Leukemia methylation markers and uses thereof

• US 10,093,986 B2
• Filed: 02/16/2017
• Issued: 10/09/2018
• Est. Priority Date: 07/06/2016
• Status: Active Grant

• Current Assignee: Regents of the University of California (University of California), Youhealth Oncotech Limited
• Original Assignee: Regents of the University of California (University of California), Youhealth Biotech, Limited
• Inventors: Zhang, Kang, Hou, Rui, Zheng, Lianghong
• Primary Examiner(s): Martinell, James
• Application Number:
  US15/435,174
• Publication Number:
  US 20180010192A1
• Time in Patent Office: 600 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/154 Methylation markers

Abstract

Disclosed herein are methods and kits for identifying a subject as having leukemia. Also provided herein are methods and kits for determining a leukemia subtype in subject. Further provided herein are methods and kits for determining the prognosis of a subject having leukemia and for determining the progression of leukemia in a subject.

Claims

1. A method of detecting a methylation pattern of a set of biomarkers in a subject suspected of having leukemia, the method comprising:

a) processing an extracted genomic DNA with a deaminating agent to generate a genomic DNA sample comprising deaminated nucleotides, wherein the extracted genomic DNA is obtained from a biological sample from the subject suspected of having leukemia; and

b) detecting the methylation pattern of one or more biomarkers selected from;

cg08261841, cg09247255, cg00142402, cg16274678, and cg02381853 from the extracted genomic DNA by contacting the extracted genomic DNA with a set of probes, wherein the set of probes hybridizes to the one or more biomarkers, and perform a DNA sequencing analysis to determine the methylation pattern of the one or more biomarkers.

2. The method of claim 1, wherein step b) comprises detecting the methylation pattern of cg08261841, cg09247255, cg00142402, cg16274678, and cg02381853.

3. The method of claim 1, further comprising detecting a methylation pattern of a biomarker selected from:

cg05304729, cg00484711, cg18518074, cg05048927, cg08960448, and cg12008047.

4. The method of claim 1, wherein the method comprises detecting the methylation of cg08261841, cg09247255, cg00142402, cg16274678, cg02381853, cg05304729, cg00484711, cg18518074, cg05048927, cg08960448, and cg12008047.

5. The method of claim 1, wherein the biological sample comprises a blood sample.

6. The method of claim 1, wherein the biological sample comprises a tissue biopsy sample.

7. The method of claim 1, wherein the biological sample comprises circulating tumor cells.

8. The method of claim 1, wherein the subject is a human.

9. The method of claim 1, wherein each probe from the set of probes is a padlock probe.

10. A method of detecting a methylation pattern of a set of biomarkers in a subject suspected of having acute lymphoblastic leukemia (ALL), comprising:

a) processing an extracted genomic DNA with a deaminating agent to generate a genomic DNA sample comprising deaminated nucleotides, wherein the extracted genomic DNA is obtained from a biological sample from the subject; and

b) detecting the methylation pattern of biomarkers cg08261841, cg09247255, cg12008047, cg05304729, cg18518074, cg05048927, and cg08960448 from the extracted genomic DNA by contacting the extracted genomic DNA with a set of probes, wherein the set of probes hybridizes to the one or more biomarkers, and perform a DNA sequencing analysis to determine the methylation pattern of the one or more biomarkers.

11. The method of claim 10, wherein each probe from the set of probes is a padlock probe.

12. The method of claim 10, wherein the biological sample comprises a blood sample.

13. The method of claim 10, wherein the biological sample comprises a tissue biopsy sample.

14. The method of claim 10, wherein the biological sample comprises circulating tumor cells.

15. The method of claim 10, wherein the subject is a human.

16. A method of detecting a methylation pattern of a set of biomarkers in a subject suspected of having acute myeloid leukemia (AML), comprising:

a) processing an extracted genomic DNA with a deaminating agent to generate a genomic DNA sample comprising deaminated nucleotides, wherein the extracted genomic DNA is obtained from a biological sample from the subject; and

b) detecting the methylation pattern of biomarkers cg00142402, cg05304729, cg00484711, and cg18518074 from the extracted genomic DNA by contacting the extracted genomic DNA with a set of probes, wherein the set of probes hybridizes to the one or more biomarkers, and perform a DNA sequencing analysis to determine the methylation pattern of the one or more biomarkers.

17. The method of claim 16, wherein each probe from the set of probes is a padlock probe.

18. The method of claim 16, wherein the biological sample comprises a blood sample.

19. The method of claim 16, wherein the biological sample comprises a tissue biopsy sample.

20. The method of claim 16, wherein the biological sample comprises circulating tumor cells.

21. The method of claim 16, wherein the subject is a human.