Multi-analyte diagnostic and prognostic assays for colorectal cancer and uses thereof
AssigneeNew Day Diagnostics, LLC
InventorsAndrew A. LUKOWIAK, Stephani D. HERNANDEZ, Denise KOTTWITZ, Jörn LEWIN, Uwe STAUB
Life of this patent
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Abstract
Provided herein are methods, assays and kits for detecting methylated genomic DNA and one or more protein biomarkers in one or more biological samples. In some aspects, the disclosure provides methods, assays and kits for detecting or prognosing a proliferative disease, such as colorectal cancer, in a subject based on the presence of methylated genomic DNA and one or more protein biomarkers in one or more biological samples.
Claims72
A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples from a subject, comprising:
- (i) detecting synthetic DNA generated from one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples, wherein the synthetic DNA is generated by converting cytosine unmethylated in the 5-position to uracil or another base that does not hybridize to guanine in the genomic DNA, and detecting unconverted cytosine in the synthetic DNA;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise carcinoembryonic antigen (CEA) and/or amphiregulin.
A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected, and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin.
A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising:
- (i) detecting DNA methylation within SEQ ID NO:
- 31 (mSEPT9) and SEQ ID NOs:
- 6 and 11 (mANKDRD13b) in the one or more biological samples, wherein cytosine unmethylated in the 5-position is converted to uracil or another base that does not hybridize to guanine, and unconverted cytosine is detected;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin.
A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, and a galectin-3 ligand.
The method of any one of claim 147, wherein the methylated genomic DNA is detected by a manual, semi-automated, or fully automated system.
A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples from a subject, comprising:
- (i) detecting one or more methylated genomic DNA sequences associated with a proliferative disease from the one or more biological samples;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin.
A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in the one or more biological samples, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin.
A method for detecting the presence or amount of methylated genomic DNA and protein in one or more biological samples, comprising:
- (i) detecting DNA methylation within SEQ ID NO:
- 31 (mSEPT9) and SEQ ID NOs:
- 6 and 11 (mANKDRD13b) in the one or more biological samples;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin.
A method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin,
- wherein the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject.
A method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma or serum samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma or serum samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin,
- wherein the presence of DNA methylation and one or more protein biomarkers in the one or more plasma or serum samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject.
A method for detecting colorectal cancer or a colorectal cell proliferative disease in a subject, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected;
- and
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, and a galectin-3 ligand,
- wherein the presence of DNA methylation and one or more protein biomarkers in the one or more plasma samples is indicative of the presence of colorectal cancer or a colorectal cell proliferative disease in the subject.
A method for prognosing colorectal cancer or a colorectal cell proliferative disease in a subject, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more biological samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and/or mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected;
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more biological samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin;
- and
- (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more biological samples.
A method for prognosing colorectal cancer or a colorectal cell proliferative disease in a subject, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma or serum samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected;
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma or serum samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin;
- and
- (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more serum or plasma samples.
A method for prognosing colorectal cancer or a colorectal cell proliferative disease in a subject, comprising:
- (i) detecting DNA methylation within at least one genomic DNA polynucleotide in one or more plasma samples from the subject, wherein the at least one genomic DNA polynucleotide comprises mSEPT9 and mANKDRD13b, wherein cytosine unmethylated in the 5-position within the genomic DNA polynucleotide is converted to uracil or another base that does not hybridize to guanine in the genomic DNA polynucleotide, and unconverted cytosine is detected;
- (ii) detecting the presence or amount of one or more protein biomarkers in the one or more plasma samples, wherein the one or more protein biomarkers comprise CEA and/or amphiregulin, and a galectin-3 ligand;
- and
- (iii) prognosing the subject with colorectal cancer or a colorectal cell proliferative disease based on the presence of DNA methylation and one or more protein biomarkers in the one or more plasma samples.
Dependencies are inferred from the claim text.