Method of analyzing chromosomal inversions

• US 9,562,259 B2
• Filed: 03/12/2012
• Issued: 02/07/2017
• Est. Priority Date: 03/14/2011
• Status: Active Grant

• Current Assignee: Ventana Medical Systems Incorporated (Roche Holding AG)
• Original Assignee: Ventana Medical Systems Incorporated (Roche Holding AG)
• Inventors: Nitta, Hiro, Farrell, Mike, Zhang, Wenjun, Grogan, Tom
• Primary Examiner(s): MYERS, CARLA J
• Application Number:
  US13/417,522
• Publication Number:
  US 20120237930A1
• Time in Patent Office: 1,793 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6841 In situ hybridisation
• CPC Class Codes: C12Q 2525/185 incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2539/115 Comparative genomic hybridisation [CGH]
• CPC Class Codes: C12Q 2543/101 in situ amplification
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels

Abstract

The present disclosure relates to systems and methods for analyzing chromosomal translocations, and in particular to analysis of chromosomal translocation by in situ hybridization.

Claims

1. A chromogenic in situ hybridization method for determining whether a sample comprises a chromosomal rearrangement, the chromosomal rearrangement occurring as a result of a breakpoint within a gene, comprising:

contacting the sample with

a first nucleic acid probe comprising a first sequence configured to hybridize to a first chromosomal DNA target located 5′

to the breakpoint,

a second nucleic acid probe comprising a second sequence configured to hybridize to a second chromosomal DNA target located 3′

to the breakpoint, and

a third nucleic acid probe comprising a third sequence having a 5′

portion and a 3′

portion, the 5′

portion configured to hybridize to a portion of a third chromosomal DNA target that is 5′ and

adjacent to the breakpoint, and the 3′

portion configured to hybridize to a portion of the third chromosomal DNA target that is 3′ and

adjacent to the breakpoint, such that in an absence of a rearrangement the third nucleic acid probe hybridizes to a region of the third chromosomal DNA target spanning the breakpoint;

establishing conditions suitable for the first, second, and third probes to hybridize to the respective chromosomal DNA targets in the sample;

contacting the sample with first, second, and third detection reagents, the first detection reagent comprising components to label the first chromosomal DNA target with a first chromogen, the second detection reagent comprising components to label the second chromosomal DNA target with a second chromogen, and the third detection reagent comprising components to label the third chromosomal DNA target with a third chromogen, where each of the first, second, and third chromogens provide different detectable signals;

detecting a colocalization of a third signal from the third labeled chromosomal DNA target with a first signal from the first labeled chromosomal DNA target;

detecting a colocalization of the third signal from the third labeled chromosomal DNA target with a second signal from the second labeled chromosomal DNA target; and

identifying the chromosomal rearrangement based on the detected colocalizations.

2. The method of claim 1, further comprising identifying a sample order and orientation, the sample order and orientation being an arrangement of the first signal, the second signal, and the third signal.

3. The method of claim 1, wherein the gene is an ALK gene.

4. The method of claim 2, further comprising comparing the sample order and orientation with a control order and orientation.

5. The method of claim 4, wherein the comparing of the sample order and orientation with a control order and orientation includes establishing whether the sample order and orientation includes inversion of the first signal and the third signal as compared to the control order and orientation.

6. The method of claim 4, wherein the comparing of the sample order and orientation with a control order and orientation includes establishing whether the sample order and orientation includes inversion of the second signal and the third signal as compared to the control order and orientation.

7. The method of claim 4, the control order and orientation is determined by analyzing a control sample known to be devoid of the chromosomal rearrangement associated with cancer comprising,

contacting the control sample with

the first nucleic acid probe comprising the first sequence configured to hybridize to genomic DNA located 5′

to the breakpoint,

the second nucleic acid probe comprising the second sequence configured to hybridize to genomic DNA located 3′

to the breakpoint, and

the third nucleic acid probe comprising the third sequence configured to hybridize to genomic DNA adjacent to and spanning the breakpoint;

establishing conditions suitable for the probes to hybridize to the genomic DNA in the control; and

detecting hybridization of the probes by detecting a first signal associated with the first nucleic acid probe, a second signal associated with the second nucleic acid probe, and a third signal associated with the third nucleic acid probe.

8. The method of claim 1, wherein nucleic acid probes comprise nucleic acids selected from the group consisting of RNA, DNA, PNA, LNA and combinations thereof.

9. The method of claim 8, wherein the first nucleic acid probe is conjugated to a first, hapten, the second nucleic acid probe is conjugated to a second hapten, and the third nucleic acid probe is conjugated to a third hapten, wherein each of the first, second, and third haptens are different.

10. The method of claim 9, wherein the different first, second and third haptens are selected from the group consisting of biotin, 2,4-dintropheyl (DNP), fluorescein derivatives, digoxygenin (DIG), 5-nitro-3-pyrozolecarbamide (nitropyrazole, NP), 4,5,-dimethoxy-2-nitrocinnamide (nitrocinnamide, NCA), 2-(3,4-dimethoxyphenyl)-quinoline-4-carbamide (phenylquinolone, DPQ), 2,1,3-benzoxadiazole-5-carbamide (benzofurazan, BF), 3-hydroxy-2-quinoxalinecarbamide (hydroxyquinoxaline, HQ), 4-(dimethylamino) azobenzene-4′

-sulfonamide (DABSYL), rotenone isoxazoline (Rot), (E)-2-(2-(2-oxo-2,3-dihydro-1H-benzo [b][1 ,4]diazepin-4-yl)phenozy)acetamide (benzodiazepine, BD), 7-(diethylamino)-2-oxo-2H-chromene-3-carboxylic acid (coumarin 343, CDO), 2-acetamido-4-methyl-5-thiazolesulfonamide (thiazolesulfonamide, TS), and p-methoxyphenylpyrazopodophyllamide (Podo).

11. The method of claim 9, wherein the first, second, and third detection reagents comprise antibodies specific for the first, second, and third haptens, respectively, where each antibody conjugated to an enzyme.

12. The method of claim 11, wherein the first, second, and third detection reagents further comprise first, second, and third chromogenic substrates, respectively.

13. A chromogenic in situ hybridization method for determining whether a sample comprises a chromosomal rearrangement associated with cancer, the chromosomal rearrangement occurring as a result of a breakpoint within a gene, comprising:

contacting the sample with

a first nucleic acid probe comprising a first sequence configured to hybridize to a first chromosomal DNA target located 5′

to the breakpoint, the first nucleic acid probe conjugated to a first hapten;

a second nucleic acid probe comprising a second sequence configured to hybridize to a second chromosomal DNA target located 3′

to the breakpoint, the second nucleic acid probe conjugated to a second hapten;

a third nucleic acid probe comprising a third sequence having a 5′

portion and a 3′

portion, the 5′

portion configured to hybridize to a portion of a third genomic DNA target that is 5′ and

adjacent to the breakpoint, and the 3′

portion configured to hybridize to a portion of the third chromosomal DNA target that is 3′ and

adjacent to the breakpoint, such that in an absence of a rearrangement the third nucleic acid probe hybridizes to a region of the third chromosomal DNA target spanning the breakpoint, the third nucleic acid probe conjugated to a third hapten;

establishing conditions suitable for the first, second, and third probes to hybridize to the respective chromosomal DNA targets in the sample;

contacting the sample with first, second, and third antibodies that are specific to the first, second, and third haptens, respectively, and wherein the first, second, and third antibodies are each conjugated to an enzyme;

contacting the sample with first, second, and third chromogenic substrates, to provide first, second, and third labeled chromosomal DNA targets, wherein each of the chromogenic substrates provide different signals;

detecting a colocalization of a third signal from the third labeled chromosomal DNA target with a first signal from the first labeled chromosomal DNA target;

detecting a colocalization of the third signal from the third labeled chromosomal DNA target with a second signal from the second labeled chromosomal DNA target; and

identifying the chromosomal rearangement based on the detected colocalizations.