Rapid analysis of variations in a genome

• US 20030186239A1
• Filed: 03/11/2002
• Published: 10/02/2003
• Est. Priority Date: 03/01/2002
• Status: Active Grant

• Current Assignee: Ravgen, Inc.
• Original Assignee: Ravgen, Inc.
• Inventors: Dhallan, Ravinder S.
• Granted Patent: US 6,977,162 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The invention provides a method useful for determining the sequence of large numbers of loci of interest on a single or multiple chromosomes. The method utilizes an oligonucleotide primer that contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′ overhang containing the locus of interest. The 5′ overhang is used as a template to incorporate nucleotides, which can be detected. The method is especially amenable to the analysis of large numbers of sequences, such as single nucleotide polymorphisms, from one sample of nucleic acid.

Claims

1. A method for determining a sequence of a locus of interest, said method comprising:

(a) amplifying a locus of interest on a template DNA using a first and second primers, wherein the second primer contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′

overhang containing the locus of interest;

(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;

(c) incorporating a nucleotide into the digested DNA of (b) by using the 5′

overhang containing the locus of interest as a template; and

(d) determining the sequence of the locus of interest by determining the sequence of the DNA of (c).

2. The method of claim 1, wherein the template DNA is obtained from a source selected from the group consisting of a bacterium, fungus, virus, protozoan, plant, animal and human.

3. The method of claim 1, wherein the template DNA is obtained from a human source.

4. The method of claim 1, wherein the template DNA is obtained from a sample selected from the group consisting of a cell, tissue, blood, serum, plasma, urine, spinal fluid, lymphatic fluid, semen, vaginal secretion, ascitic fluid, saliva, mucosa secretion, peritoneal fluid, fecal matter, or body exudates.

5. The method of claim 1, wherein the amplification in (a) comprises polymerase chain reaction (PCR).

6. The method of claim 1, wherein the restriction enzyme cuts DNA at the recognition site.

7. The method of claim 6, wherein a 5′

region of the second primer does not anneal to the template DNA.

8. The method of claim 6, wherein a 5′

region of the first primer does not anneal to the template DNA.

9. The method of claim 6, wherein the restriction enzyme is selected from the group consisting of BsaJ I, Bssk I, Dde I, EcoN I, Fnu4H I, and Hinf I.

10. The method of claim 1, wherein the restriction enzyme cuts DNA at a distance from the recognition site.

11. The method of claim 10, wherein a 5′

region of the second primer does not anneal to the template DNA.

12. The method of claim 10, wherein a 5′

region of the first primer does not anneal to the template DNA.

13. The method of claim 11, wherein an annealing length of the 3′

region of the second primer is selected from the group consisting of 25-20, 20-15, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, and less than 4 bases.

14. The method of claim 1, wherein an annealing temperature for cycle 1 of PCR is about the melting temperature of the 3′

region of the second primer that anneals to the template DNA.

15. The method of claim 14, wherein an annealing temperature for cycle 2 of PCR is about the melting temperature of the 3′

region of the first primer that anneals to the template DNA.

16. The method of claim 15, wherein an annealing temperature for the remaining cycles is at about the melting temperature of the entire second primer.

17. The method of claim 1, wherein the 3′

end of the second primer is adjacent to the locus of interest.

18. The method of claim 10, wherein the recognition site is for a Type IIS restriction enzyme.

19. The method of claim 18, wherein the Type IIS restriction enzyme is selected from the group consisting of:

Alw I, Alw26 I, Bbs I, Bbv I, BceA I, Bmr I, Bsa I, Bst71 I, BsmA I, BsmB I, BsmF I, BspM I, Ear I, Fau I, Fok I, Hga I, Ple I, Sap I, SSfaN I, and Sthi32 I.

20. The method of claim 18, wherein the Type IIS restriction enzyme is BceA I or BsmF I.

21. The method of claim 1, wherein the first primer contains a recognition site for a restriction enzyme that is different from the recognition site for the restriction enzyme on the second primer.

22. The method of claim 21, further comprising digesting the DNA of (c) with a restriction enzyme that recognizes the recognition site on the first primer.

23. The method of claim 1, wherein the first or second primer contains a tag at the 5′

terminus.

24. The method of claim 1, wherein the first primer contains a tag at the 5′

terminus.

25. The method of claim 23, wherein the tag is used to separate the amplified DNA from the template DNA.

26. The method of claim 25, wherein the tag is used to separate the amplified DNA containing the incorporated nucleotide from the amplified DNA that does not contain the incorporated nucleotide.

27. The method of claim 23, wherein the tag is selected from the group consisting of:

radioisotope, fluorescent reporter molecule, chemiluminescent reporter molecule, antibody, antibody fragment, hapten, biotin, derivative of biotin, photobiotin, iminobiotin, digoxigenin, avidin, enzyme, acridinium, sugar, enzyme, apoenzyme, homopolymeric oligonucleotide, hormone, ferromagnetic moiety, paramagnetic moiety, diamagnetic moiety, phosphorescent moiety, luminescent moiety, electrochemiluminescent moiety, chromatic moiety, moiety having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity, and combinations thereof.

28. The method of claim 23, wherein the tag is biotin.

29. The method of claim 28, wherein the biotin tag is used to separate amplified DNA from the template DNA using a streptavidin matrix.

30. The method of claim 29, wherein the streptavidin matrix is coated on wells of a microtiter plate.

31. The method of claim 1, wherein the incorporation of a nucleotide in (c) is by a DNA polymerase selected from the group consisting of E. coli DNA polymerase, Klenow fragment of E. coli DNA polymerase I, T7 DNA polymerase, T4 DNA polymerase, Taq polymerase, Pfu DNA polymerase, Vent DNA polymerase and sequenase.

32. The method of claim 1, wherein the incorporation of a nucleotide in (c) comprises incorporation of a labeled nucleotide.

33. The method of claim 1, wherein the incorporation of a nucleotide in (c) further comprises using a mixture of labeled and unlabeled nucleotides.

34. The method of claim 32, wherein the labeled nucleotide is selected from the group consisting of a dideoxynucleotide triphosphate and deoxynucleotide triphosphate.

35. The method of claim 32, wherein the labeled nucleotide is labeled with a molecule selected from the group consisting of radioactive molecule, fluorescent molecule, antibody, antibody fragment, hapten, carbohydrate, biotin, derivative of biotin, phosphorescent moiety, luminescent moiety, electrochemiluminescent moiety, chromatic moiety, and moiety having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity.

36. The method of claim 32, wherein the labeled nucleotide is labeled with a fluorescent molecule.

37. The method of claim 36, wherein the incorporation of a fluorescent labeled nucleotide further comprises using a mixture of fluorescent and unlabeled nucleotides.

38. The method of claim 1, wherein the determination of the sequence of the locus of interest in (d) comprises detecting the nucleotide.

39. The method of claim 32, wherein the determination of the sequence of the locus of interest in (d) comprises detecting labeled nucleotide.

40. The method of claim 39, wherein the detection is by a method selected from the group consisting of gel electrophoresis, polyacrylamide gel electrophoresis, fluorescence detection system, sequencing, ELISA, mass spectrometry, fluorometry, hybridization, microarray, and Southern Blot.

41. The method of claim 39, wherein the detection method is DNA sequencing.

42. The method of claim 39, wherein the detection method is a fluorescence detection system.

43. The method of claim 1, wherein the locus of interest is suspected of containing a single nucleotide polymorphism or mutation.

44. The method of claim 1, wherein the method is used for determining sequences of multiple loci of interest concurrently.

45. The method of claim 44, wherein the template DNA comprises multiple loci from a single chromosome.

46. The method of claim 44, wherein the template DNA comprises multiple loci from different chromosomes.

47. The method of claim 44, wherein the loci of interest on template DNA are amplified in one reaction.

48. The method of claim 44, wherein each of the loci of interest on template DNA is amplified in a separate reaction.

49. The method of claim 48, wherein the amplified DNA are pooled together prior to digestion of the amplified DNA.

50. The method of claim 44, wherein each of the labeled DNA in (c) containing a locus of interest is separated prior to (d).

51. The method of claim 44, wherein at least one of the loci of interest is suspected of containing a single nucleotide polymorphism or a mutation.

52. A method for determining a sequence of a locus of interest, said method comprising:

(a) amplifying a locus of interest on a template DNA using a first and second primers, wherein the second primer contains a portion of a recognition site for a restriction enzyme, wherein a full recognition site for the restriction enzyme is generated upon amplification of the template DNA such that digestion with the restriction enzyme generates a 5′

overhang containing the locus of interest;

(b) digesting the amplified DNA with the restriction enzyme that recognizes the full recognition site generated by the second primer and the template DNA;

(c) incorporating a nucleotide into the digested DNA of (b) by using the 5′

overhang containing the locus of interest as a template; and

(d) determining the sequence of the locus of interest by determining the sequence of the DNA of (c).

53. The method of claim 52, wherein the 3′

region of the second primer contains a mismatch with the template DNA.

54. The method of claim 53, wherein the mismatch occurs at the last 1, 2 or 3 bases at the 3′

region.

55. A method for determining a sequence of a locus of interest, said method comprising:

(a) amplifying a locus of interest on a template DNA using a first and second primers, wherein the second primer contains a recognition site for a restriction enzyme that cuts DNA at a distance from the recognition site and digestion with the restriction enzyme generates a 5′

overhang containing the locus of interest, and wherein the first primer contains a recognition site for a restriction enzyme that is different from the recognition site for the restriction enzyme on the second primer and contains a tag at the 5′

end;

(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;

(c) incorporating a labeled nucleotide into the digested DNA of (b) by using the 5′

overhang containing the locus of interest as a template;

(d) digesting the DNA of (c) with the restriction enzyme that recognizes the recognition site on the first primer; and

(e) determining the sequence of the locus of interest by determining the sequence of the digested DNA of (d) containing the labeled nucleotide.

56. A method for determining a sequence of a locus of interest, said method comprising:

(a) amplifying a locus of interest on a template DNA using a first and second primers, wherein the second primer contains a recognition site for a restriction enzyme that cuts DNA at a distance from the recognition site and digestion with the restriction enzyme generates a 5′

overhang containing the locus of interest, wherein the first primer contains a recognition site for a restriction enzyme that is different from the recognition site for the restriction enzyme on the second primer, and contains a tag at the 5′

end, and wherein the annealing temperature for cycle 1 of PCR is at about the melting temperature of the 3′

region, which anneals to the template DNA, of the second primer, the annealing temperature for cycle 2 of PCR is at about the melting temperature of the 3′

region, which anneals to the template DNA, of the first primer, and the annealing temperature for the remaining cycles is at about the melting temperature of the entire second primer;

(b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer;

(c) incorporating a labeled nucleotide into the digested DNA of (b) by using the 5′

overhang containing the locus of interest as a template;

(d) digesting the DNA of (c) with the restriction enzyme that recognizes the recognition site on the first primer; and

(e) determining the sequence of the locus of interest by determining the sequence of the digested DNA of (d) containing the labeled nucleotide.

57. The method of claim 56, wherein the tag is used to separate the amplified DNA from the template DNA.