Detecting neoplasm
AssigneeMayo Foundation for Medical Education and Research
InventorsDavid A. Ahlquist, John B. Kisiel, William R. Taylor, Tracy C. Yab, Douglas W. Mahoney
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Abstract
Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as pancreatic and colorectal cancer.
Claims57
A method of screening for a neoplasm in a sample obtained from a subject, the method comprising:
- 1) assaying a methylation state of a marker in a sample obtained from a subject;
- and
- 2) identifying the subject as having a neoplasm when the methylation state of the marker is different than a methylation state of the marker assayed in a subject that does not have a neoplasm,
- wherein the marker comprises a base in a differentially methylated region (DMR) selected from a group consisting of DMR 1-107.
An oligonucleotide comprising a sequence selected from the group consisting of SEQ ID NO:
- 1-202.
An oligonucleotide comprising a sequence complementary to a chromosomal region having a base in a DMR.
An oligonucleotide sensitive to methylation state of a DMR.
A kit comprising:
- 1) a bisulfite reagent;
- and
- 2) a control nucleic acid comprising a sequence from a DMR selected from a group consisting of DMR 1-107 and having a methylation state associated with a subject who does not have a cancer.
A kit comprising:
- 1) a bisulfite reagent;
- and
- 2) a control nucleic acid comprising a sequence from a DMR selected from a group consisting of DMR 1-107 and having a methylation state associated with a subject who has a cancer.
A composition comprising a nucleic acid comprising a DMR and a bisulfite reagent.
A composition comprising a nucleic acid comprising a DMR and a methylation-sensitive restriction enzyme.
A composition comprising a nucleic acid comprising a DMR and a polymerase.
A method for screening for a neoplasm in a sample obtained from a subject, the method comprising:
- a) determining a methylation state of a marker in the sample comprising a base in a DMR selected from a group consisting of DMR 1-107;
- b) comparing the methylation state of the marker from the subject sample to a methylation state of the marker from a normal control sample from a subject who does not have a cancer;
- c) determining a confidence interval and/or a p value of the difference in the methylation state of the subject sample and the normal control sample.
A method for screening for a neoplasm in a sample obtained from a subject, the method comprising reacting a nucleic acid comprising a DMR with a bisulfite reagent to produce a bisulfite-reacted nucleic acid;
- sequencing the bisulfite-reacted nucleic acid to provide a nucleotide sequence of the bisulfite-reacted nucleic acid;
- comparing the nucleotide sequence of the bisulfite-reacted nucleic acid with a nucleotide sequence of a nucleic acid comprising the DMR from a subject who does not have a cancer to identify differences in the two sequences;
- and identifying the subject as having a neoplasm when a difference is present.
A system for screening for a neoplasm in a sample obtained from a subject, the system comprising an analysis component configured to determine the methylation state of a sample, a software component configured to compare the methylation state of the sample with a control sample or a reference sample methylation state recorded in a database, and an alert component configured to determine a single value based on a combination of methylation states and alert a user of a cancer-associated methylation state.
A set of isolated nucleic acids, each nucleic acid having a sequence comprising a DMR.
Dependencies are inferred from the claim text.