Methods for discovering tumor biomarkers and diagnosing tumors
AssigneeIrm LLC
InventorsGarret M. Hampton, John B. Welsh
Life of this patent
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Abstract
This invention provides methods for discovery of biomarkers that are useful for diagnosing, prognosticating, and monitoring the treatment efficacy, of various cancers. The invention also provides methods for diagnosing various forms of cancers using biomarkers identified in accordance with the invention.
Claims30
A method for identifying a biomarker that is diagnostic for the presence of a cancer in a mammal, the method comprising:
- analyzing one or more polynucleotide sequences using an algorithm that determines whether the polynucleotide sequence is predicted to encode a polypeptide that is secreted from a cell in which the polypeptide is expressed;
- and
- determining whether an mRNA that corresponds to one or more of the polynucleotide sequences that are predicted to encode secreted polypeptides is differentially expressed in one or more types of cancer cells compared to non-cancer cells;
- wherein an mRNA that is differentially expressed in cancer cells compared to non-cancer cells, or a polypeptide encoded by the differentially expressed mRNA, is useful as a biomarker that is diagnostic for the presence of the cancer in a mammal.
A method of diagnosing a cancer in a mammal, the method comprising detecting in a sample obtained from the mammal an increase in the level of a biomarker, wherein the biomarker was identified using a method that comprises:
- analyzing one or more polynucleotide sequences using an algorithm that determines whether the polynucleotide sequence is predicted to encode a polypeptide that is secreted from a cell in which the polypeptide is expressed;
- and
- determining whether an mRNA that corresponds to one or more of the polynucleotide sequences that are predicted to encode secreted polypeptides is differentially expressed in one or more types of cancer cells compared to non-cancer cells;
- wherein an mRNA that is differentially expressed in cancer cells compared to non-cancer cells, or a polypeptide encoded by the differentially expressed mRNA, is useful as a biomarker that is diagnostic for the presence of the cancer in a mammal.
A method for monitoring the efficacy of a cancer treatment in a mammal, the method comprising detecting an increase or decrease in the level of a biomarker that is diagnostic for the presence of the cancer in a mammal in a plurality of samples obtained from the mammal at different times, wherein the biomarker was identified using a method that comprises:
- analyzing one or more polynucleotide sequences using an algorithm that determines whether the polynucleotide sequence is predicted to encode a polypeptide that is secreted from a cell in which the polypeptide is expressed;
- and
- determining whether an mRNA that corresponds to one or more of the polynucleotide sequences that are predicted to encode secreted polypeptides is differentially expressed in one or more types of cancer cells compared to non-cancer cells;
- wherein an mRNA that is differentially expressed in cancer cells compared to non-cancer cells, or a polypeptide encoded by the differentially expressed mRNA, is useful as a biomarker that is diagnostic for the presence of the cancer in a mammal.
- The method of claim 23, wherein the mammal was subjected to a cancer treatment in between obtaining two or more of the samples.
A method for diagnosing, or identifying a predisposition to the development of, prostate cancer in a mammal, comprising (a) obtaining a biological sample from the mammal suspected to have or be predisposed to develop prostate cancer;
- and (b) detecting in the biological sample an abnormal level of at least one secreted biomarker of prostate cancer, thereby diagnosing or identifying a predisposition to the development of prostate cancer in the mammal;
- wherein the at least one secreted biomarker of prostate cancer is selected from the group consisting of relaxin 1 (H1), neuropeptide Y, MIC-1, pancreatic thread protein-like (rat), prostate-specific membrane antigen, prostate-specific membrane antigen, prostate-specific membrane antigen, and single-minded homolog 2 (Drosophila).
A method for diagnosing, or identifying a predisposition to the development of, colon cancer in a mammal, comprising (a) obtaining a biological sample from the mammal suspected to have or be predisposed to develop colon cancer, and (b) detecting in the biological sample an elevated level of mucin 2 (MUC-2).
A method for diagnosing, or identifying a predisposition to the development of, a carcinoma in a mammal, comprising (a) obtaining a biological sample from the mammal suspected to have or be predisposed to develop a carcinoma, and (b) detecting in the biological sample from the mammal an elevated level of mapsin;
- wherein said carcinoma is colon cancer, gastroesophagous cancer, lung cancer, or pancreas cancer.
Dependencies are inferred from the claim text.