Methylation markers for diagnosing hepatocellular carcinoma and lung cancer

Abstract

Disclosed herein, in certain embodiments, are methods and kits for diagnosing a subject as having hepatocellular carcinoma (HCC) or lung cancer. In some instances, also described herein are methods of determining the prognosis of the subject having HCC or lung cancer. In additional instances, described herein are methods of determining the specific staging of HCC or lung cancer in a subject.

What is claimed is: 
     
         1 - 30 . (canceled) 
     
     
         31 . A method of determining a methylation profile of a subject, wherein the methylation profile comprises one or more biomarkers, the method comprising: 
 (a) contacting treated DNA from the subject with one or more probes to generate amplified products, 
 wherein each probe hybridizes to the treated DNA to detect the methylation status of the one or more biomarkers, 
 wherein each of the one or more biomarkers is selected from the group consisting of cg10673833, cg11225410, cg00338116, cg00552226, cg24496475, cg05414338, cg12041340, cg08343881, cg03431741, cg17126142, cg18004756, cg26205771, cg08436738, cg01604601, cg27252696, cg24917945, cg11252953, cg03550506, cg06903569, cg12865837, cg18440897, cg19255783, and cg20634573, and 
 wherein the treated DNA is processed from a biological sample obtained from the subject to allow for determination of the methylation status of the one or more biomarkers; and 
   (b) analyzing the amplified products to generate the methylation status of the one or more biomarkers, 
thereby determining the methylation profile of the one or more biomarkers in the subject. 
     
     
         32 . The method of  claim 31 , wherein the one or more biomarkers is a set of biomarkers comprising cg11225410, cg00338116, cg00552226, cg24496475, cg05414338, cg12041340, cg08343881, cg03431741, cg17126142, and cg18004756. 
     
     
         33 . The method of  claim 31 , wherein the one or more biomarkers is a set of biomarkers comprising cg26205771, cg08436738, cg01604601, cg27252696, cg24917945, cg11252953, cg03550506, cg06903569, cg12865837, cg18440897, cg19255783, and cg20634573. 
     
     
         34 . The method of  claim 31 , wherein the methylation profile comprises a combined diagnostic score (cd-score), 
 wherein the cd-score is based on the methylation status of the one or more biomarkers.   
     
     
         35 . The method of  claim 34 , wherein the cd-score correlates to an amount of methylated circulating tumor DNA comprising the one or more biomarkers present in the biological sample. 
     
     
         36 . The method of  claim 34 , wherein the cd-score is determined utilizing an algorithm selected from one or more of the following: a principal component analysis, a logistic regression analysis, a nearest neighbor analysis, a support vector machine, and a neural network model. 
     
     
         37 . The method of  claim 31 , wherein the methylation profile comprises a combined prognostic score (cp-score), 
 wherein the cp-score is based on the methylation status of the one or more biomarkers.   
     
     
         38 . The method of  claim 37 , wherein the cp-score correlates to an amount of methylated circulating tumor DNA comprising the one or more biomarkers present in the biological sample. 
     
     
         39 . The method of  claim 38 , wherein the cp-score is determined utilizing an algorithm selected from one or more of the following: a principal component analysis, a logistic regression analysis, a nearest neighbor analysis, a support vector machine, and a neural network model. 
     
     
         40 . The method of  claim 31 , further comprising comparing the methylation profile of the subject to a model. 
     
     
         41 . The method of  claim 40 , wherein the model comprises a methylation profile of one or more biomarkers from a hepatocellular carcinoma (HCC) positive sample. 
     
     
         42 . The method of  claim 41 , wherein the HCC positive sample comprises cells from a metastatic HCC sample. 
     
     
         43 . The method of  claim 40 , wherein the model comprises a methylation profile of one or more biomarkers from a lung cancer positive sample. 
     
     
         44 . The method of  claim 43 , wherein the lung cancer positive sample comprises cells from a metastatic lung cancer sample. 
     
     
         45 . The method of  claim 40 , wherein the model further comprises a methylation profile of one or more biomarkers from a normal sample. 
     
     
         46 . The method of  claim 31 , wherein the one or more probes are droplet digital PCR (ddPCR) probes. 
     
     
         47 . The method of  claim 31 , wherein the treated DNA is treated with a deaminating agent. 
     
     
         48 . The method of  claim 31 , wherein the subject is a human. 
     
     
         49 . The method of  claim 48 , wherein the subject is suspected of having hepatocellular carcinoma (HCC) or lung cancer. 
     
     
         50 . The method of  claim 31 , wherein the biological sample is a blood sample, tissue biopsy sample, or a circulating tumor cell sample. 
     
     
         51 . The method of  claim 31 , wherein the method comprises performing a next-generation sequencing technique on the amplified products to generate sequencing reads, and mapping sequencing reads from the next-generation sequencing technique to a reference genome.