Source tagging and normalization of DNA for parallel DNA sequencing, and direct measurement of mutation rates using the same

• US 20080318233A1
• Filed: 03/31/2008
• Published: 12/25/2008
• Est. Priority Date: 03/30/2007
• Status: Abandoned Application

• Current Assignee: University of South Carolina
• Original Assignee: University of South Carolina
• Inventors: Szalai, Gabor J., Jones, Kenneth L., Lance, Stacey L., Felder, Michael R., Glenn, Travis C.
• Application Number:
  US12/078,466
• Publication Number:
  US 20080318233A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2527/143 Concentration of primer or probe
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• 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

Abstract

This invention allows efficient tagging and normalization of DNA molecules prior to pooling and characterization using parallel DNA sequencing (e.g., commercially available 454 sequencers). The invention provides novel ways to process independent DNA samples (sources) so that similar numbers of molecules from each source are represented in the pool (i.e., the pool is normalized for representation among the sources). These approaches would save researchers time and energy relative to approaches currently available. In other embodiments, the invention provides novel ways to process large numbers of independently derived DNA samples that can be uniquely tagged in ways that allow the source of the DNA (e.g., an individual) to be tracked. The invention also provides novel ways for processing DNA to consistently obtain various portions of the genome to compare DNA sequences and directly measure mutations using state of the art massively parallel DNA sequencing (e.g., commercially available 454 sequencers and others. The invention is useful for the production of diagnostic assays for individuals prior to reproduction (e.g., cancer survivors who wish to procreate) and also for diagnostics of cancer (thus affecting the choice of treatment for cancer).

Claims

1. A method to tag one or more DNA fragments from one or more subjects to investigate one or more loci of interest comprising:

(a) normalizing the concentration of the one or more DNA fragments;

(b) pooling the one or more DNA fragments;

(c) ligating distinct identification linker tags to each of the DNA fragments;

(d) optionally pooling the distinctly tagged DNA fragments;

(e) processing the distinctly tagged DNA fragments through parallel sequencing; and

(f) using the identification linker tag to differentiate the one or more DNA fragments to investigate one or more loci of interest.

2. The method of claim 1, wherein the one or more DNA fragments comprise DNA fragments from different sources.

3. The method of claim 2, wherein the different sources comprise different tissue types.

4. The method of claim 2, wherein the different sources comprise different subjects.

5. The method of claim 1, wherein the distinctly tagged DNA fragments of step (d) are pooled from a plurality of different sources.

6. The method of claim 4, wherein each source has a distinct identification linker tag.

7. The method of claim 1, wherein one or more additional linkers are ligated to the DNA fragment prior to parallel sequencing.

8. The method of claim 5, wherein the one or more additional linkers contain unique DNA sequences.

9. The method of claim 1, wherein the identification linker tag is a 1 mer to about a 100 mer.

10. The method of claim 1, wherein only one end of the one or more DNA fragments is tagged with the identification linker tag.

11. The method of claim 1, wherein both ends of the one or more DNA fragments are tagged with the same identification linker tag.

12. The method of claim 1, wherein the identification linker tag comprises biotin, digoxigenin, or FITC.

13. The method of claim 1, wherein the identification linker tag comprises topoisomerase.

14. The method of claim 1, wherein the identification linker tags are ligated individually, simultaneously, or in multiple steps.

15. The method of claim 1, wherein the one or more DNA fragments are isolated or amplified from genomic DNA, plasmid DNA, or mitochondrial DNA.

16. The method of claim 1, wherein the identification linker tag is captured for sequencing through hybridization to oligonucleotides attached to a solid support.

17. A method to efficiently tag and/or normalize one or more DNA fragments comprising:

(a) ligating a predefined amount of an identification linker tag to one or more DNA fragments;

(b) pooling the one or more tagged DNA fragments;

(c) repeating steps (a)-(b) for each subject;

(d) optionally pooling the one or more tagged DNA fragments for all subjects;

(e) capturing the one or more tagged DNA fragments;

(f) purifying the one or more tagged DNA fragments;

(g) releasing and reconstituting the one or more tagged DNA fragments;

(h) processing the one or more tagged DNA fragments through parallel sequencing; and

(i) using the identification linker tag to differentiate the one or more tagged DNA fragments from one or more subjects.

18. The method of claim 17, wherein one or more additional linkers are ligated to the DNA fragment prior to parallel sequencing.

19. The method of claim 17, wherein the one or more additional linkers contain unique DNA sequences.

23. The method of claim 17, wherein step 17(d) is omitted and/or both ends of the one or more DNA fragments are ligated to linkers lacking unique identification sequences.

25. The method of claim 17, wherein the identification linker tag is captured for sequencing through hybridization to oligonucleotides attached to a solid support.

26. The method of claim 17, wherein the identification linker tag is phosphorylated.

27. The method of claim 17, wherein the identification linker tag comprises topoisomerase.

30. The method of claim 17, wherein the one or more DNA fragments are isolated or amplified from genomic DNA, plasmid DNA, or mitochondrial DNA.

20-22. -22. (canceled)

24. (canceled)

28-29. -29. (canceled)

31. A method for the measurement of mutations in the genome of a cell population by identifying and sequencing a region of interest comprising:

(a) ligating a universal linker to one or more DNA fragments;

(b) denaturing the one or more DNA fragments;

(c) hybridizing the one or more DNA fragments with a tagged oligonucleotide, wherein the tagged oligonucleotide is complementary to the region of interest;

(d) capturing the tagged oligonucleotide;

(e) recovering the one or more DNA fragments containing the region of interest;

(f) making the one or more DNA fragments double-stranded;

(g) optionally removing the universal linker; and

(h) processing the one or more DNA fragments through parallel sequencing to aid in the direct measurement of mutations in the genome of the cell population.

32. The method of claim 31, wherein steps (c)-(f) are repeated before proceeding to step (g).

33. The method of claim 31, wherein the DNA is obtained by whole genome amplification.

34. The method of claim 31, wherein the tagged oligonucleotide is captured for sequencing through hybridization to oligonucleotides attached to a solid support.

35. The method of claim 31, wherein the region of interest contains a region or regions with at least one microsatellite repeat.

36. The method of claim 31, wherein the universal linker comprises an identification linker tag.

37. The method of claim 31, wherein a peptide nucleic acid is used at step (c).

38. The method of claim 31, wherein the universal linker is not removed.

39. A method of comparing a portion of the genomes of one or more cells comprising:

(a) ligating a universal linker to one or more DNA fragments;

(b) denaturing the one or more DNA fragments;

(c) hybridizing the one or more DNA fragments with tagged oligonucleotides, wherein the tagged oligonucleotides are complementary to the region of interest;

(d) capturing the tagged oligonucleotide;

(e) recovering the one or more DNA fragments containing the region of interest;

(f) making the one or more DNA fragments double-stranded;

(g) optionally removing the universal linker; and

(h) processing the one or more DNA fragments through parallel sequencing to aid in comparing the genomes of one or more cells.

40. The method of claim 39, wherein steps (c)-(f) are repeated before proceeding to step (g).

44. The method of claim 39, wherein the region of interest contains a region or regions with at least one microsatellite repeat.

45. The method of claim 39, wherein the region of interest is identified from DNA sequences conserved among divergent taxa.

46. The method of claim 39, wherein the oligonucleotides complementary to the region of interest include a repetitive element or flank repetitive elements.

50. The method of claim 39, wherein a peptide nucleic acid is used at step (c).

51. The method of claim 39, wherein the universal linker is not removed.

41-43. -43. (canceled)

47-49. -49. (canceled)

52. (canceled)

53. A method for diagnosing a disease comprising:

(a) ligating a universal linker to one or more DNA fragments;

(b) denaturing the one or more DNA fragments;

(c) hybridizing the one or more DNA fragments with a tagged oligonucleotide, wherein the tagged oligonucleotide is complementary to the region of interest;

(d) capturing the tagged oligonucleotide;

(e) recovering the one or more DNA fragments containing the region of interest;

(f) making the one or more DNA fragments double-stranded;

(g) optionally removing the universal linker;

(h) processing the one or more DNA fragments through parallel sequencing; and

(i) comparing the genomes of one or more cells to diagnose the disease in the patient.

54. The method of claim 53, wherein steps (c)-(f) are repeated before proceeding to step (g).

55-65. -65. (canceled)

66. A method for determining choice of treatment in a patient previously diagnosed with cancer and other diseases comprising:

(a) ligating a universal linker to one or more DNA fragments;

(b) denaturing the one or more DNA fragments;

(c) hybridizing the one or more DNA fragments with a tagged oligonucleotide, wherein the tagged oligonucleotide is complementary to the region of interest;

(d) capturing the tagged oligonucleotide;

(e) recovering the one or more DNA fragments containing the region of interest;

(f) making the one or more DNA fragments double-stranded;

(g) optionally removing the universal linker; and

(h) processing the one or more DNA fragments through parallel sequencing to aid in determining choice of treatment in a patient previously diagnosed with cancer and other diseases involving altered DNA repair.

67. The method of claim 66, wherein steps (c)-(f) are repeated before proceeding to step (g).

68-78. -78. (canceled)