Unbiased DNA methylation markers define an extensive field defect in histologically normal prostate tissues associated with prostate cancer: new biomarkers for men with prostate cancer
AssigneeWisconsin Alumni Research Foundation
InventorsDavid Frazier Jarrard, Bing Yang
Life of this patent
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Abstract
A method of detecting the presence of a prostate cancer field defect in a human subject comprising the step of (a) obtaining genomic DNA from the human subject and (b) quantitating methylation in at least one target region selected from the group consisting of PLA2G16, CAV1, EVX1, MCF2L, FGF1, NCR2 and WNT2 and EXT1 and SPAG4 target, wherein significant methylation changes indicate the presence of prostate cancer or a prostate cancer field defect, wherein the change is relative to tissue from a second human subject who does not have prostate cancer.
Claims15
A method of preparing a separated, amplified target loci DNA sample for analysis comprising the steps of:
- (a) providing a reaction mixture comprising bisulfite modified DNA from histologically normal prostate tissue of a subject, and (i) a pair of primers designed to amplify specifically target loci DNA consisting essentially of SEQ ID NO:
- 102, wherein the primer pair comprises a first and a second primer, (ii) a polymerase, and (iii) a plurality of free nucleotides comprising adenine, thymine, cytosine and guanine;
- (b) heating the reaction mixture to a first predetermined temperature for a first predetermined time;
- (c) cooling the reaction mixture to a second predetermined temperature for a second predetermined time under conditions to allow the first and second primers to hybridize with their complementary sequences on the bisulfite modified DNA;
- (d) repeating steps (b) and (c) at least 10 times wherein an amplified DNA sample comprising amplified target loci DNA of SEQ ID NO:
- 102 is formed;
- and
- (e) separating the amplified target loci DNA of SEQ ID NO:
- 102 from the amplified DNA sample, wherein a separated, amplified target loci DNA sample is formed, wherein the primer pair consists of SEQ ID NO:
- 98 and SEQ ID NO:
- 99 or the amplicon consists of SEQ ID NO:
- 102.
A method of preparing a separated, amplified target loci DNA sample for analysis comprising the steps of:
- (a) providing a reaction mixture comprising bisulfite modified DNA from a urine or semen sample from a subject, and (i) a pair of primers designed to amplify target loci DNA consisting essentially of SEQ ID NO:
- 102, wherein the primer pair comprises a first and a second primer, (ii) a polymerase and (iii) a plurality of free nucleotides comprising adenine, thymine, cytosine and guanine;
- (b) heating the reaction mixture to a first predetermined temperature for a first predetermined time;
- (c) cooling the reaction mixture to a second predetermined temperature for a second predetermined time under conditions to allow the first and second primers to hybridize with their complementary sequences on the bisulfite modified DNA;
- (d) repeating steps (b) and (c) at least 10 times wherein an amplified DNA sample comprising amplified target loci DNA of SEQ ID NO:
- 102 is formed;
- and
- (e) separating the amplified target loci DNA of SEQ ID NO:
- 102 from the amplified DNA sample, wherein a separated, amplified target loci DNA sample is formed, wherein the primer pair consists of SEQ ID NO:
- 98 and SEQ ID NO:
- 99 or the amplicon consists of SEQ ID NO:
- 102.
Dependencies are inferred from the claim text.