coli ligase.

44. The method of claim 41, wherein the buffer comprises T4 ligase buffer and the ligase comprises T4 DNA ligase.