Patent ID: 6893820

Claim:
A method of identifying CpG islands which are preferentially methylated in malignant cells contained within a tumor or neoplasm, comprising: a) digesting genomic DNA obtained from the malignant cells with an infrequently-cutting, methylation-sensitive, restriction enzyme to provide a set of malignant cell restriction fragments; b) digesting genomic DNA obtained from non-malignant, control cells with an infrequently-cutting, methylation-sensitive, restriction enzyme to provide a set of control cell restriction fragments; c) attaching a detectable label to the ends of the malignant cell restriction fragments and the control restriction fragments; d) digesting the labeled malignant cell and control cell restriction fragments with a second restriction enzyme; e) separating the labeled malignant cell restriction fragments and the labeled control cell restriction fragments, wherein the malignant cell restriction fragments and the control cell restriction fragments are separated by electrophoresis on two different gels; f) digesting the restriction fragments in each of said gels with a third restriction enzyme; g) electrophoresing the restriction fragments in each of said gels in a direction perpendicular to the first direction to provide a first pattern of detectable malignant cell restriction fragments and a second pattern of detectable control cell restriction fragments; and h) comparing the first pattern to the second pattern to identify diagnostic control cell restriction fragments in said second pattern which are absent or exhibit a decreased intensity in the first pattern, wherein said diagnostic control cell restriction fragments comprise a CpG island that is unmethylated in the DNA of the control cells and methylated in the DNA of the malignant cells, wherein the tumor or neoplasm is selected from the group: colon, glioma, lung, and non-medulloblastoma primitive neuroectodermal tumors (PNET).