Direct sequence identification of mutations by cleavage- and ligation-associated mutation-specific sequencing

• US 5,707,806 A
• Filed: 06/07/1995
• Issued: 01/13/1998
• Est. Priority Date: 06/07/1995
• Status: Expired due to Term

• Current Assignee: Esoterix Genetic Laboratories LLC (Laboratory Corporation Of America Holdings)
• Original Assignee: Genzyme Corporation (Sanofi )
• Inventors: Shuber, Anthony P.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): REES, DIANE
• Application Number:
  US08/488,013
• Time in Patent Office: 951 Days
• Field of Search: 435/6, 435/5, 435/91.2, 530/300, 530/350, 536/24.31-24.33
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2521/131 Terminal transferase
• CPC Class Codes: C12Q 2525/186 incorporating a non-extendable or blocking moiety
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target

Abstract

The present invention provides methods for identifying the presence, location and sequence of one or more genetic alterations in one or more DNA molecules. Further provided are methods for positional cloning of a gene of interest.

Claims

1. A method for identifying one or more genetic alterations in a target sequence present in a DNA sample, which comprises:

a) immobilizing a first DNA sample, said first DNA having a 5'"'"' end and a 3'"'"' end on a solid support under conditions such that said 5'"'"' end is bound to said support and said 3'"'"' end is unbound;

b) hybridizing said immobilized sample with a second DNA having a 5'"'"' end and a 3'"'"' end wherein said second DNA does not contain the alteration(s), to form heteroduplex DNA containing a mismatch region at the site of an alteration(s);

c) cleaving one or both strands of said heteroduplex adjacent to said mismatch region to form a gap at or in the vicinity of said alteration;

d) subjecting said cleaved heteroduplex to conditions of denaturation to dissociate said second DNA and cleaved first DNA 3'"'"' to the site of cleavage from immobilized remaining first DNA;

e) removing DNA strands cleaved in step c and dissociated in step d from said immobilized remaining first DNA;

f) ligating a single-stranded oligonucleotide primer of known sequence to the unbound end of said immobilized remaining first DNA to form a ligation product;

(g) treating said ligation product with a DNA polymerase and an oligonucleotide complementary to said primer of known sequence in the presence of dideoxynucleotides or four nucleotide triphosphates and determining the nucleotide sequence adjacent to the ligated primer sequence; and

h) comparing said nucleotide sequence with a predetermined cognate wild-type sequence to identify said genetic alteration(s).

2. The method of claim 1, wherein the alterations are selected from the group consisting of additions, deletions, and substitutions of one or more nucleotides and combinations thereof.

3. The method of claim 1 further comprising blocking unbound ends on said heteroduplex DNA prior to the cleaving step.

4. The method of claim 3, wherein the blocking step comprises a method selected from the group consisting of removal of 5'"'"' phosphate groups, homopolymeric tailing of 3'"'"' ends with dideoxynucleotides, and ligation of modified double-stranded oligonucleotides.

5. The method of claim 1, wherein said target sequence is amplified prior to the immobilizing step.

6. The method of claim 1, wherein the solid support is selected from the group consisting of nitrocellulose filter, nylon filter, glass beads, and plastic.

7. The method of claim 1, wherein said cleaving step comprises exposing said heteroduplex DNA to one or more mismatch repair proteins under conditions appropriate for mismatch recognition and cleavage.

8. The method of claim 7, wherein the one or more mismatch repair proteins are selected from the group consisting of Eschericia coli proteins MutY, MutS, MutL, MutH, and combinations thereof, or functional homologues thereof.

9. The method of claim 8, wherein the functional homologues are derived from species selected from the group consisting of Salmonella typhimurium, Streptococcus pneumoniae, Saccharomyces cerevisiae, Schizosaccharomyces pombe, mouse and human.

10. The method of claim 1, wherein said cleaving step comprises exposing said heteroduplex DNA to a mixture of nucleotide excision repair proteins under conditions appropriate for mismatch recognition and cleavage.

11. The method of claim 10, wherein the mixture comprises E. coli proteins UvrA, UvrB, and UvrC, or functional homologues thereof.

12. The method of claim 11, wherein the functional homologues are derived from species selected from the group consisting of Saccharomyces cerevisiae and human.

13. The method of claim 1, wherein said cleaving step comprises exposing said heteroduplex DNA to one or more resolvase proteins under conditions appropriate for mismatch recognition and cleavage.

14. The method of claim 13, wherein the resolvases are selected from the group consisting of bacteriophage T4 Endonuclease VII and bacteriophage T7 endonuclease I.

15. The method of claim 1, wherein said cleaving step comprises the steps of:

(i) exposing said heteroduplex DNA to one or more chemical reagents under conditions appropriate for mismatch recognition and modification; and

(ii) contacting recognized and modified heteroduplex DNA with one or more reagents to selectively cleave one strand in the vicinity of the modification.

16. The method of claim 15, wherein the chemical reagent is selected from the group consisting of hydroxylamine and osmium tetroxide.

17. The method of claim 1, wherein the single-stranded oligonucleotide primer is from about 15 to about 35 nucleotides.

18. The method of claim 1, wherein the ligating step is performed in the presence of RNA ligase.

19. The method of claim 1, wherein the determining step is performed by enzymatic DNA sequencing.

20. The method of claim 1, wherein the determining step is performed by hybridization to oligonucleotide arrays.

24. The method of claim 1 wherein the DNA samples are denatured prior to hybridization.

21. A method for identifying one or more genetic alterations in a target sequence present in a genomic DNA sample, which comprises:

a) immobilizing a first DNA sample, said first DNA having a 5'"'"' end and a 3'"'"' end on a solid support under conditions such that said 5'"'"' end is bound to said support and said 3'"'"' end is unbound;

b) hybridizing said immobilized DNA sample with a second DNA sample, said second DNA having a 5'"'"' end and a 3'"'"' end, and wherein said second sample does not contain the alteration(s), to form heteroduplex DNA containing a mismatch region at the site of an alteration(s);

c) treating said heteroduplex with terminal transferase in the presence of a dideoxynucleotide to block unbound ends thereof;

d) contacting said heteroduplex with bacteriophage T4 endonuclease 7 to cleave one or both strands of said heteroduplex adjacent to said mismatch region to form a gap at or in the vicinity of said alteration;

e) subjecting said cleaved heteroduplex to conditions of denaturation to dissociate said second DNA and cleaved first DNA 3'"'"' to the site of cleavage from immobilized remaining first DNA;

f) removing DNA strands cleaved in step d and dissociated in step (e) from said immobilized remaining first DNA;

g) ligating a single-stranded oligonucleotide primer having the sequence 5'"'"'-CAGTAGTACAACTGACCCTTTTGGGACCGC-3'"'"' (SEQ ID NO;

1) to the unbound end of immobilized remaining first DNA to form a ligation product;

(h) treating said ligation product with a DNA polymerase and an oligonucleotide complementary to said primer of known sequence in the presence of dideoxynucleotides or four nucleotide triphosphates and determining the nucleotide sequence adjacent to ligated primer sequence; and

i) comparing said nucleotide sequence with a predetermined cognate wild-type sequence to identify said alteration(s).

25. The method of claim 21 wherein the DNA samples are denatured prior to hybridization.

22. A method for identification of one or more mutation(s) in a DNA, which comprises:

a) immobilizing one or more first DNA samples, said first DNA having a respective 5'"'"' end and a respective 3'"'"' end, on a solid support under conditions such that said 5'"'"' end is bound to said support and said 3'"'"' and is unbound;

b) hybridizing said immobilized sample(s) with a second DNA sample, said second DNA having a respective 5'"'"' end and a respective 3'"'"' end, and wherein said second sample does not contain the mutation(s), to form heteroduplex DNA containing a mismatch region at the site of a mutation;

c) chemically blocking unbound ends on said heteroduplex DNA;

d) treating said heteroduplex DNA so that one or both strands are cleaved within or adjacent to said mismatch region to form a gap at or in the vicinity of said alteration;

e) subjecting said cleaved heteroduplex to conditions of denaturation to dissociate said second DNA and cleaved first DNA 3'"'"' to the site of cleavage from immobilized remaining first DNA;

f) removing DNA strands cleaved in step (d) and dissociated in step (e) from immobilized remaining first DNA;

g) ligating a single-stranded oligonucleotide primer of known sequence to the unbound end of said immobilized remaining first DNA to form a ligation product;

(h) treating said ligation product with a DNA polymerase and an oligonucleotide complementary to said primer of known sequence in the presence of dideoxynucleotides or four nucleotide triphosphates and determining the nucleotide sequence adjacent to ligated primer sequence; and

i) comparing said nucleotide sequence with one or more predetermined cognate wild-type sequences to identify said mutation(s).

26. The method of claim 22 wherein the DNA samples are denatured prior to hybridization.

23. A method for multiplex identification of one or more mutations in a DNA, the method comprising:

a) obtaining one or more first DNA samples, said DNA having a respective 5'"'"' end and a respective 3'"'"' end;

b) amplifying one or more target sequences in each of said samples;

c) immobilizing said amplified sequences on a solid support under conditions such that said 5'"'"' end is bound to said support and said 3'"'"' end is unbound;

d) hybridizing said immobilized sample(s) with a second DNA sample, said second DNA having a respective 5'"'"' end and a respective 3'"'"' end, and wherein said second sample does not contain the mutation(s), to form heteroduplex DNA containing a mismatch region at the site of a mutation;

e) chemically blocking unbound ends on said heteroduplex DNA;

f) treating said heteroduplex DNA so that one or both strands are cleaved within or adjacent to said mismatch region to form a gap at or in the vicinity of said mutation;

g) subjecting said cleaved heteroduplex to conditions of denaturation to dissociate said second DNA and cleaved first DNA 3'"'"' to site of cleavage from immobilized remaining first DNA;

h) removing DNA strands cleaved in step (f) and dissociated in step (g) from said immobilized remaining first DNA;

i) ligating a single-stranded oligonucleotide primer of known sequence to the unbound end of said immobilized remaining first DNA to form a ligation product;

(j) treating said ligation product with a DNA polymerase and an oligonucleotide complementary to said primer of known sequence in the presence of dideoxynucleotides or four nucleotide triphosphates and determining the nucleotide sequence adjacent to ligated primer sequence; and

k) comparing said nucleotide sequence with one or more predetermined cognate wild-type sequences to identify said mutation(s).

27. The method of claim 23 wherein the DNA samples are denatured prior to hybridization.

28. A method for positional cloning of a gene of interest, the method comprising:

a) immobilizing a first DNA sample from an individual displaying a given phenotype, said first DNA having a 5'"'"' end and a 3'"'"' end on a solid support under conditions such that said 5'"'"' end is bound to said support and said 3'"'"' end unbound;

b) hybridizing said immobilized sample with a second DNA sample, said second DNA having a 5'"'"' end and a 3'"'"' end, and wherein said second DNA sample is from one or more individual(s) not displaying said phenotype to form heteroduplex DNA containing a mismatch region at the site of a genetic alteration;

c) cleaving one or both strands of said heteroduplex DNA to form a gap at or in the vicinity of said alteration;

d) subjecting said cleaved heteroduplex to conditions of denaturation to dissociate said second DNA from said first DNA;

e) removing DNA strands cleaved in step (c) and dissociated in step (d) from said first DNA;

f) ligating a single-stranded oligonucleotide primer of known sequence to the 3'"'"' end of first cleaved DNA to form a ligation product;

g) treating said ligation product with a DNA polymerase and an oligonucleotide complementary to said primer of known sequence in the presence of dideoxynucleotides or four nucleotide triphosphates and determining the nucleotide sequence adjacent to ligated primer sequence;

h) preparing a synthetic oligonucleotide comprising all or part of said determined nucleotide sequence; and

i) identifying a DNA clone that hybridizes to said oligonucleotide.

29. The method of claim 28 which comprises chemically blocking free terminal ends of said heteroduplex prior to said cleaving steps.

30. The method of claim 28, wherein the genetic alterations are selected from the group consisting of additions, deletions, and substitutions of one or more nucleotides and combinations thereof.

31. The method of claim 28, wherein the cleaving step comprises exposing the heteroduplex DNA to a mixture of mismatch repair proteins under conditions appropriate for mismatch recognition and cleavage.

32. The method of claim 31, wherein the mismatch repair proteins are selected from the group consisting of Escherichia coli proteins MutY, MutS, MutL, MutH, and combinations thereof, or functional homologues thereof.

33. The method of claim 32, wherein the functional homologues are from species selected from the group consisting of Salmonella typhimurium, Streptococcus pneumoniae, Saccharomyces cerevisiae, Schizosaccharomyces pombe, mouse and human.

34. The method of claim 28, wherein the cleaving step comprises exposing the heteroduplex DNA to a mixture of nucleotide excision repair proteins under conditions appropriate for mismatch recognition and cleavage.

35. The method of claim 34, wherein the mixture comprises Escherichia coli proteins UvrA, UvrB, and UvrC, or functional homologues thereof.

36. The method of claim 35, wherein the functional homologues are from species selected from the group consisting of Saccharomyces cerevisiae and human.

37. The method of claim 28, wherein the cleaving step comprises exposing the heteroduplex DNA to one or more resolvase proteins under conditions appropriate for mismatch recognition and cleavage.

38. The method of claim 37, wherein the resolvases are selected from the group consisting of bacteriophage T4 Endonuclease VII and bacteriophage T7 endonuclease I.

39. The method of claim 28, wherein the cleaving step comprises the steps of:

(i) exposing the heteroduplex to one or more chemical reagents under conditions appropriate for mismatch recognition and modification; and

(ii) contacting said recognized and modified heteroduplex DNA with one or more reagents to selectively cleave one strand in the vicinity of the alteration.

40. The method of claim 39, wherein the chemical reagent is selected from the group consisting of hydroxylamine and osmium tetroxide.

41. The method of claim 28, wherein the single-stranded oligonucleotide primer is from about 15 to about 35 nucleotides.

42. The method of claim 28, wherein the ligating step is performed in the presence of RNA ligase.

43. The method of claim 28, wherein the determining step performed by enzymatic DNA sequencing.

44. The method of claim 28, wherein the determining step is performed by hybridization to oligonucleotide arrays.

45. The method of claim 28, wherein the identifying step is achieved using a method selected from the group consisting of colony hybridization, identification of tissue-specific expression, reverse transcription-amplification of mRNA, and screening of an affected population for genotype/phenotype association.

46. The method of claim 28, wherein the DNA samples are denatured prior to hybridization.

47. The method of claim 28, wherein the first DNA is immobilized on a solid support under conditions such that said 5'"'"' end is bound to said support and said 3'"'"' end is unbound.