Detection method

Abstract

Provided herein are materials and methods for detecting colorectal neoplasms and colon cancer based on the expression levels of stool-derived eukaryotic RNA biomarkers in eukaryotic nucleic acid present in a stool sample from a subject, for example, a patient. The methods can be used for the detection of high-risk adenomas and colorectal neoplasm molecular subtypes.

1 . A method of detecting colorectal neoplasia in a subject, the method comprising:
 a) measuring the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers selected from the biomarkers listed in Table 1 or Table 2 or a combination of Table 1 and Table 2 in eukaryotic nucleic acid extracted from a stool sample from the subject;   b) comparing the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers in the stool sample with the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, or 29 stool-derived eukaryotic RNA biomarkers in a control, wherein a difference in the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers in the stool sample relative to the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers in the control indicates that the subject has colorectal neoplasia.   
     
     
         2 . The method of  claim 1 , wherein the subject is human. 
     
     
         3 . The method of  claim 1 , wherein the colorectal neoplasia is selected from the group consisting of colorectal cancer, high-risk adenoma, medium-risk adenoma, and low-risk adenoma. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 1 , wherein the nucleic acid comprises RNA, total RNA, mRNA, seRNA, tRNA, rRNA, ncRNA, smRNA, or snoRNA, or a combination of any of RNA, total RNA, mRNA, seRNA, tRNA, rRNA, ncRNA, smRNA, or snoRNA. 
     
     
         6 . The method of  claim 1 , wherein the expression level is measured by nucleic acid sequencing, microarray sequencing, molecular barcoding, amplicon sequencing, probe capture, polymerase chain reaction (PCR), ddPCR, dPCR, RT-PCR, or RT-qPCR. 
     
     
         7 . The method of  claim 1 , further comprising determining the subject's demographic information. 
     
     
         8 . The method of  claim 1 , further comprising administering a fecal immunochemical test (FIT) to the subject. 
     
     
         9 . A method of selecting a clinical plan for a subject having or at risk for colorectal neoplasia, the method comprising:
 a) measuring the level of expression of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers selected from the biomarkers listed in Table 1 or Table 2 or a combination of Table 1 and Table 2 in eukaryotic nucleic acid present in a stool sample from the subject;   b) comparing the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers in the stool sample with the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers in a control, wherein a difference in the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers in the stool sample relative to the measured expression level of the 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers in the control indicates that the subject has or is at risk for colorectal neoplasia;   c) administering a diagnostic procedure or a treatment or a combination of a diagnostic procedure and a treatment.   
     
     
         10 . The method of  claim 9 , wherein the subject is a human. 
     
     
         11 . The method of  claim 9 , wherein the colorectal neoplasia is selected from the group consisting of colorectal cancer, high-risk adenoma, medium-risk adenoma, and low-risk adenoma. 
     
     
         12 . (canceled) 
     
     
         13 . The method of  claim 9 , wherein the nucleic acid comprises RNA, total RNA, mRNA, seRNA, tRNA, rRNA, ncRNA, smRNA, or snoRNA, or a combination of any of RNA, total RNA, mRNA, seRNA, tRNA, rRNA, ncRNA, smRNA, or snoRNA. 
     
     
         14 . The method of  claim 9 , wherein the expression level is measured by nucleic acid sequencing, microarray sequencing, molecular barcoding, amplicon sequencing, probe capture, polymerase chain reaction (PCR), ddPCR, dPCR, RT-PCR, or RT-qPCR. 
     
     
         15 . The method of  claim 9 , further comprising determining the subject's demographic information. 
     
     
         16 . The method of  claim 9 , further comprising administering a fecal immunochemical test (FIT) to the subject. 
     
     
         17 . The method of  claim 9 , wherein the clinical plan comprises a diagnostic procedure or a treatment. 
     
     
         18 . The method of  claim 9 , wherein the diagnostic procedure comprises a colonoscopy. 
     
     
         19 . (canceled) 
     
     
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         26 . A method of treating a colorectal neoplasia in a subject, the method comprising:
 a) determining that a stool sample from the patient expresses elevated levels of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 stool-derived eukaryotic RNA biomarkers selected from the biomarkers listed in Table 1 or Table 2 or a combination of Table 1 and Table 2 in eukaryotic nucleic acid present in a stool sample from the subject; and   b) administering to the subject a colonoscopy, surgery, chemotherapy, radiation therapy, targeted therapy, or immunotherapy.   
     
     
         27 . A method of detecting colorectal neoplasia in a subject, the method comprising:
 a) measuring the variant allele frequency of one or more variant biomarker genes selected from the biomarker genes listed in Table 3 in eukaryotic nucleic acid extracted from a stool sample from the subject;   b) comparing the measured variant allele frequency of the one or more variant biomarker genes in the stool sample with the measured variant allele frequency of the one or more variant biomarker genes in a control, wherein a difference in the variant allele frequency of the one or more variant biomarker genes relative to the variant allele frequency of the one or more variant biomarker genes in the control indicates that the subject has or is at risk for colorectal cancer.   
     
     
         28 . A method of determining whether a subject has or is at risk for colorectal cancer, the method comprising:
 a) measuring the variant allele frequency of one or more variant biomarker genes selected from the biomarker genes listed in Table 3 in eukaryotic nucleic acid extracted from a stool sample from the subject;   b) comparing the measured variant allele frequency of the one or more variant biomarker genes in the stool sample with the measured variant allele frequency of the one or more variant biomarker genes in a control, wherein a difference in the variant allele frequency of the one or more variant biomarker genes relative to the variant allele frequency of the one or more variant biomarker genes in the control indicates that the subject has or is at risk for colorectal cancer.   
     
     
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         37 . A method of detecting a molecular subtype of colorectal cancer in a subject, the method comprising:
 a) measuring the level of expression of two or more biomarker genes selected from any of the colorectal neoplasm molecular subtype biomarker genes listed in Table 4 in eukaryotic nucleic acid extracted from a stool sample from the subject;   b) comparing the measured expression level of the two or more colorectal neoplasm molecular subtype biomarker genes in the biological sample with the measured expression level of the two or more colorectal neoplasm molecular subtype biomarker genes in a control, wherein a difference in the measured expression level of the two or more colorectal neoplasm molecular subtype biomarker genes in the biological sample with the measured expression level of the two or more colorectal neoplasm molecular subtype biomarker genes relative to the two or more colorectal neoplasm molecular subtype biomarker genes in the control indicates the molecular subtype of colorectal cancer.   
     
     
         38 . (canceled) 
     
     
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         48 . (canceled) 
     
     
         49 . A method comprising:
 a) determining that a stool sample from a patient comprises elevated levels of two or more stool-derived eukaryotic biomarkers selected from the biomarkers listed in Table 1 or Table 2 or a combination of Table 1 and Table 2 or Table 3 or Table 4 in eukaryotic nucleic acid present in a stool sample from the subject relative to a control;   b) based on that determination, determining the patient is at risk for a colorectal neoplasia; and   c) administering a colonoscopy to the patient.   
     
     
         50 . The method of  claim 49 , further comprising step of providing a stool sample.