Dna methylation markers for metastatic prostate cancer
AssigneeThe Johns Hopkins University
InventorsSrinivasan Yegnasubramanian, G. Steven Bova, Martin Aryee, William B. Isaacs, William G. Nelson
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Abstract
The present invention relates to the field of cancer. More specifically, the present invention provides methods and compositions useful for assessing prostate cancer. In a specific embodiment, present inventors have developed and applied a new technology and associated computation methods enabling simultaneous genome-scale analysis of genetic (copy number) and epigenetic (total methylation (TM) and allele-specific methylation (ASM) alternation, This method, called MBD-SNP, features affinity enrichment or methylated genomic DNA fragments using a methyl-binding domain polypeptide.
Claims15
A method for enabling simultaneous genome-scale analysis of genetic and epigenetic alterations in an individual comprising the steps of:
- a. digesting a first genomic DNA sample from the individual with a first restriction enzyme;
- b. digesting a second genomic DNA sample from the individual with a second restriction enzyme (total input fraction);
- c. ligating digested ends of the resulting genomic DNA fragments from steps (a) and (b) with adaptors;
- d. enriching the genomic DNA fragments from step (a) for methylated DNA fragments with a methylation-binding domain polypeptide (enriched methylated fraction);
- e. amplifying the total input fraction and the enriched methylated fraction using polymerase chain reaction (PCR);
- f. labeling the amplified total input fraction and the enriched methylated fraction;
- g. hybridizing the amplified total input fraction and the enriched methylated fraction to a single nucleotide polymorphism (SNP) microarray;
- and
- h. analyzing the enriched methylated fraction and total input fraction to assess total methylation (TM) and allele-specific methylation (ASM).
A method for diagnosing prostate cancer in an individual comprising the steps of:
- a. isolating DNA from a biological sample taken from the individual;
- b. contacting the DNA with a primer specific for a SNP biomarker of prostate cancer to form a DNA:primer complex, wherein the SNP biomarker of prostate cancer is a SNP located in the promoter region of one or more genes selected from the group consisting of EYA4, ADAMTS12, ESR1, ESR2 and TNFRSF10D;
- c. amplifying the DNA:primer complex using methylation-specific PCR;
- d. identifying the individual as having prostate cancer if the biomarkers are hypermethylated relative to a control.
Dependencies are inferred from the claim text.