# US 12,110,558 B2 · Methods and nucleic acids for determining the prognosis of a cancer subject > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 12,110,558 B2 - Document ID: US12110558B2 - Status: Granted - Kind: B2 - Application number: 17/577,836 - Filed: 2022-01-18 - Published: 2022-08-04 - Granted: 2024-10-08 - Earliest claimed: 2020-03-10 - Assignees: New Day Diagnostics, LLC - Applicants: New Day Diagnostics, LLC - Inventors: Jörn Lewin; Manuel Krispin - Web page: https://patentgrep.com/patent/US12110558B2 ## CPC - C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575) - C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism - C12Q 2600/118: Prognosis of disease development - C12Q 2600/154: Methylation markers - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract The invention provides methods, nucleic acids and kits for determining the prognosis of a subject having cancer. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of said disorder, thereby enabling the improved diagnosis and treatment of patients. ## Claims ### Claim 1 A method for determining methylation of SEPTIN-9 (SEQ ID NO: 1) genomic colon or colorectal tumor cell DNA of a human subject with colorectal cancer following removal of a primary colon or colorectal tumor but prior to further treatment, the method comprising: detecting the presence of, or measuring the level of, methylated genomic SEPTIN-9 DNA in a stool, blood, serum or plasma sample obtained from the human subject following the removal of the primary colon or colorectal tumor but prior to further treatment, wherein the methylated genomic SEPTIN-9 DNA is from colon or colorectal tumor cells, and wherein the detection uses a primer pair in which one of the primers hybridizes under stringent conditions to at least 9 nucleotides of the nucleic acid sequence of SEQ ID NO:26 or a complement thereof, and the other primer of the primer pair hybridizes under stringent conditions to at least 9 nucleotides of the nucleic acid sequence of SEQ ID NO:25 or a complement thereof, thereby determining methylation of the SEPTIN-9 genomic colon or colorectal tumor cell DNA of the human subject after removal of the primary colon or colorectal tumor, wherein: the colorectal cancer is Stage I, II, or III according to the Tumor-Node-Metastasis (TNM) staging system, and when the colorectal cancer is Stage III, the removal of the primary colon or colorectal tumor includes the removal of nearby lymph nodes. ### Claim 2 (depends on 1) The method of claim 1, wherein the colorectal cancer is Stage I according to the TNM staging system when the primary tumor is removed by surgery or resection. ### Claim 3 (depends on 2) The method of claim 2, wherein the surgery or resection includes nearby lymph nodes. ### Claim 4 (depends on 1) The method of claim 1, wherein the colorectal cancer is Stage II according to the TNM staging system when the primary tumor is removed by surgery or resection. ### Claim 5 (depends on 4) The method of claim 4, wherein the surgery or resection includes nearby lymph nodes. ### Claim 6 (depends on 1) The method of claim 1, wherein the colorectal cancer is Stage III according to the TNM staging system when the primary tumor is removed by surgery or resection. ### Claim 7 (depends on 1) The method of claim 1, wherein one of the primers of the primer pair comprises the nucleic acid sequence of SEQ ID NO: 26, or a complement thereof, and the other primer of the primer pair hybridizes under stringent conditions to at least 9 nucleotides of the nucleic acid sequence of SEQ ID NO:25 or a complement thereof. ### Claim 8 (depends on 1) The method of claim 1, further comprising using a blocker that hybridizes under stringent conditions to at least 9 nucleotides of the nucleic acid sequence of SEQ ID NO: 27. ### Claim 9 (depends on 1) The method of claim 1, further comprising using a probe that hybridizes under stringent conditions to at least 9 nucleotides of the nucleic acid sequence of SEQ ID NO: 28. ### Claim 10 (depends on 1) The method of claim 1, wherein at least one primer of the primer pair comprises SEQ ID NO: 26, or a complement thereof. ### Claim 11 (depends on 1) The method of claim 1, wherein at least one primer of the primer pair comprises SEQ ID NO: 25, or a complement thereof. ### Claim 12 (depends on 1) The method of claim 1, wherein determining methylation of the SEPTIN-9 genomic colon or colorectal tumor cell DNA further comprises using primers consisting of SEQ ID NOs: 25-26, a blocker consisting of SEQ ID NO: 27, and a probe consisting of SEQ ID NO: 28. ### Claim 13 (depends on 1) The method of claim 1, wherein the presence of methylated genomic SEPTIN-9 DNA in the stool, blood, serum or plasma sample following the removal of the primary colon or colorectal tumor, but prior to further treatment, indicates that the colorectal cancer of the human subject is aggressive. ### Claim 14 (depends on 1) The method of claim 1, wherein detecting the presence of or measuring the level of methylated genomic SEPTIN-9 DNA further comprises: detecting the presence of or measuring the level of a nucleic acid sequence comprising SEQ ID NO: 33 in the stool, blood, serum, or plasma sample of the human subject. ### Claim 15 (depends on 1) The method of claim 1, wherein the detection step is performed using quantitative PCR. ### Claim 16 (depends on 15) The method of claim 15, wherein the detection step is performed without confirmation. ### Claim 17 (depends on 15) The method of claim 15, wherein the detection step is performed without confirmation using sequencing. ### Claim 18 (depends on 1) The method of claim 1, wherein one of the primers of the primer pair comprises a complement of the nucleic acid sequence of SEQ ID NO: 26, and the other primer of the primer pair hybridizes under stringent conditions to a complement of at least 9 nucleotides of the nucleic acid sequence of SEQ ID NO:25. ### Claim 19 (depends on 1) The method of claim 1, wherein one of the primers of the primer pair comprises the nucleic acid sequence of SEQ ID NO: 26, and the other primer of the primer pair hybridizes under stringent conditions to a complement of at least 9 nucleotides of the nucleic acid sequence of SEQ ID NO:25. ### Claim 20 (depends on 1) The method of claim 1, wherein one of the primers of the primer pair comprises a complement of the nucleic acid sequence of SEQ ID NO: 26, and the other primer of the primer pair hybridizes under stringent conditions to at least 9 nucleotides of the nucleic acid sequence of SEQ IDNO:25.