Method for the detection of clonal populations of transformed cells in a genomically heterogeneous cellular sample

• US 5,670,325 A
• Filed: 08/14/1996
• Issued: 09/23/1997
• Est. Priority Date: 08/14/1996
• Status: Expired due to Term

• Current Assignee: Esoterix Genetic Laboratories LLC (Laboratory Corporation Of America Holdings)
• Original Assignee: Exact Laboratories, Inc.
• Inventors: Shuber, Anthony P., Lapidus, Stanley N., Ulmer, Kevin M.
• Primary Examiner(s): Ketter, James
• Assistant Examiner(s): Yucel, Irem
• Application Number:
  US08/700,583
• Time in Patent Office: 405 Days
• Field of Search: 435/6, 435/7.2, 435/91.1, 435/91.3, 435/240.2, 435/252.3, 435/254.11
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Methods are provided for detecting the presence of mutant sequences in a subpopulation of gene sequences in a biological sample. These methods are particularly useful for identifying individuals with gene mutations indicative of early colorectal cancer.

Claims

1. A method for detecting the presence of a clonal subpopulation of transformed cells in a biological sample obtained from an organism, comprising the steps of:

a) determining from the biological sample a number X of a first wild-type polynucleotide characteristic of a genomic region of said organism that is not mutated in said subpopulation of transformed cells;

b) determining from the biological sample a number Y of a second wild-type polynucleotide in a genomic region of said organism suspected of being mutated in said subpopulation of transformed cells; and

c) determining whether a difference exists between number X and number Y,

the presence of a statistically-significant difference being indicative of a clonal subpopulation of transformed cells in said biological sample.

2. The method according to claim 1, wherein said transformed cells are malignant.

3. The method according to claim 1, wherein said biological sample is selected from the group consisting of pus, sputum, semen, urine, blood, saliva, cerebrospinal fluid and biopsy tissue.

4. The method according to claim 1, wherein said biological sample is a stool sample.

5. The method according to claim 1, wherein step a) comprises exposing said biological sample to a first oligonucleotide probe having a nucleotide sequence complementary to at least a portion of nucleotide sequence of said first polynucleotide.

6. The method according to claim 5, wherein said first oligonucleotide probe is detectably labeled.

7. The method according to claim 5, wherein said number x is proportional to the number of said first oligonucleotide probes that forms duplex with said first polynucleotide.

8. The method according to claim 1, wherein step b) comprises exposing said biological sample to a second oligonucleotide probe having a nucleotide sequence complementary to at least a portion of said second polynucleotide.

9. The method according to claim 8, where said number y is proportional to a number of said second oligonucleotide probes that forms duplex with said second polynucleotide.

10. The method according to claim 8, wherein said second oligonucleotide probe is detectably labeled.

11. A method for detecting the presence of a colorectal cancer or precancerous lesion in a mammalian tissue or body fluid sample, comprising the steps of:

(a) exposing the sample to a plurality of a first oligonucleotide probe and to a plurality of a second oligonucleotide probe under hybridization conditions, thereby to hybridize

(1) said first oligonucleotide probes to copies of a first polynucleotide segment characteristic of wild-type cells of the organism, and

(2) said second oligonucleotide probes to copies of a second polynucleotide segment characteristic of a wild-type genomic region suspected to be deleted or mutated in colorectal cancer cells;

(b) detecting a first number of duplexes formed between said first probe and said first segment and a second number of duplexes formed between said second probe and said second segment; and

(c) determining whether there is a difference between the number of duplexes formed between said first probe and said first segment and the number of duplexes formed between said second probe and said second segment,

the presence of a statistically-significant difference being indicative of the presence in said sample of a colorectal cancer or precancerous lesion.

12. The method according to claim 11, wherein said first and second oligonucleotide probes each are coupled to a distinct detectable label.

13. The method according to claim 11, wherein

said first oligonucleotide probes are attached to a first particle in a ratio of one first oligonucleotide probe to one particle and said second oligonucleotide probes are attached to a second particle detectably distinct from said first particle in a ratio of one second oligonucleotide probe to one second particle, wherein

said detecting step comprises separating hybridized from unhybridized first and second oligonucleotide probes and subsequently passing hybridized first and second oligonucleotide probes through a detector to determine said first and second numbers.

14. The method of claim 13, wherein said first and second particles are of detectably different sizes.

15. The method according to claim 13, wherein said first and second particles are of detectably different colors.

16. The method according to claim 11, further comprising, prior to step a) the steps of converting double-stranded DNA in said sample to single-stranded DNA and removing complement to said first and second polynucleotide segments.

17. The method according to claim 16, wherein said removing step comprises hybridizing said complement to a nucleic acid probe attached to a magnetic particle and subsequently removing said magnetic particle from the sample.

18. A method for detecting a nucleic acid sequence change in a target allele in a subpopulation of cells in a biological sample, comprising the steps of:

(a) determining

(i) an amount of wild-type target allele in the biological sample, and

(ii) an amount of a reference allele in the biological sample; and

(b) detecting a nucleic acid sequence change in the target allele in a subpopulation of cells in the biological sample as

a statistically significant difference in the amount of wild-type target allele and the amount of reference allele obtained in said determining step.

19. The method according to claim 18, wherein said determining step comprises exposing said biological sample to a first oligonucleotide probe which hybridizes with a portion of said wild-type allele and to a second oligonucleotide probe capable of hybridizing to a portion of said reference allele, and removing from said biological sample any unhybridized first or second oligonucleotide probe.

20. The method according to claim 18, wherein said biological sample is stool.

21. The method according to claim 18, wherein said target allele is a tumor suppressor allele.

22. The method according to claim 18, wherein said tumor suppressor allele is a p53 allele.

23. A method for detecting a change in the nucleotide sequence in a subpopulation of a target allele in a heterogeneous sample of cellular material, comprising the steps of:

a) exposing the heterogeneous sample, under hybridization conditions, to a plurality of isolation probes, each of which hybridizes to at least a portion of only one member selected from a first group consisting of a coding strand of said target allele and complement of a coding strand of said target allele;

b) exposing the heterogeneous sample, under hybridization conditions, to a plurality of second isolation probes, each of which hybridizes to at least a portion of only one member selected from a second group consisting of a coding strand of a reference allele and a complement of a coding strand of said reference allele;

c) contacting said heterogeneous sample, under hybridization conditions, with a plurality of first hybridization probes, each of which hybridizes to at least a portion of the member of said first group to which said first isolation probe does not hybridize;

d) contacting the heterogeneous sample, under hybridization conditions, with a plurality of second hybridization probes, each of which hybridizes with at least a portion of the member of said second group to which said second isolation probe does not hybridize;

e) removing non-hybridizing first and second hybridization probes from said heterogeneous sample;

f) determining an amount of each of said first and second hybridization probes remaining in the heterogeneous sample after said removing step; and

g) detecting allelic loss in a subpopulation of target allele as a statistically-significant difference in the amount of said first hybridization probe and said second hybridization probe obtained in said determining step.

24. The method according to claim 23, wherein said first and second hybridization probes are differentially labeled.

25. The method according to claim 23, wherein said first and second hybridization probes are attached to first and second hybridization beads, respectively, in a ratio of one probe to one bead.

26. The method according to claim 25, wherein said first hybridization beads are of a size distinct from said second hybridization beads.

27. The method according to claim 26, wherein said detecting step comprises passing said first and second hybridization beads through a Coulter counter.

28. The method according to claim 23, wherein said target allele is an allele, the mutation of which is associated with disease.

29. The method according to claim 28, wherein said disease is cancer.

30. The method according to claim 28, wherein said sample of cellular material is a stool sample obtained from a patient.

31. The method according to claim 30, further comprising the step of performing an endoscopy procedure on a patient in whose stool sample allelic loss is detected.

32. A method for detecting a deletion in polymorphic locus in a subpopulation of cells in a biological sample, comprising the steps of:

a) detecting an amount of a maternal allele at a polymorphic locus in the biological sample;

b) detecting an amount of a paternal allele at the polymorphic locus in the biological sample; and

c) determining whether a statistically-significant difference exists between the amount of maternal allele and the amount of paternal allele at the polymorphic locus,

The presence of a statistically-significant difference being indicative of a deletion at the polymorphic locus in a subpopulation of cells in the biological sample.

33. The method according to claim 32, wherein said polymorphic locus is a single base polymorphism and is heterozygous between said maternal and paternal alleles.

34. The method according to claim 33, wherein said detecting steps comprise,

a) hybridizing probe to a portion of said polymorphic locus on both maternal and paternal alleles that is immediately adjacent to said single-base polymorphism;

b) exposing said sample to a mixture of detectably-labeled dideoxy nucleotide triphosphates under conditions which allow appropriate binding of said dideoxy nucleotide triphosphates to said single-base polymorphism;

c) washing the sample; and

d) counting an amount of each detectably-labeled dideoxy nucleotide triphosphate remaining for the sample.

35. The method according to claim 34, wherein said detectable label is selected from the group consisting of radioisotopes, fluorescent compounds, and particles.

36. The method according to claim 32, wherein said biological sample is selected from the group consisting of pus, blood, urine, sputum, semen, saliva, cerebrospinal fluid, biopsy tissue, and stool.

37. The method according to claim 32, wherein said polymorphic locus is identified from a database of nucleotide sequences.

38. A method for detecting heterozygosity at a single-nucleotide polymorphic locus in a biological sample, comprising the steps of:

a) hybridizing probes to a sequence immediately adjacent to a single-base polymorphism;

b) exposing the sample to a plurality of different labeled dideoxy nucleotides

c) washing the sample;

d) determining which of said dideoxy nucleotides are incorporated into said probes; and

e) detecting heterozygosity at the single-nucleotide polymorphic site as the detection of two dideoxy nucleotides having been incorporated into the probe.