Methods for rapid forensic analysis of mitochondrial DNA and characterization of mitochondrial DNA heteroplasmy

• US 8,802,372 B2
• Filed: 10/30/2007
• Issued: 08/12/2014
• Est. Priority Date: 03/02/2001
• Status: Expired due to Fees

• Current Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Original Assignee: Ibis Biosciences Incorporated (Abbott Laboratories)
• Inventors: Ecker, David J., Griffey, Richard H., Sampath, Rangarajan, Hofstadler, Steven A., McNeil, John, Crooke, Stanley T., Blyn, Lawrence, Hall, Thomas A., Jiang, Yun, Hannis, James C., White, Neill, Samant, Vivek, Eshoo, Mark W., Drader, Jared James
• Primary Examiner(s): Chunduru, Prabha
• Application Number:
  US11/929,930
• Publication Number:
  US 20090182511A1
• Time in Patent Office: 2,478 Days
• Field of Search: 435/6, 435/91.2, 536/24.33
• US Class Current: 435/6.12
• 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 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C12Q 1/6888 for detection or identification of organisms
• CPC Class Codes: C12Q 1/689 for bacteria
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2545/113 with an external standard/control, i.e. control reaction is separated from the test/target reaction
• CPC Class Codes: C12Q 2563/167 Mass label
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 2333/28 from Vibrionaceae (F)
• CPC Class Codes: G01N 2333/32 from Bacillus (G)
• CPC Class Codes: G01N 2333/35 from Mycobacteriaceae (F)
• CPC Class Codes: G01N 2333/36 from Actinomyces; from Streptomyces (G)

Abstract

The present invention provides methods for rapid forensic analysis of mitochondrial DNA and methods for characterizing heteroplasmy of mitochondrial DNA, which can be used to assess the progression of mitochondrial diseases.

Claims

1. A method of identifying a nucleic acid sequence from a human sample, comprising:

a) contacting nucleic acid from said human sample with two or more oligonucleotide primers that hybridize to sequence regions of said nucleic acid that are conserved among different bioagents, wherein said conserved sequence regions flank a variable sequence region to produce an amplification product;

b) determining the base composition of said amplification product wherein said base composition of said amplification product comprises identification of the number of A residues, C residues, T residues, G residues, U residues, analogs thereof and/or mass tag residues thereof and wherein said base composition is determined without sequencing said amplification product; and

c) identifying said nucleic acid sequence from said human sample by comparing said determined base composition to a database of base compositions from a plurality of different bioagents wherein said base composition of said amplification product comprises identification of the number but not the nucleic acid sequence order of A residues, C residues, T residues, G residues, U residues, analogs thereof and/or mass tag residues thereof.

2. The method of claim 1, wherein said bioagent is selected from the group of bioagents consisting of a viral bioagent, a bacterial bioagent, a fungal bioagent, a protozoal bioagent, a parasitic bioagent, a mammalian bioagent, and a human bioagent.

3. The method of claim 1, wherein said bioagent is selected from the group of bioagents consisting of an evolving bioagent, a mutating bioagent, a recombinant bioagent, a replicating bioagent, a living bioagent, a dead bioagent, and an engineered bioagent.

4. The method of claim 1, wherein said bioagent is not previously known to exist.

5. The method of claim 1, wherein said human sample is selected from the group consisting of a body fluid sample, a urine sample, a blood sample, a serum sample, a plasma sample, a spinal fluid sample, a sputum sample, a bile sample, a stool sample, a saliva sample, a tear sample, a mucus sample, a gastric content sample, a sweat sample, an exocrine gland sample, an endocrine gland sample, a pus sample, a wound swab sample, a culture swab sample, a surgical sample, a tissue sample, a biopsy sample, a brush sample, a culture media sample, a forensic sample, a body surface sample, a skin sample, a mucus membrane sample, a hair sample, a nail sample, a cosmetic sample, a clothing sample, a bedding sample, an environmental sample, a stored sample, a preserved sample, a formalin sample, a paraffin sample, an immunohistochemistry sample, a histology sample, a living sample, and a post-mortem sample.

6. The method of claim 1, wherein said human sample comprises at least two bioagents of different genus, and wherein said nucleic acid from said sample is contacted with two or more oligonucleotide primers configured to identify two or more bioagents of different genus.

7. The method of claim 1, wherein said human sample comprises at least two bioagents of different species, and wherein said nucleic acid from said sample is contacted with two or more oligonucleotide primers configured to identify two or more bioagents of different species.

8. The method of claim 1, further comprising purifying said nucleic acid prior to production of said amplification product.

9. The method of claim 1, further comprising modifying said nucleic acid prior to production of said amplification product.

10. The method of claim 1, wherein said nucleic acid is selected from the group consisting of genomic DNA, RNA, DNA that is complementary to RNA, DNA that is synthesized from RNA, double-stranded DNA, single stranded DNA, DNA that is the product of amplification, DNA that is fragmented, nuclear DNA, mitochondrial DNA, cytoplasmic DNA and extracellular DNA.

11. The method of claim 1, wherein said two or more oligonucleotide primers are about 15-35 nucleobases in length, and wherein said two or more oligonucleotide primers comprise at least 70%, at least 80%, at least 90%, at least 95%, or at least 100% sequence identify with said conserved sequence regions.

12. The method of claim 1, wherein said amplification product is 45 to 200 nucleobases in length.

13. The method of claim 1, wherein a non-templated T residue on the 5′

-end of at least one of said two or more oligionucleotide primers is removed.

14. The method of claim 1, wherein at least one of said two or more oligonucleotide primers comprises a non-templated T residue on the 5′

-end.

15. The method of claim 1, wherein at least one of said two or more oligonucleotide primers comprises at least one molecular mass modifying tag.

16. The method of claim 1, wherein at least one of said two or more oligonucleotide primers comprises at least one modified nucleobase.

17. The method of claim 16, wherein said modified nucleobase is 5-propynyluracil or 5-propynylcytosine.

18. The method of claim 16, wherein said modified nucleobase is a mass modified nucleobase.

19. The method of claim 18, wherein said mass modified nucleobase is 5-Iodo-C.

20. The method of claim 16, wherein said modified nucleobase is a universal nucleobase.

21. The method of claim 20, wherein said universal nucleobase is inosine.

22. The method of claim 1, wherein said bioagent is identified at the genus, species, sub-species, strain, sub-type or nucleotide polymorphism levels.

23. The method of claim 1, wherein said two or more oligonucleotide primers comprise multiple oligonucleotide primer sets configured for identification of diverse bioagents.

24. The method of claim 1, wherein said conserved sequence regions are within a gene.

25. The method of claim 1, wherein said conserved sequence regions are within a coding region of a gene.

26. The method of claim 1, wherein said conserved sequence regions are within a regulatory region of a gene.

27. The method of claim 1, wherein said variable sequence region is within a gene.

28. The method of claim 1, wherein said variable sequence region is within a coding region of a gene.

29. The method of claim 1, wherein said variable sequence region is within a regulatory region of a gene.

30. The method of claim 1, wherein said conserved sequence regions are about 10 to 100 nucleobases in length.

31. The method of claim 1, wherein said variable sequence region is about 10 to 200 nucleobases in length.

32. The method of claim 1, wherein said amplification product is produced by polymerase chain reaction.

33. The method of claim 1, further comprising purifying said amplification product.

34. The method of claim 1, wherein said base composition is determined by mass spectrometry.

35. The method of claim 34, wherein said mass spectrometry is ESI mass spectrometry.

36. The method of claim 1, wherein said comparing comprises identifying a match between said determined base composition and at least one entry within said database of base compositions from a plurality of different bioagents.

37. The method of claim 1, wherein said identifying said bioagent requires two or more oligonucleotide primer pairs.

38. The method of claim 1, wherein said database of base compositions from a plurality of different bioagents comprises base compositions of genus specific amplification products, family specific amplification products, species specific amplification products, strain specific amplification products, sub-type specific amplification products, or nucleotide polymorphism specific amplification products produced with said two or more oligonucleotide primers, wherein one or more matches between said determined base composition of said amplification product and one or more entries in said database identifies said bioagent, classifies a major classification of said bioagent, or differentiates between subgroups of known and unknown bioagents.

39. The method of claim 1, wherein said database of base compositions comprises base composition information for at least 3 different bioagents.

40. The method of claim 1, wherein said database of base compositions comprises base composition information for at least 4 different bioagents.

41. The method of claim 1, wherein said database of base compositions comprises base composition information for at least 8 different bioagents.

42. The method of claim 1, wherein said database of base compositions comprises base composition information for at least 19 different bioagents.

43. The method of claim 1, wherein said database of base compositions comprises base composition information for at least 30 different bioagents.

44. The method of claim 1, wherein said database of base compositions comprises at least 12 unique base compositions.

45. The method of claim 1, wherein said database of base compositions comprises at least 40 unique base compositions.

46. The method of claim 1, wherein said database of base compositions comprises base composition information for a bioagent from two or more genuses selected from the group consisting ofAcinetobacter, Aeromonas, Bacillus, Bacteroides, Bartonella, Bordetella, Borrelia, Brucella, Burkholderia, Campylobacter, Chlamydia, Chlamydophila, Clostridium, Coxiella, Enterococcus, Escherichia, Francisella, Fusobacterium, Haemophilus, Helicobacter, Klebsiella, Legionella, Leptospira, Listeria, Moraxella, Mycobacterium, Mycoplasma, Neisseria, Proteus, Pseudomonas, Rhodobacter, Rickettsia, Salmonella, Shigella, Staphylococcus, Streptobacillus, Streptomyces, Treponema, Ureaplasma, Vibrio, or Yersinia.

47. The method of claim 1, wherein said database of base compositions comprises base composition information for a bioagent from each of the genuses of Acinetobacter, Aeromonas, Bacillus, Bacteroides, Bartonella, Bordetella, Borrelia, Brucella, Burkholderia, Campylobacter, Chlamydia, Chlamydophila, Clostridium, Coxiella, Enterococcus, Escherichia, Francisella, Fusobacterium, Haemophilus, Helicobacter, Klebsiella, Legionella, Leptospira, Listeria, Moraxella, Mycobacterium, Mycoplasma, Neisseria, Proteus, Pseudomonas, Rhodobacter, Rickettsia, Salmonella, Shigella, Staphylococcus, Streptobacillus, Streptomyces, Treponema, Ureaplasma, Vibrio, or Yersinia.

48. The method of claim 1, wherein said database of base compositions comprises base composition information for a bioagent from two or more orders or families selected from the group consisting of Smallpox virus, Arenavirus, Bunyaviruses, Mononegavirales, Picornaviruses, Astroviruses, Calciviruses, Nidovirales, Flaviviruses, and Togaviruses.

49. The method of claim 1, wherein said database of base compositions comprises base composition information for a bioagent from each of the orders or families of Smallpox virus, Arenavirus, Bunyaviruses, Mononegavirales, Picornaviruses, Astroviruses, Calciviruses, Nidovirales, Flaviviruses, and Togaviruses.

50. The method of claim 1, wherein said base compositions in said database are associated with bioagent identity.

51. The method of claim 1, wherein said base compositions in said database are associated with bioagent geographic origin.

52. The method of claim 1, wherein said comparing step is performed by a computer.

53. The method of claim 52, wherein said computer identifies a match between said determined base composition of said amplification product and one or more entries in database of base compositions from a plurality of different bioagents with a probability algorithm.

54. The method of claim 1, wherein said database is stored on a computer.

55. The method of claim 54, wherein said computer is a local computer.

56. The method of claim 54, wherein said computer is a remote computer.

57. The method of claim 1, wherein said identifying a nucleic acid sequence from a human sample comprises interrogation of said database with two or more different base compositions associated with said plurality of bioagents.

58. The method of claim 1, wherein said database of base compositions comprises at least 10 base compositions.

59. The method of claim 1, wherein said database of base compositions comprises at least 20 base compositions.

60. The method of claim 1, wherein said database of base compositions comprises at least 30 base compositions.

61. The method of claim 1, wherein said database of base compositions comprises at least 40 base compositions.

62. The method of claim 1, wherein said database of base compositions comprises at least 50 base compositions.

63. The method of claim 1, wherein said database of base compositions comprises at least 60 base compositions.

64. The method of claim 1, wherein said database of base compositions comprises at least 70 base compositions.

65. The method of claim 1, wherein said database of base compositions comprises at least 80 base compositions.

66. The method of claim 1, wherein said database of base compositions comprises at least 90 base compositions.

67. The method of claim 1, wherein said database of base compositions comprises at least 100 base compositions.

68. The method of claim 1, wherein said database of base compositions comprises at least 500 base compositions.

69. The method of claim 1, wherein said database of base compositions comprises at least 1000 base compositions.

70. The method of claim 1, wherein said two or more oligonucleotide primers hybridize to sequence regions of human nucleic acid.

71. The method of claim 1, wherein said human sample comprises human nucleic acid and nucleic acid from a bioagent wherein said bioagent is selected from the group consisting of a viral bioagent, a bacterial bioagent, a fungal bioagent, a protozoal bioagent, a parasitic bioagent, and a mammalian bioagent.