Leukemia methylation markers and uses thereof
View Patent ↗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.
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.