DNA diagnostics based on mass spectrometry

• US 6,197,498 B1
• Filed: 04/06/1999
• Issued: 03/06/2001
• Est. Priority Date: 03/17/1995
• Status: Expired due to Term

• Current Assignee: Agena Bioscience Inc. (Mesa Laboratories Inc.)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Köster, Hubert
• Primary Examiner(s): Horlick, Kenneth R.
• Application Number:
  US09/287,141
• Time in Patent Office: 700 Days
• Field of Search: 435/5, 435/6, 435/91.1, 435/91.2
• US Class Current: 435/5
• 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 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/706 for hepatitis
• CPC Class Codes: C12Q 2521/325 Single stranded exonuclease
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents
• CPC Class Codes: C12Q 2523/319 Photocleavage, photolysis, photoactivation
• CPC Class Codes: C12Q 2525/107 incorporating a peptide nucleic acid
• CPC Class Codes: C12Q 2535/113 Cycle sequencing
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2537/113 Heteroduplex formation
• CPC Class Codes: C12Q 2565/625 being a nucleic acid test strip device, e.g. dipsticks, strips, tapes, CD plates
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: G01N 35/1067 for transfer to or from containers having different spacing
• CPC Class Codes: H01J 49/00 : Particle spectrometers or separator tubes
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]
• CPC Class Codes: Y10T 436/24 : Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry

Abstract

Fast and highly accurate mass spectrometry-based processes for detecting particular nucleic acid molecules and sequences in the molecules are provided. Depending upon the sequence to be detected, the processes, for example, can be used to diagnose a genetic disease or a chromosomal abnormality, a predisposition to a disease or condition, or infection by a pathogen, or for determining identity or heredity.

Claims

1. A process for identifying the presence or absence of a mutation in a target sequence in a nucleic acid molecule, comprising the steps of:

a) hybridizing a nucleic acid molecule comprising the target nucleic acid sequence with an oligonucleotide probe, which is complementary to a region of the target nucleic acid sequence that can contain a mutation, thereby forming a heteroduplex;

b) contacting the heteroduplex with a single strand specific endonuclease, which can cleave the heteroduplex at a site of a mismatch, if present, to produce a cleavage product comprising a cleaved probe, a cleaved target nucleic acid sequence, or both; and

c) detecting the product of step b) by mass spectrometry, thereby identifying the presence or absence of a mutation in the target nucleic acid sequence.

2. A process of claim 1, wherein the oligonucleotide probe is complementary to a wild type target nucleic acid sequence, and detecting a cleavage product by mass spectrometry identifies the presence of a mutation in the target nucleic acid sequence.

3. A process of claim 1, wherein the oligonucleotide probe is complementary to a mutant target nucleic acid sequence, and detecting a cleavage product by mass spectrometry identifies the absence of a mutation in the target nucleic acid sequence.

4. A process of claim 1, wherein the oligonucleotide probe is an oligonucleotide mimetic.

5. A process of claim 4, wherein the oligonucleotide mimetic is a peptide nucleic acid.

6. A process of claim 1, wherein the nucleic acid molecule comprising the target nucleic acid sequence is immobilized on a solid support.

7. A process of claim 6, wherein the nucleic acid molecule is immobilized by hybridizing a portion of the nucleic acid molecule, which is distinct from the site to which the oligonucleotide probe hybridizes, to a complementary capture nucleic acid sequence, which is immobilized to the solid support.

8. A process of claim 6, wherein the nucleic acid molecule is immobilized by direct bonding to the solid support.

9. A process of claim 6, wherein the solid support is selected from the group consisting of beads, flat surfaces, pins, combs and wafers.

10. A process of claim 6, wherein the nucleic acid molecule is one of a plurality of nucleic acid molecules comprising a target nucleic acid sequence, which are immobilized by hybridizing a portion of the nucleic acid molecules, which is distinct from the site to which the oligonucleotide probe hybridizes, to an array of complementary capture nucleic acid sequences, which are immobilized to the solid support.

11. A process of claim 10, wherein the complementary capture nucleic acid sequences are oligonucleotide mimetics.

12. A process of claim 11, wherein the oligonucleotide mimetics are peptide nucleic acids.

13. A process of claim 6, wherein the immobilization is reversible.

14. A process of claim 13, wherein the immobilization is via a thiol linkage.

15. A process of claim 13, wherein the immobilization is via a photocleavable linkage.

16. A process of claim 1, wherein, prior to contacting the heteroduplex with the single strand specific nuclease, the target nucleic acid sequence is amplified.

17. A process of claim 1, wherein the mass spectrometry is selected from the group consisting of matrix-assisted laser desorption/ionization time-of-flight, electrospray, ion cyclotron resonance, Fourier transform, and combinations thereof.

18. A process of claim 1, wherein, prior to mass spectrometry, the product to be detected is conditioned.

19. A process of claim 1, wherein the nucleic acid molecule comprises one of a plurality of nucleic acid molecules comprising a target nucleic acid sequence, and said hybridizing is performed with at least two oligonucleotide probes, each of which can hybridize to a target nucleic acid sequence in the plurality, wherein the products to be detected are mass differentiated to detect and distinguish the presence or absence of a mutation in the target nucleic acid sequences in the plurality simultaneously.

20. A process of claim 19, wherein mass differentiation is achieved by differences in the length or sequence of the products to be detected.

21. A process of claim 19, wherein mass differentiation is achieved by the introduction of mass modifying functionalities in the base, sugar or phosphate moiety of the products to be detected.

22. A process of claim 19, wherein mass differentiation is achieved by exchange of cations at the phosphodiester bonds of the products to be detected.

23. A process of claim 19, wherein the target nucleic acid sequences in the plurality comprise alleles of a gene.

24. A process of claim 19, wherein the oligonucleotide probes comprise a probe complementary to a wild type target nucleic acid sequence and a probe complementary to a mutant target nucleic acid sequence.

25. A process of claim 1, wherein the nucleic acid molecule comprising the target nucleic acid sequence is obtained from an individual, and wherein the presence or absence of a mutation in the target nucleic acid sequence provides a DNA fingerprint or is indicative of a disease or condition selected from the group consisting of a genetic disease, a chromosomal abnormality, a genetic predisposition, a viral infection, a fungal infection, a bacterial infection and a protist infection.

26. A process for identifying the presence or absence of one or more mutations in a plurality of target nucleic acid sequences, comprising the steps of:

a) hybridizing a plurality of nucleic acid molecules comprising the target nucleic acid sequences with a plurality of oligonucleotide probes, which are complementary to regions of the target nucleic acid sequences that can contain a mutation, wherein a probe that hybridizes to one target nucleic acid sequence in the plurality is distinguishable from each probe that hybridizes to a different target nucleic acid sequence, thereby forming one or more heteroduplexes, which are distinguishable;

b) contacting the one or more heteroduplexes with a single strand specific endonuclease, which can cleave a heteroduplex at a site of a mismatch, if present, to produce a cleavage product comprising a cleaved probe, a cleaved target nucleic acid, or both; and

c) detecting the products of step b) by mass spectrometry, thereby identifying the presence or absence of a mutation in each target nucleic acid sequence in the plurality.

27. A process of claim 26, wherein the products to be detected are mass differentiated.

28. A process of claim 27, wherein the products to be detected are mass differentiated due to differences in their length or sequence.

29. A process of claim 27, wherein the products to be detected are mass differentiated due to the introduction of mass modifying functionalities in the base, sugar or phosphate moiety.

30. A process of claim 27, wherein the products to be detected are mass differentiated due to an exchange of cations at the phosphodiester bonds.

31. A process of claim 26, wherein the nucleic acid molecules in the plurality are immobilized to a solid support.

32. A process of claim 31, wherein the solid support is selected from the group consisting of beads, flat surfaces, pins, combs and wafers.

33. A process of claim 31, wherein the nucleic acid molecules in the plurality are immobilized in an array.

34. A process of claim 31, wherein the nucleic acid molecules in the plurality are reversibly immobilized.

35. A process of claim 34, wherein the nucleic acid molecules in the plurality are immobilized via a bond that can be cleaved by a process selected from the group consisting of a chemical process, an enzymatic process and a physical process.

36. A process of claim 35, wherein the bond is a photocleavable bond.

37. A process of claim 34, wherein the nucleic acid molecules in the plurality are immobilized by hybridizing a portion of the nucleic acid molecules, which is distinct from the site to which the oligonucleotide probe hybridizes, to an array of complementary capture nucleic acid sequences, which are immobilized to the solid support.

38. A process of claim 37, wherein the complementary capture nucleic acid sequences are oligonucleotide mimetics.

39. A process of claim 26, wherein the target nucleic acid sequences in the plurality are amplified.

40. A process of claim 26, wherein, prior to mass spectrometry, products to be detected are conditioned.

41. A process of claim 26, wherein the target nucleic acid sequences in the plurality comprise alleles of a gene.

42. A process of claim 26, wherein the plurality of oligonucleotide probes comprise a probe complementary to a wild type target nucleic acid sequence and a probe complementary to a mutant target nucleic acid sequence.

43. A process of claim 26, wherein the plurality of nucleic acid molecules is obtained from one or more individuals, and wherein the presence or absence of a mutation in a target nucleic acid sequence in the plurality provides a DNA fingerprint or is indicative of a disease or condition selected from the group consisting of a genetic disease, a chromosomal abnormality, a genetic predisposition, a viral infection, a fungal infection, a bacterial infection and a protist infection.

44. A method of detecting mutations in a target nucleic acid molecule comprising:

hybridizing the target nucleic acid molecule to one or more probes;

fragmenting the target nucleic acid with a reagent that specifically cleaves at any regions of nucleotide mismatch that form between molecule target nucleic acid molecule and any of the probes to produce a set of fragments; and

determining masses of the members of said set by mass spectrometry, thereby identifying any mutations in the target nucleic acid molecule.

45. The method of claim 44, wherein at least one member of the set has one or more nucleotides replaced with mass-modified nucleotides.