Method for detecting chromosomal rearrangements

• US 10,385,401 B2
• Filed: 11/21/2014
• Issued: 08/20/2019
• Est. Priority Date: 11/21/2013
• Status: Active Grant

• Current Assignee: Assistance Publique - Hopitaux De Paris
• Original Assignee: Assistance Publique - Hopitaux De Paris
• Inventors: Saffroy, Raphael, Lemoine, Antoinette
• Primary Examiner(s): Whisenant, Ethan C
• Application Number:
  US15/038,122
• Publication Number:
  US 20160319365A1
• Time in Patent Office: 1,733 Days
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2565/627 being a mass spectrometer
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

An object of the invention is an in vitro method for detecting chromosomal rearrangements between at least two specific chromosomal regions in a biological sample of a human subject, which comprises the steps of: a) isolating deoxyribonucleic acid (DNA) molecules comprising said specific chromosomal regions from said biological sample, wherein said DNA molecules have an average length of X base pairs; b)amplifying the DNA molecules of step a) by a multiplex polymerase chain reaction assay, said assay comprising at least two sets of primers, wherein each set of primers is capable of hybridizing with a specific reference chromosomal region, and each set of primer comprises a plurality of primers, said primers being capable of hybridizing to a nucleic acid strand of one of the said specific chromosomal regions at sites regularly spaced of less than X/2 base pairs; and hybridizing the product of the amplification of step b) with at least one set of nucleic probes.

Claims

1. An in vitro method for detecting chromosomal rearrangements between at least two specific chromosomal regions in a biological sample of a human subject, wherein said rearrangement is a ELM4-ALK, ROS1-CD74, ROS1-EZR, or ROS1-SLC34A2 chromosomal rearrangement, said method comprising the steps of:

a) isolating deoxyribonucleic acid (DNA) molecules comprising said specific chromosomal regions from said biological sample, wherein said DNA molecules have an average length of X base pairs;

b) amplifying the DNA molecules of step a) by a multiplex polymerase chain reaction assay,

said assay comprising at least two sets of primers, wherein each set of primers is capable of hybridizing with a specific chromosomal region, and

each set of primer comprises a plurality of primers,

said primers being capable of hybridizing to a nucleic acid strand of one of the said specific chromosomal regions at sites regularly spaced of less than X/2 base pairs; and

c) hybridizing the product of the amplification of step b) with at least one set of nucleic probes,

wherein said set of nucleic acid probes comprises a plurality of nucleic acid probes,

said probes being capable of hybridizing to a nucleic acid strand of one of the said specific chromosomal regions at sites regularly spaced of less than X/2 base pairs; and

the 5′

end of said probe being capable of hybridizing within 0 to 30 bases from the 3′

end of a primer capable of hybridizing to the same specific chromosomal region; and

wherein the successful hybridization of at least one probe of said set of nucleic probes to product of the amplification of step b) indicates the presence of a chromosomal rearrangement.

2. The method of claim 1, wherein X is inferior or equal to 600.

3. The method of claim 1, wherein said biological sample is a formalin-fixed, paraffin-embedded (FFPE) tissue sample or a blood-derived sample.

4. The method of claim 1, wherein said biological sample is a tumor tissue.

5. The method of claim 4, wherein said tumor is selected from the group consisting of carcinoma, including that of the bladder, breast, colon, kidney, liver, lung, ovary, pancreas, stomach, cervix, thyroid and skin;

including squamous cell carcinoma;

tumors of mesenchymal origin, including fibrosarcoma and rhabdomyoscarcoma;

other tumors, including melanoma, seminoma, tetratocarcinoma, neuroblastoma and glioma;

tumors of the central and peripheral nervous system, including astrocytoma, neuroblastoma, glioma, and schwannomas;

tumors of mesenchymal origin, including fibrosarcoma, rhabdomyoscarama, and osteosarcoma; and

other tumors, including melanoma, xeroderma pigmentosum, keratoactanthoma, seminoma, thyroid follicular cancer and teratocarcinoma.

6. The method of claim 5, wherein the said tumor is a lung tumor.

7. The method of claim 1, further comprising a step of detecting the hybridization of step c).

8. The method of claim 7, wherein said detection is performed by mass spectrometry.

9. The method of claim 1, said method further comprising a step of sequencing the product of amplification of step b).

10. The method of claim 1, said method being for detecting chromosomal rearrangements between two specific chromosomal regions.

11. The method of claim 1, wherein said specific chromosomal regions comprise at least the anaplastic lymphoma kinase gene (ALK) of sequence SEQ ID No.1.

12. The method of claim 11, wherein said specific chromosomal regions further comprise the echinoderm microtubule-associated protein-like 4 gene (EML4) of SEQ ID No.4.

13. The method of claim 1, wherein said specific chromosomal regions further comprise the ROS1 gene of sequence SEQ ID No.5.

14. An in vitro method for diagnosing cancer, wherein the method comprises detecting chromosomal rearrangements between at least two specific chromosomal regions in a biological sample of said human subject with the method of claim 1.

15. The method of claim 14, wherein said cancer is non-small cell lung cancer.

16. The method of claim 14, wherein said specific chromosomal regions comprise at least the ROS1 gene of sequence SEQ ID No.5 and at least one of the CD74 gene (CD74) of sequence SEQ ID No.312, the EZR gene (EZR) of sequence SEQ ID No.313, and the SLC34A2 gene (SLC34A2) of sequence SEQ ID No.314.

17. The method of claim 14, wherein said method comprises:

a) detecting chromosomal rearrangements between at least two specific chromosomal regions in a biological sample of said human subject;

b) diagnosing cancer in said human subject if a chromosomal rearrangement has been detected in step a).

18. A method for the treatment of cancer in a human subject in need thereof, comprising diagnosing cancer in a human subject with the method of claim 14 and administering an effective amount of anti-cancer therapy to said subject.

19. The method of claim 18 comprising diagnosing non-small cell lung cancers that comprise a chromosomal rearrangement involving the gene ALK or the gene ROS1 in a human subject and administering an effective amount of ALK inhibitors to said subject.