WO2023273257A1 - 一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用 - Google Patents

一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用 Download PDF

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WO2023273257A1
WO2023273257A1 PCT/CN2021/142201 CN2021142201W WO2023273257A1 WO 2023273257 A1 WO2023273257 A1 WO 2023273257A1 CN 2021142201 W CN2021142201 W CN 2021142201W WO 2023273257 A1 WO2023273257 A1 WO 2023273257A1
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chr18
region
nucleic acid
acid combination
methylation
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PCT/CN2021/142201
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English (en)
French (fr)
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张良禄
周谛晗
董兰兰
梁嘉琳
孙帆
李婷婷
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武汉艾米森生命科技有限公司
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/154—Methylation markers

Definitions

  • the present disclosure relates to the technical field of tumor detection, in particular, to a diagnostic or auxiliary diagnostic reagent, nucleic acid combination, kit and application for colorectal cancer or precancerous lesions.
  • Colorectal cancer is one of the most common malignant tumors in my country, mainly including colon cancer and rectal cancer.
  • the prognosis of colorectal cancer is related to the severity of the disease at the time of diagnosis, and the 5-year survival rate of colorectal cancer patients in the United States is 67%. From 2004 to 2013, the incidence of colorectal cancer in the United States decreased by 3% per year, and the overall mortality rate decreased by an average of 2.7% per year, with early screening contributing more than 50%. Due to the lack of symptoms in the early stage of colorectal cancer, the current early diagnosis rate of colorectal cancer is only about 10%, and more than 80% of patients have reached the middle and late stages when they are diagnosed.
  • fecal occult blood test fecal immune test
  • colonic barium enema colonic barium enema
  • sigmoidoscopy colonoscopy
  • colonoscopy fecal occult blood test and fecal immune test
  • endoscopy has improved the detection rate of colorectal cancer in high-risk groups, it has low patient acceptance and is not flexible enough.
  • Colorectal tumors generally occur in the colorectal epithelial tissue. During the growth process, tumor cells are continuously shed into the intestinal lumen and excreted with feces. Tumor cells are more likely to fall off from the intestinal tract due to abnormal proliferation. Therefore, the feces of patients with intestinal tumors contain a large number of diseased cells and diseased components. Detection of tumor cell components in stool can provide a non-invasive method for auxiliary diagnosis of colorectal tumors . In addition, tumor cells will also release DNA into the blood (cfDNA, circulating free DNA). Therefore, colorectal cancer can also be detected by detecting tumor DNA in blood. However, cfDNA has the characteristics of low content and short half-life, which makes it easy to be lost during the extraction process, so detection is extremely difficult.
  • Some detection markers disclosed in the prior art have a good detection effect on colorectal cancer, but have poor detection sensitivity and specificity on colorectal precancerous lesions. In addition, markers with excellent detection effects in both feces and blood are currently lacking.
  • the present disclosure provides a diagnostic or auxiliary diagnostic reagent, nucleic acid combination, kit and application for colorectal cancer or precancerous lesions to solve the above technical problems.
  • the disclosure provides the application of a diagnostic or auxiliary diagnostic reagent for colorectal cancer or precancerous lesions in the preparation of diagnostic or auxiliary diagnostic products for colorectal cancer or precancerous lesions.
  • the diagnostic or auxiliary diagnostic reagents are used to detect DOK6 gene A reagent for methylation of the target region, the target region is selected from the full-length or partial region of at least one of the following regions of the DOK6 gene: region I, region II and region III;
  • region I is selected from Chr18:69400274-69401932 positive chain or Chr18:69401932-69400274 negative chain
  • region II is selected from Chr18:69402698-69402935 positive chain or Chr18:69402935-69402698 negative chain
  • region III is selected from Chr18:69469672- 69470012 positive strand or Chr18: 69470012-69469672 negative strand.
  • the DOK6 gene is located on the negative-sense strand of human chromosome 18, and the specific position is 69400888-69849087bp. It should be noted that the positions of the sites or regions mentioned in this disclosure are all based on GRCh38.p13.
  • DOK6 docking Protein 6, DOK6
  • DOK6 docking Protein 6
  • NS1 protein influenza virus nonstructural protein 1
  • DOK6 belongs to the Dok family, which includes DOK1, DOK2, DOK3, DOK4, DOK5, DOK6, and DOK7, among which DOK1, DOK2, and DOK3 are the first category, mainly distributed in blood system tissues and cells, and all of them are negative regulators , while the other four members are the second largest group, mainly distributed in non-blood system tissues and cells.
  • DOK6 belongs to the Dok family, which includes DOK1, DOK2, DOK3, DOK4, DOK5, DOK6, and DOK7, among which DOK1, DOK2, and DOK3 are the first category, mainly distributed in blood system tissues and cells, and all of them are negative regulators , while the other four members are the second largest group, mainly distributed in non-blood system tissues and cells.
  • the target region in the present disclosure includes not limited to the promoter region, coding region, non-coding region and regulatory region of the DOK6 gene.
  • colorectal cancer or its adenoma can be diagnosed or assisted in diagnosis by detecting the increase in the methylation level of the CpG island region (i.e. the target region) using the DOK6 gene as a marker, which has high sensitivity and Specificity helps to improve the detection rate of colorectal cancer or its adenoma.
  • the CpG island is a region rich in CpG dinucleotides, the length is between 200-3000bp, and the G+C content exceeds 50%.
  • the CpG island region of DOK6 includes the Chr18:69400274-69401932 region, Chr18:69402698-69402935 region and Chr18: 69469672-69470012 region.
  • the above-mentioned target region is selected from the full-length region or partial region of at least one of the following regions of the DOK6 gene:
  • Area 1 Area 2, Area 3, Area 4, Area 5, Area 6, Area 7, Area 8, Area 9, Area 10, Area 11, Area 12, Area 13, Area 14, Area 15, Area 16, Area 17 , area 18, area 19 and area 20;
  • region 1 is selected from Chr18:69400290-69400480 positive chain
  • region 2 is selected from Chr18:69400531-69400649 positive chain
  • region 3 is selected from Chr18:69400739-69400893 positive chain
  • region 4 is selected from Chr18:69400997-69401110 positive chain
  • Region 5 is selected from Chr18:69401156-69401286 positive strand
  • region 6 is selected from Chr18:69401302-69401453 positive strand
  • region 7 is selected from Chr18:69401500-69401649 positive strand
  • region 8 is selected from Chr18:69401777-69401902 positive strand
  • region 9 Chr18:69402740-69402896 positive chain
  • region 10 selected from Chr18:69469693-69469908 positive chain
  • region 11 selected from Chr18:69401868-69401735 negative chain
  • region 12 selected from Chr18:69401755-69401590 negative chain
  • region 13 selected from Chr18:69401564-694
  • the above-mentioned target region is selected from the full-length region or partial region of at least one of the following regions of the DOK6 gene: region 2, region 4, region 9, region 13, region 14, region 18 and area 19.
  • Regions 1-8 are located on the positive strand of Chr18:69400274-69401932 of the region I, region 9 is located on the positive strand of Chr18:69402698-69402935 of the region II, and region 10 is located on the positive strand of Chr18:69469672-69470012 of the region III
  • region 11-18 is located on the negative strand of Chr18: 69401932-69400274 of the region I, region 19 is located on the negative strand of Chr18: 69402935-69402698 of the region II, and region 20 is located on the Chr18 of the region III: 69470012 -69469672 on the negative chain.
  • Region 2 is selected from Chr18:69400531-69400649 positive strand
  • region 4 is selected from Chr18:69400997-69401110 positive strand
  • region 9 is selected from Chr18:69402740-69402896 positive strand
  • region 13 is selected from Chr18:69401564-69401424 negative strand
  • region 14 Chr18:69401261-69401139 negative strand
  • region 18 is selected from Chrl8:69400577-69400468 negative strand
  • region 19 is selected from Chr18:69402905-69402736 negative strand.
  • the above diagnostic or auxiliary diagnostic reagents are used to detect Chr18:69400301, Chr18:69400306, Chr18:69400310, Chr18:69400338, Chr18:69400341, Chr18 on the positive strand of region 1 on the DOK6 gene Methylation of cytosine at least one position in Chr18:69400344, Chr18:69400348, Chr18:69400461 and Chr18:69400479.
  • the diagnostic or auxiliary diagnostic reagent is used to detect the methyl group of cytosine at least one position of Chr18:69400539, Chr18:69400545, Chr18:69400587, Chr18:69400601, Chr18:69400631 and Chr18:69400634 on the positive strand of region 2 on the DOK6 gene change.
  • the diagnostic or auxiliary diagnostic reagent is used to detect the methyl group of cytosine at least one position of Chr18:69400751, Chr18:69400753, Chr18:69400787, Chr18:69400874, Chr18:69400879 and Chr18:69400891 on the positive strand of region 3 of the DOK6 gene change.
  • the diagnostic or auxiliary diagnostic reagent is used to detect Chr18:69401159, Chr18:69401166, Chr18:69401168, Chr18:69401176, Chr18:69401196, Chr18:69401202, Chr18:69401209, Chr1826209, Chr18:694 on the positive strand of region 5 on the DOK6 gene Methylation of cytosine at least one position in Chr18:69401283;
  • the diagnostic or auxiliary diagnostic reagent is used to detect the methyl group of cytosine at least one position of Chr18:69401518, Chr18:69401545, Chr18:69401556, Chr18:69401560, Chr18:69401633 and Chr18:69401645 on the positive strand of region 7 on the DOK6 gene change;
  • Diagnostic or auxiliary diagnostic reagents are used to detect Chr18:69401780, Chr18:69401783, Chr18:69401785, Chr18:69401787, Chr18:69401796, Chr18:69401818, Chr18:69401821, Chr18:6940 on the positive strand of region 8 on the DOK6 gene Methylation of cytosine at least one position of Chr18:69401833 and Chr18:69401902;
  • the diagnostic or auxiliary diagnostic reagent is used to detect the methylation of cytosine at least one position of Chr18:69469702, Chr18:69469711, Chr18:69469740, Chr18:69469887 and Chr18:69469905 on the positive strand of region 10 of the DOK6 gene;
  • the diagnostic or auxiliary diagnostic reagent is used to detect at least one position of Chr18:69401754, Chr18:69401736, Chr18:69401705, Chr18:69401703, Chr18:69401699, Chr18:69401607 and Chr18:69401600 on the negative strand of DOK6 gene Methylation of pyrimidines;
  • the diagnostic or auxiliary diagnostic reagent is used to detect Chr18:69401238, Chr18:69401222, Chr18:69401217, Chr18:69401215, Chr18:69401210, Chr18:69401160, Chr18:69401150, Chr101464 and 69 on the region 14 negative strand of the DOK6 gene Methylation of cytosine at least one position in Chr18:69401143;
  • Diagnostic or auxiliary diagnostic reagents are used to detect Chr18:69401083, Chr18:69401071, Chr18:69401068, Chr18:69401042, Chr18:69401040, Chr18:69401035, Chr18:69401033, Chr100995, Chr18:69401035, Chr18:69401033, Chr18:64 on the negative strand of region 15 on the DOK6 gene Methylation of cytosine at least one position of Chr18:69400992, Chr18:69400990, and Chr18:69400981;
  • Diagnostic or auxiliary diagnostic reagents are used to detect Chr18:69400933, Chr18:69400927, Chr18:69400915, Chr18:69400898, Chr18:69400895, Chr18:69400892, Chr18:69400880, Chr18:69 on the negative strand of region 16 of the DOK6 gene Methylation of cytosine at least one position of Chr18:69400761, Chr18:69400754, and Chr18:69400752;
  • the diagnostic or auxiliary diagnostic reagent is used to detect at least one position of Chr18:69400559, Chr18:69400557, Chr18:69400546, Chr18:69400540, Chr18:69400486, Chr18:69400484 and Chr18:69400480 on the negative strand of DOK6 gene Methylation of pyrimidines;
  • the diagnostic or auxiliary diagnostic reagent is used to detect methylation of cytosine at least one position of Chr18:69469985, Chr18:69469971, Chr18:69469963, Chr18:69469947 and Chr18:69469888 on the negative strand of region 20 of the DOK6 gene.
  • the above reagents are selected from at least one of the following nucleic acid combinations:
  • nucleic acid combination 1 for detection area 1, nucleic acid combination 2 for detection area 2, nucleic acid combination 3 for detection area 3, nucleic acid combination 4 for detection area 4, nucleic acid combination 5 for detection area 5, Nucleic acid combination 6 for detection area 6, nucleic acid combination 7 for detection area 7, nucleic acid combination 8 for detection area 8, nucleic acid combination 9 for detection area 9, nucleic acid combination 10 for detection area 10, Nucleic acid combination 11 for detection area 11, nucleic acid combination 12 for detection area 12, nucleic acid combination 13 for detection area 13, nucleic acid combination 14 for detection area 14, nucleic acid combination 15 for detection area 15, The nucleic acid combination 16 for the detection area 16, the nucleic acid combination 17 for the detection area 17, the nucleic acid combination 18 for the detection area 18, the nucleic acid combination 19 for the detection area 19 and the nucleic acid combination 20 for the detection area 20;
  • the base sequence of nucleic acid combination 1 is shown in SEQ ID NO.1-3
  • the base sequence of nucleic acid combination 2 is shown in SEQ ID NO.4-6
  • the base sequence of nucleic acid combination 3 is shown in SEQ ID NO.7-
  • the base sequence of nucleic acid combination 4 is shown in SEQ ID NO.10-12
  • the base sequence of nucleic acid combination 5 is shown in SEQ ID NO.13-15
  • the base sequence of nucleic acid combination 6 is shown in SEQ ID As shown in NO.16-18
  • the base sequence of nucleic acid combination 7 is shown in SEQ ID NO.19-21
  • the base sequence of nucleic acid combination 8 is shown in SEQ ID NO.22-24
  • the base sequence of nucleic acid combination 9 The sequence is shown in SEQ ID NO.25-27
  • the base sequence of nucleic acid combination 10 is shown in SEQ ID NO.28-30
  • the base sequence of nucleic acid combination 11 is shown in SEQ ID NO.31-33
  • the base sequence of nucleic acid combination 18 is shown in SEQ ID NO.52-54
  • the base sequence of nucleic acid combination 19 is shown in SEQ ID NO.55-57
  • the base sequence of nucleic acid combination 20 is shown in Shown in SEQ ID NO.58-60.
  • the reagent is selected from at least one of the following nucleic acid combinations:
  • Nucleic acid combination 2 for detection zone 2 nucleic acid combination 4 for detection zone 4, nucleic acid combination 9 for detection zone 9, nucleic acid combination 13 for detection zone 13, nucleic acid combination 14 for detection zone 14, Nucleic acid combination 18 for detection zone 18 and nucleic acid combination 19 for detection zone 19 .
  • the above-mentioned diagnostic or auxiliary diagnostic products for colorectal cancer or precancerous lesions are selected from at least one of the following products: kits, chips, and sequencing libraries. It should be noted that the above-mentioned diagnostic or auxiliary diagnostic products for colorectal cancer or precancerous lesions can be in any form of in vitro diagnostic products, and are not limited to the above-mentioned product types of kits, chips and sequencing libraries, as long as they meet the requirements The diagnosis or auxiliary diagnosis of rectal cancer or precancerous lesions is within the protection scope of the present disclosure.
  • the present disclosure provides a nucleic acid combination for detecting the methylation level of the CpG island of the DOK6 gene.
  • the nucleic acid combination for detecting the CpG island of the DOK6 gene is selected from at least one of the following nucleic acid combinations: nucleic acid combination 1, nucleic acid combination 2, and nucleic acid combination 3 , nucleic acid combination 4, nucleic acid combination 5, nucleic acid combination 6, nucleic acid combination 7, nucleic acid combination 8, nucleic acid combination 9, nucleic acid combination 10, nucleic acid combination 11, nucleic acid combination 12, nucleic acid combination 13, nucleic acid combination 14, nucleic acid combination 15, nucleic acid combination Combination 16, nucleic acid combination 17, nucleic acid combination 18, nucleic acid combination 19 and nucleic acid combination 20;
  • the base sequence of nucleic acid combination 1 is shown in SEQ ID NO.1-3
  • the base sequence of nucleic acid combination 2 is shown in SEQ ID NO.4-6
  • the base sequence of nucleic acid combination 3 is shown in SEQ ID NO.7-
  • the base sequence of nucleic acid combination 4 is shown in SEQ ID NO.10-12
  • the base sequence of nucleic acid combination 5 is shown in SEQ ID NO.13-15
  • the base sequence of nucleic acid combination 6 is shown in SEQ ID As shown in NO.16-18
  • the base sequence of nucleic acid combination 7 is shown in SEQ ID NO.19-21
  • the base sequence of nucleic acid combination 8 is shown in SEQ ID NO.22-24
  • the base sequence of nucleic acid combination 9 The sequence is shown in SEQ ID NO.25-27
  • the base sequence of nucleic acid combination 10 is shown in SEQ ID NO.28-30
  • the base sequence of nucleic acid combination 11 is shown in SEQ ID NO.31-33
  • the base sequence of nucleic acid combination 18 is shown in SEQ ID NO.52-54
  • the base sequence of nucleic acid combination 19 is shown in SEQ ID NO.55-57
  • the base sequence of nucleic acid combination 20 is shown in Shown in SEQ ID NO.58-60.
  • nucleic acid combination has at least 85% (such as 85%, 86%, 87%, 88%, 89%, 90% of the base sequence shown in the above nucleic acid combination (nucleic acid combination 1-20) %, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%) or more sequence identity, and the nucleic acid combination also has certain colorectal cancer or precancerous
  • the diagnostic function of lesions is also within the protection scope of the present disclosure.
  • nucleic acid combinations 1-20 correspond to the detection of regions 1-20, respectively.
  • the present disclosure provides a detection reagent for the diagnosis or auxiliary diagnosis of colorectal cancer or precancerous lesions, which includes the above-mentioned nucleic acid combination for detecting the methylation level of the CpG island of DOK6 gene.
  • the above-mentioned detection reagent is a reagent for detecting the methylation state of the CpG island of the DOK6 gene
  • the detection means of the methylation state includes at least one of the following methods: methylation-specific PCR method , bisulfite sequencing, methylation-specific microarray, genome-wide methylation sequencing, pyrosequencing, methylation-specific high performance liquid chromatography, digital PCR, methylation-specific High-resolution melting curve method, methylation-sensitive restriction enzyme method, fluorescence quantification method and flap endonuclease method.
  • the precancerous lesion is a colorectal adenoma, such as tubular adenoma, villous adenoma, and villous tubular adenoma.
  • precancerous lesions also include adenomatosis, inflammatory bowel disease-associated dysplasia, traditional serrated adenoma, and broad-based serrated adenoma/polyp.
  • Precancerous lesions include, but are not limited to, other bowel diseases.
  • the present disclosure provides a detection kit for the diagnosis or auxiliary diagnosis of colorectal cancer or precancerous lesions, which includes the above-mentioned nucleic acid combination for detecting the methylation level of DOK6 gene CpG island or the above-mentioned colorectal cancer or precancerous lesions detection reagents for diagnosis or auxiliary diagnosis.
  • the detection sample of the above kit is a blood sample, a stool sample or a tissue sample.
  • the above detection kit further includes PCR buffer, water, amplification enzyme and other substances.
  • the present disclosure provides a method for diagnosing or assisting in diagnosing colorectal cancer or precancerous lesions in a subject, characterized in that the method includes
  • the region I is selected from the Chr18:69400274-69401932 positive chain or the Chr18:69401932-69400274 negative chain
  • the region II is selected from the Chr18:69402698-69402935 positive chain or the Chr18:69402935-69402698 negative chain
  • the region III selected from Chr18:69469672-69470012 plus strand or Chr18:69470012-69469672 minus strand;
  • the step b) includes comparing the assay results of the subject's sample with the methyl group of the target region on the DOK6 gene in the sample of a normal individual who does not suffer from colorectal cancer or precancerous lesions. Wherein the test result of the tester's sample is higher than the methylation level of the target region on the DOK6 gene in the sample of a normal individual who does not suffer from colorectal cancer or precancerous lesions indicates that the subject has Colorectal cancer or precancerous lesions.
  • the sample is a blood sample, a stool sample, or a tissue sample.
  • the detection in step a) of the method is selected from methylation-specific PCR, bisulfite sequencing, methylation-specific microarray, genome-wide methylation Methylation sequencing, pyrosequencing, methylation-specific high-performance liquid chromatography, digital PCR, methylation-specific high-resolution melting curve method, methylation-sensitive restriction endonuclease method, fluorescence Quantitative method and flap endonuclease method.
  • step a) the sample is assayed using the nucleic acid combination as defined in claim 6 .
  • the diagnostic or auxiliary diagnostic reagents, detection kits, and nucleic acid compositions for colorectal cancer or precancerous lesions use the methylation of the CpG island of the human DOK6 gene as a marker. Methylation levels were significantly higher in rectal cancer/precancer samples than in normal samples. Colorectal cancer or precancerous lesions can be diagnosed or assisted in diagnosis by detecting the increase in the methylation level of the CpG island of the DOK6 gene in the sample, which has high sensitivity and specificity.
  • the detection reagent and kit provided by the present disclosure can effectively improve the detection rate of colorectal cancer/precancerous lesions, thereby meeting the clinical needs of early screening and early diagnosis of colorectal cancer/precancerous lesions.
  • the genetic testing products provided by this disclosure can also provide better intestinal health assessment services for the physical examination population, realize early detection, early diagnosis, and early treatment of intestinal lesions, and help save the family's medical burden costs.
  • positive strand refers to the strand carrying the nucleotide sequence encoding the amino acid information of the protein in the DNA double strand of the gene, also known as the coding strand and the sense strand.
  • the nucleotides of the positive strand are identical to the nucleotide sequence of the mRNA.
  • minus strand refers to the single strand that serves as a template for mRNA synthesis during transcription among the DNA double strands of a gene, also referred to as the template strand or the antisense strand.
  • diagnosis refers to a medical judgment about a person's mental and physical state. Specifically, a process of determining which disease or condition could explain a subject's symptoms and signs. For example, the presence of rectal cancer or adenoma is determined by using the kits or nucleotide sets described herein.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes a nucleotide combination 1, and the nucleic acid combination 1 includes the nucleotides shown in SEQ ID NO.1-3.
  • the nucleotide combination 1 can detect the methylation of the positive strand of Chr18:69400290-69400480 (region 1) on the DOK6 gene;
  • the positive strand base sequence (5'-3') of region 1 is as follows:
  • the nucleotides shown in SEQ ID NO.1-3 can detect Chr18:69400301, Chr18:69400306, Chr18:69400310, Chr18:69400338, Chr18:69400341, Chr18:69400344, Chr18:69400348, Chr18 on the positive strand of this region Methylation of cytosine at positions Chr18:69400461 and Chr18:69400479.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes a nucleotide combination 2, and the nucleic acid combination 2 includes the nucleotides shown in SEQ ID NO.4-6.
  • the nucleotide combination 2 can detect the methylation of the positive strand of Chr18:69400531-69400649 (region 2) on the DOK6 gene;
  • the positive strand base sequence (5'-3') of region 2 is as follows:
  • the nucleotides shown in SEQ ID NO.4-6 can detect the formazan of cytosine located at Chr18:69400539, Chr18:69400545, Chr18:69400587, Chr18:69400601, Chr18:69400631 and Chr18:69400634 on the positive strand of this region Basicization.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes a nucleotide combination 3, and the nucleic acid combination 3 includes the nucleotides shown in SEQ ID NO.7-9.
  • the nucleotide combination 3 can detect the methylation of the positive strand of Chr18:69400739-69400893 (region 3) on the DOK6 gene;
  • the positive strand base sequence (5'-3') of region 3 is as follows:
  • the nucleotides shown in SEQ ID NO.7-9 can detect the formazan of cytosine located at Chr18:69400751, Chr18:69400753, Chr18:69400787, Chr18:69400874, Chr18:69400879 and Chr18:69400891 on the positive strand of this region Basicization.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 4, and nucleic acid combination 4 includes the nucleotides shown in SEQ ID NO.10-12.
  • the nucleotide combination 4 can detect the methylation of the positive strand of Chr18:69400997-69401110 (region 4) on the DOK6 gene;
  • the positive strand base sequence (5'-3') of region 4 is as follows:
  • the nucleotides shown in SEQ ID NO.10-12 can detect Chr18:69401001, Chr18:69401011, Chr18:69401047, Chr18:69401054, Chr18:69401061, Chr18:69401099, Chr18:69401102 and Chr18 on the positive strand of this region : Methylation of cytosine at position 69401110.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 5, and nucleic acid combination 5 includes the nucleotides shown in SEQ ID NO.13-15.
  • the nucleotide combination 5 can detect the methylation of the positive strand of Chr18:69401156-69401286 (region 5) on the DOK6 gene;
  • the nucleotides shown in SEQ ID NO.13-15 can detect Chr18:69401159, Chr18:69401166, Chr18:69401168, Chr18:69401176, Chr18:69401196, Chr18:69401202, Chr18:69401209, Chr18 on the positive strand of this region Methylation of cytosine at positions Chr18:69401262 and Chr18:69401283.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 6, and nucleic acid combination 6 includes the nucleotides shown in SEQ ID NO.16-18.
  • the nucleotide combination 6 can detect the methylation of the negative strand of Chr18:69401302-69401453 (region 6) on the DOK6 gene;
  • the nucleotides shown in SEQ ID NO.16-18 can detect Chr18:69401321, Chr18:69401341, Chr18:69401344, Chr18:69401348, Chr18:69401352, Chr18:69401357, Chr18:69401433 and Chr18 on the positive strand of this region : Methylation of cytosine at position 69401442.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 7, and nucleic acid combination 7 includes the nucleotides shown in SEQ ID NO.19-21.
  • the nucleotide combination 7 can detect the methylation of the positive strand of Chr18:69401500-69401649 (region 7) on the DOK6 gene;
  • the nucleotides shown in SEQ ID NO.19-21 can detect the alpha of cytosine located at Chr18:69401518, Chr18:69401545, Chr18:69401556, Chr18:69401560, Chr18:69401633 and Chr18:69401645 on the positive strand of this region Basicization.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 8, and nucleic acid combination 8 includes the nucleotides shown in SEQ ID NO.22-24.
  • the nucleotide combination 8 can detect the methylation of the positive strand of Chr18:69401777-69401902 (region 8) on the DOK6 gene;
  • the nucleotides shown in SEQ ID NO.22-24 can detect Chr18:69401780, Chr18:69401783, Chr18:69401785, Chr18:69401787, Chr18:69401796, Chr18:69401818, Chr18:69401821, Chr18 on the positive strand of this region Methylation of cytosine at Chr18:69401827, Chr18:69401833 and Chr18:69401902.
  • Example 9 This example provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 9, and nucleic acid combination 13 includes nucleotides shown in SEQ ID NO.25-27.
  • the nucleotide combination 9 can detect the methylation of the positive strand of Chr18:69402740-69402896 (region 9) on the DOK6 gene;
  • the nucleotides shown in SEQ ID NO.25-27 can detect Chr18:69402751, Chr18:69402755, Chr18:69402761, Chr18:69402778, Chr18:69402792, Chr18:69402876, Chr18:69402884 and Chr18 on the positive strand of this region : Methylation of cytosine at position 69402896.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes a nucleotide combination 10, and the nucleic acid combination 10 includes the nucleotides shown in SEQ ID NO.28-30.
  • the nucleotide combination 10 can detect the methylation of the positive strand of Chr18:69469693-69469908 (region 10) on the DOK6 gene;
  • the positive strand base sequence of the region 10 is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.28-30 can detect the methylation of cytosine at Chr18:69469702, Chr18:69469711, Chr18:69469740, Chr18:69469887 and Chr18:69469905 on the positive strand of this region.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 11, and nucleic acid combination 11 includes the nucleotides shown in SEQ ID NO.31-33.
  • the nucleotide combination 11 can detect the methylation of the negative strand of Chr18:69401868-69401735 (region 11) on the DOK6 gene;
  • the nucleotides shown in SEQ ID NO.31-33 can detect Chr18:69401866, Chr18:69401848, Chr18:69401828, Chr18:69401822, Chr18:69401819, Chr18:69401813, Chr18:69401754 and Chr18 on the negative strand of this region Methylation of cytosine at position :69401736.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 12, and nucleic acid combination 12 includes the nucleotides shown in SEQ ID NO.34-36.
  • the nucleotide combination 12 can detect the methylation of the negative strand of Chr18:69401755-69401590 (region 12) on the DOK6 gene;
  • the base sequence of the 12 negative strands in the region is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.34-36 can detectably be located on the Chr18:69401754, Chr18:69401736, Chr18:69401705, Chr18:69401703, Chr18:69401699, Chr18:69401607 and Chr18:69401600 positions on the negative strand of this region Methylation of cytosine.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 13, and nucleic acid combination 13 includes the nucleotides shown in SEQ ID NO.37-39.
  • the nucleotide combination 13 can detect the methylation of the negative strand of Chr18:69401564-69401424 (region 13) on the DOK6 gene;
  • the negative strand base sequence of region 13 is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.37-39 can detect Chr18:6940562, Chr18:6940558, Chr18:6940554, Chr18:6940543, Chr18:6940534, Chr18:6940516, Chr18:6940443 and Chr18 on the negative strand of this region : Methylation of cytosine at position 6940434.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 14, and nucleic acid combination 14 includes the nucleotides shown in SEQ ID NO.40-42.
  • the nucleotide combination 14 can detect the methylation of the negative strand of Chr18:69401261-69401139 (region 14) on the DOK6 gene;
  • the negative strand base sequence of region 14 is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.40-42 can detect Chr18:69401238, Chr18:69401222, Chr18:69401217, Chr18:69401215, Chr18:69401210, Chr18:69401160, Chr18:69401150, Chr18 on the negative strand of this region Methylation of cytosine at positions :69401146 and Chr18:69401143.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 15, and nucleic acid combination 15 includes the nucleotides shown in SEQ ID NO.43-45.
  • the nucleotide combination 15 can detect the methylation of the negative strand of Chr18:69401085-69400981 (region 15) on the DOK6 gene;
  • the base sequence of 15 negative strands in the region is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.43-45 can detect Chr18:69401083, Chr18:69401071, Chr18:69401068, Chr18:69401042, Chr18:69401040, Chr18:69401035, Chr18:69401033, Chr18 on the negative strand of this region Methylation of cytosine at Chr18:69400995, Chr18:69400992, Chr18:69400990 and Chr18:69400981.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 16, and nucleic acid combination 16 includes the nucleotides shown in SEQ ID NO.46-48.
  • the nucleotide combination 16 can detect the methylation of the negative strand of Chr18:69400934-69400749 (region 16) on the DOK6 gene;
  • the negative strand base sequence of region 16 is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.46-48 can detect Chr18:69400933, Chr18:69400927, Chr18:69400915, Chr18:69400898, Chr18:69400895, Chr18:69400892, Chr18:69400880, Chr18 on the negative strand of this region Methylation of cytosine at Chr18:69400765, Chr18:69400761, Chr18:69400754 and Chr18:69400752.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 17, and nucleic acid combination 17 includes the nucleotides shown in SEQ ID NO.49-51.
  • the nucleotide combination 17 can detect the methylation of the negative strand of Chr18:69400729-69400630 (region 17) on the DOK6 gene;
  • the negative strand base sequence of region 17 is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.49-51 can detect Chr18:69400723, Chr18:69400717, Chr18:69400714, Chr18:69400711, Chr18:69400676, Chr18:69400665, Chr18:69400658, Chr18 on the negative strand of this region Methylation of cytosine at positions :69400635 and Chr18:69400632.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 18, and nucleic acid combination 18 includes the nucleotides shown in SEQ ID NO.52-54.
  • the nucleotide combination 18 can detect the methylation of the negative strand of Chr18:69400577-69400468 (region 18) on the DOK6 gene;
  • the base sequence of the 18 negative strands in the region is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.52-54 can detectably be located on the Chr18:69400559, Chr18:69400557, Chr18:69400546, Chr18:69400540, Chr18:69400486, Chr18:69400484 and Chr18:69400480 positions on the negative strand of this region Methylation of cytosine.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes nucleotide combination 19, and nucleic acid combination 19 includes the nucleotides shown in SEQ ID NO.55-57.
  • the nucleotide combination 19 can detect the methylation of the negative strand of Chr18:69402905-69402736 (region 19) on the DOK6 gene;
  • the negative strand base sequence of region 19 is as follows (5'-3'):
  • Nucleotides shown in SEQ ID NO.55-57 can detect the alpha of cytosine located at Chr18:69402897, Chr18:69402885, Chr18:69402810, Chr18:69402793, Chr18:69402756 and Chr18:69402752 on the negative strand of this region Basicization.
  • This embodiment provides a kit for the diagnosis or auxiliary diagnosis of colorectal cancer or adenoma, which includes a nucleotide combination 20, and the nucleic acid combination 20 includes the nucleotides shown in SEQ ID NO.58-60.
  • the nucleotide combination 20 can detect the methylation of the negative strand of Chr18:69469992-69469868 (region 20) on the DOK6 gene;
  • the negative strand base sequence of the region 20 is as follows (5'-3'):
  • the nucleotides shown in SEQ ID NO.58-60 can detect the methylation of cytosine at Chr18:69469985, Chr18:69469971, Chr18:69469963, Chr18:69469947 and Chr18:69469888 on the negative strand of the region.
  • This embodiment provides a method for diagnosing colorectal cancer or adenoma carcinoma using any one of the kits in embodiments 1-20, which includes the following steps:
  • the stools of patients with colorectal cancer, patients with colorectal adenoma and normal people were collected by Zhongnan Hospital of Wuhan University, and all patients signed informed consent, and each sample was anonymized.
  • the sample used is a feces sample
  • the human DOK6 gene in the feces is extracted using a nucleic acid extraction kit from Wuhan Amison Life Science and Technology Co., Ltd. (Ehan Jibei No. 20200225).
  • the capture probe is labeled with biotin, and the positive-strand region and the negative-strand region are captured and extracted separately, that is, the positive-strand capture probe is added when the positive-strand genome is extracted, and the negative-strand capture probe is added when the negative-strand region is extracted.
  • the samples used were blood samples, and plasma cfDNA was extracted using Tiangen Biochemical Technology (Beijing) Co., Ltd. Magnetic Bead Serum/Plasma Free DNA Extraction Kit (DP709).
  • DP709 Magnetic Bead Serum/Plasma Free DNA Extraction Kit
  • the genome extracted in the above step 1 was subjected to bisulfite conversion.
  • the nucleic acid conversion kit used was the nucleic acid purification reagent of Wuhan Aimison Life Science and Technology Co., Ltd. (Ehan Jibei 20500843). For specific experimental operations, please refer to the kit manual.
  • the methylation-specific PCR reaction was performed on the bisulfite-converted DNA to detect the methylation status of regions 1-20 of the DOK6 gene. Each region was tested separately, that is, only one region was added to a PCR tube at a time. Detect primers and probes, and add detection probes for internal reference genes at the same time. Using ACTB as an internal reference gene, the PCR reaction system is shown in Table 3.
  • ACTB is used as an internal reference gene, wherein the upstream primer of ACTB is: AAGGTGGTTGGGTGGTTGTTTTG (SEQ ID NO.75); the downstream primer of ACTB is: AATAACACCCCCACCCCTGC (SEQ ID NO.76); the probe of ACTB is: GGAGTGGTTTTTGGGTTTG (SEQ ID NO.77).
  • the reporter group at the 5' end of the probe for detecting the target region is FAM
  • the quencher group at the 3' end is MGB
  • the reporter group at the 5' end of the ACTB probe is VIC
  • the quencher group at the 3' end is BHQ1.
  • the added DNA of the sample to be tested is the positive strand DNA extracted by the aforementioned capture and converted by bisulfite; when the detection area is 11-20, the added DNA of the sample to be tested is the aforementioned The extracted negative-strand DNA is captured and converted by bisulfite; for blood samples, when the detection area is 1-20, the DNA of the sample to be tested added is converted from the extracted cfDNA.
  • Ct value reading After PCR is completed, adjust the baseline, set the fluorescence value before the minimum Ct value of the sample in one PCR 1-2 cycles earlier as the baseline value, set the threshold at the inflection point of the S-type amplification curve, and obtain the sample Ct values of individual genes.
  • the negative control was purified water.
  • the preparation method of the positive control is: artificially synthesizing the bisulfite-converted sequence corresponding to the amplified region of ACTB, and cloning it into a vector to form an artificially synthesized plasmid.
  • the bisulfite-converted sequences corresponding to fully methylated regions 1-20 were artificially synthesized and cloned into an artificially synthesized plasmid.
  • the positive control of area 1-20 is a 1:1 mixture of 10 3 copies/ ⁇ l of the artificially synthesized plasmid ACTB and 10 3 copies/ ⁇ l of the artificially synthesized plasmid of area 1-20, such as the positive control of area 1 is 10 3 copies/ ⁇ l of ACTB artificially synthesized plasmid and 10 3 copies/ ⁇ l of region 1 artificially synthesized plasmid were mixed 1:1.
  • the negative control should have no amplification, the Ct value of the positive control should be between 26-30, and the Ct value of the internal reference gene of the sample to be tested should be ⁇ 35. After the negative control, positive control and internal reference gene all meet the above requirements, it indicates that this experiment If it is valid, the next sample result can be judged. Otherwise, the test is invalid and must be tested again.
  • Result analysis and interpretation method If the Ct value of a certain detection area on the sample is ⁇ 38.5, the sample is considered to be methylation-positive in this detection area; if the Ct value of a certain detection area on the sample is >38.5, then The sample was considered negative for methylation in this region of detection.
  • the methylation detection results of the samples were compared with the pathological results to calculate the sensitivity and specificity of the methylation detection. Sensitivity is the proportion of methylation-positive samples with pathologically positive results, and specificity is the proportion of methylation-negative samples with pathologically negative results.
  • This embodiment provides a diagnostic or auxiliary diagnostic reagent for colorectal cancer or precancerous lesions, which includes nucleic acid combination 3 for detection region 3 (same as in Example 3) and nucleic acid combination 4 for detection region 4 (same as Example 4).
  • This embodiment provides a diagnostic or auxiliary diagnostic reagent for colorectal cancer or precancerous lesions, which includes the nucleic acid combination 9 for the detection area 9 (same as in Example 9), and the nucleic acid combination 14 for the detection area 14 (same as Example 14).
  • This embodiment provides a diagnostic or auxiliary diagnostic reagent for colorectal cancer or precancerous lesions, which includes a nucleic acid combination 13 (same as in Example 13) for the detection region 13, and a nucleic acid combination 18 for the detection region 18 (same as Example 18) and the nucleic acid combination 19 for the detection region 19 (same as Example 19).
  • the calculation method of colorectal adenoma sensitivity is the number of detected colorectal adenoma PCR positives divided by the summed number of rectal adenoma cases
  • the calculation method of colorectal cancer sensitivity is the detection of colorectal cancer PCR positive number divided by The number of rectal cancer cases was summed; specificity was calculated as the number of PCR negatives detected divided by the number of normal samples without disease.
  • regions 1-20 can better distinguish colorectal adenoma samples, colorectal cancer samples and normal samples, but the detection effects of each region are slightly different. , the detection sensitivity of regions 1-20 to colorectal adenoma is greater than 40%, the detection sensitivity to colorectal cancer samples is greater than 80%, and the specificity is greater than 80%.
  • region 2 region 4, region 9, region 13, region 14, region 18, and region 19 were significantly better than those of other regions, and in stool samples, the methylation levels of these regions were detected to increase
  • the detection sensitivities to colorectal adenomas are all over 60%, the detection sensitivities to colorectal cancer are all over 90%, and the specificities are all over 90%.
  • Plasma samples from patients with colorectal cancer, adenoma patients and healthy people diagnosed by colonoscopy and tissue biopsy were collected in Zhongnan Hospital of Wuhan University. Each person collected 5 mL. A total of 108 cases of colorectal cancer plasma samples and colorectal adenoma plasma samples were collected. There were 130 samples and 90 normal plasma samples. According to the method provided in Example 10, plasma DNA extraction and bisulfite conversion were carried out, and the specific primers and probe combinations based on 20 regions for DOK6 in Examples 1-9 were selected for PCR detection. The PCR detection results are shown in Table 6. shown.
  • region 2 region 4, region 9, region 13, region 14, region 18, and region 9 were significantly better than those of other regions, and in plasma samples, the increased methylation levels of these regions were detected
  • the detection sensitivities to colorectal adenomas are all over 60%
  • the detection sensitivities to colorectal cancer are all over 90%
  • the specificities are all over 90%.
  • the diagnostic or auxiliary diagnostic reagents, detection kits, and nucleic acid compositions for colorectal cancer or precancerous lesions use the methylation of the CpG island of the human DOK6 gene as a marker. Methylation levels were significantly higher in rectal cancer/precancer samples than in normal samples. Colorectal cancer or precancerous lesions can be diagnosed or assisted in diagnosis by detecting the increase in the methylation level of the CpG island of the DOK6 gene in the sample, which has high sensitivity and specificity.
  • the detection reagent and kit provided by the present disclosure can effectively improve the detection rate of colorectal cancer/precancerous lesions, thereby meeting the clinical needs of early screening and early diagnosis of colorectal cancer/precancerous lesions.
  • the genetic detection products provided by the present disclosure can also provide better intestinal health assessment services for the physical examination population, realize early detection, early diagnosis, and early treatment of intestinal lesions, and help save the family's medical burden costs.

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Abstract

提供了一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用，涉及肿瘤检测技术领域。以人DOK6基因CpG岛的甲基化作为标志物，通过检测样本中DOK6基因的CpG岛的甲基化水平的增加可以对结直肠癌或癌前病变进行诊断或辅助诊断，具有较高的灵敏度和特异性。采用提供的检测试剂和试剂盒能有效地提高结直肠癌的检出率，从而满足结直肠癌／癌前病变早筛早诊的临床需求。提供的基因检测产品也可以为体检人群提供更好的肠道健康评估服务，实现对肠道病变的早发现、早诊断、早治疗，有利于节约家庭的医疗负担成本。

Description

一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用
相关申请的交叉引用
本申请要求于2021年6月30日提交中国专利局的申请号为2021107329471、名称为“一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用”的中国专利申请的优先权，其全部内容通过引用结合在本申请中。
技术领域
本公开涉及肿瘤检测技术领域，具体而言，涉及一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用。
背景技术
结直肠癌是我国常见的恶性肿瘤之一，主要包括结肠癌与直肠癌两大类。结直肠癌的预后与疾病诊断时的严重程度相关，美国结直肠癌患者5年生存率为67％。2004年至2013年，美国结直肠癌的发病率每年下降3％，整体死亡率平均每年下降2.7％，早期筛查在其中的贡献率超过50％。由于结直肠癌在早期缺少症状，目前结直肠癌的早期诊断率仅为10％左右，超过80％患者确诊时已到中晚期。
因此，提高腺瘤的检出率对于降低结直肠癌的发病率和死亡率极为重要。而结直肠癌传统的筛查方法包括粪便潜血试验、粪便免疫试验、结肠钡剂灌肠检查、乙状结肠镜检查以及结肠镜检查。其中，粪便潜血试验和粪便免疫试验具有一定的特异性和灵敏性，但前提是患者已存在明显的肿瘤大小，因此不适用于结直肠癌的早期检测。内窥镜检查虽然提高了高危人群中结直肠癌的检出率，但患者接受度低、且操作不够灵活。
近期分子生物学方面的进展为开发简便、有效的早期诊断方法提供了新的方向，结直肠癌组织中存在多基因、多位点的甲基化，并且在结直肠癌发生的早期即出现DNA甲基化的改变，因此，甲基化改变可以作为食管癌早期诊断的标志物，从DNA甲基化角度探索结直肠癌诊断策略已成为一种新的思路。
结直肠肿瘤一般发生在结直肠上皮组织中，在其生长过程中，不断地有肿瘤细胞脱落至肠腔内并随着粪便排出。肿瘤细胞由于增生异常更容易从肠道脱落，因此肠道肿瘤患者的粪便中包含有大量的病变细胞和病变成分，检测粪便中的肿瘤细胞成分就可以提供一种无创的辅助诊断结直肠肿瘤方法。另外，肿瘤细胞也会释放DNA到血液中(cfDNA,circulating free DNA)，因此，也可通过检测血液中的肿瘤DNA对结直肠癌进行检测。但cfDNA具有含量少、半衰期短的特点，使其在提取过程中容易丢失，因此检测难度巨大。
现有技术中公开的一些检测标记物对结直肠癌具有良好的检测效果，但对结直肠癌前病变的检测灵敏性和特异性较差。另外，目前尚缺少在粪便和血液中均具有优异检测效果的标记物。
发明内容
本公开提供一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用以解决上述技术问题。
本公开提供了一种结直肠癌或癌前病变的诊断或辅助诊断试剂在制备结直肠癌或癌前病变的诊断或辅助诊断产品中的应用，诊断或辅助诊断试剂为用于检测DOK6基因上的靶区域的甲基化的试剂，靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：区域I、区域II和区域III；
其中，区域I选自Chr18:69400274-69401932正链或Chr18:69401932-69400274负链，区域II选自 Chr18:69402698-69402935正链或Chr18:69402935-69402698负链，区域III选自Chr18：69469672-69470012正链或Chr18：69470012-69469672负链。
以GRCh38.p13为参考基因组，DOK6基因位于人18号染色体的负义链上，具体位置为69400888-69849087bp。需要说明的是，本公开所提到的位点或区域的位置均是以GRCh38.p13为参考。
DOK6基因编码停泊蛋白6(Docking Protein 6,DOK6)，现有的研究表明DOK6蛋白与NS1蛋白(流感病毒非结构蛋白1)存在相互作用，NS1能够与DOK6蛋白的PTB结构域发生相互作用。DOK6属于Dok家族，该家族包括DOK1、DOK2、DOK3、DOK4、DOK5、DOK6和DOK7，其中DOK1、DOK2、DOK3为第一大类，主要分布在血液系统组织和细胞中，而且均为负调控因子，而其他的四个成员为第二大类，主要分布在非血液系统组织和细胞中。其中，在2004年由Crowder R.J.等人克隆了人的dok6基因，并证明其参与c-Ret信号通路，促进GDNF诱导的Neuro2A细胞的突起生长，之后有研究人员证明了DOK6作为TrkC受体的底物，参与了NT-3介导的原代培养的小鼠大脑皮层神经元的神经突起生长过程(李玮琪，北京协和医学院基础学院)。需要说明的是，本公开中的靶区域包括不限于DOK6基因的启动子区、编码区、非编码区和调控区。
而发明人发现，以DOK6基因作为标志物，通过检测其CpG岛区域(即靶区域)甲基化水平的增加可以对结直肠癌或其腺瘤进行诊断或辅助诊断，具有较高的灵敏度和特异性，有助于提高结直肠癌或其腺瘤的检出率。
CpG岛是富含CpG二核苷酸的区域，长度在200-3000bp之间，G+C的含量超过50％，DOK6的CpG岛区域包括Chr18:69400274-69401932区域、Chr18:69402698-69402935区域和Chr18：69469672-69470012区域。
在本公开应用较佳的实施方式中，上述靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：
区域1、区域2、区域3、区域4、区域5、区域6、区域7、区域8、区域9、区域10、区域11、区域12、区域13、区域14、区域15、区域16、区域17、区域18、区域19和区域20；
其中，区域1选自Chr18：69400290-69400480正链，区域2选自Chr18:69400531-69400649正链，区域3选自Chr18:69400739-69400893正链，区域4选自Chr18:69400997-69401110正链，区域5选自Chr18:69401156-69401286正链，区域6选自Chr18:69401302-69401453正链，区域7选自Chr18:69401500-69401649正链，区域8选自Chr18:69401777-69401902正链，区域9选自Chr18:69402740-69402896正链，区域10选自Chr18:69469693-69469908正链，区域11选自Chr18:69401868-69401735负链，区域12选自Chr18:69401755-69401590负链，区域13选自Chr18:69401564-69401424负链，区域14选自Chr18:69401261-69401139负链，区域15选自Chr18:69401085-69400981负链，区域16选自Chr18:69400934-69400749负链，区域17选自Chr18:69400729-69400630负链，区域18选自Chr18:69400577-69400468负链，区域19选自Chr18:69402905-69402736负链，区域20选自Chr18:69469992-69469868负链。
在本公开应用较佳的实施方式中，上述靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：区域2、区域4、区域9、区域13、区域14、区域18和区域19。
区域1-8位于所述区域I的Chr18:69400274-69401932正链上，区域9位于所述区域II的Chr18:69402698-69402935正链上，区域10位于所述区域III的Chr18：69469672-69470012正链上，区域11-18位于所述区域I的Chr18:69401932-69400274负链上，区域19位于所述区域II的Chr18: 69402935-69402698负链上，区域20位于所述区域III的Chr18：69470012-69469672负链上。
发明人发现：区域1-20均能对结直肠腺瘤样本、结直肠癌症样本和正常样本实现较好区分。其中，区域2、区域4、区域9、区域13、区域14、区域18和区域19的检测灵敏度和特异性均显著优于其他区域，在粪便样本和血浆样本中，检测这几个区域的甲基化水平的增加对结直肠腺瘤的检测灵敏度均超过60％，对结直肠癌的检测灵敏度均超过90％，特异性均大于90％。
区域2选自Chr18:69400531-69400649正链，区域4选自Chr18:69400997-69401110正链，区域9选自Chr18:69402740-69402896正链，区域13选自Chr18:69401564-69401424负链，区域14选自Chr18:69401261-69401139负链，区域18选自Chr18:69400577-69400468负链，区域19选自Chr18:69402905-69402736负链。
在一种或多种实施方式中，上述诊断或辅助诊断试剂用于检测DOK6基因上的区域1正链上的Chr18:69400301、Chr18:69400306、Chr18:69400310、Chr18:69400338、Chr18:69400341、Chr18:69400344、Chr18:69400348、Chr18:69400461和Chr18:69400479至少一个位置上胞嘧啶的甲基化。
诊断或辅助诊断试剂用于检测DOK6基因上的区域2正链上的Chr18:69400539、Chr18:69400545、Chr18:69400587、Chr18:69400601、Chr18:69400631和Chr18:69400634至少一个位置上胞嘧啶的甲基化。
诊断或辅助诊断试剂用于检测DOK6基因上的区域3正链上的Chr18:69400751、Chr18:69400753、Chr18:69400787、Chr18:69400874、Chr18:69400879和Chr18:69400891至少一个位置上胞嘧啶的甲基化。
诊断或辅助诊断试剂用于检测DOK6基因上的区域4正链上的Chr18:69401001、Chr18:69401011、Chr18:69401047、Chr18:69401054、Chr18:69401061、Chr18:69401099、Chr18:69401102和Chr18:69401110至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域5正链上的Chr18:69401159、Chr18:69401166、Chr18:69401168、Chr18:69401176、Chr18:69401196、Chr18:69401202、Chr18:69401209、Chr18:69401262和Chr18:69401283至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域6正链上的Chr18:69401321、Chr18:69401341、Chr18:69401344、Chr18:69401348、Chr18:69401352、Chr18:69401357、Chr18:69401433和Chr18:69401442至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域7正链上的Chr18:69401518、Chr18:69401545、Chr18:69401556、Chr18:69401560、Chr18:69401633和Chr18:69401645至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域8正链上的Chr18:69401780、Chr18:69401783、Chr18:69401785、Chr18:69401787、Chr18:69401796、Chr18:69401818、Chr18:69401821、Chr18:69401827、Chr18:69401833和Chr18:69401902至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域9正链上的Chr18:69402751、Chr18:69402755、Chr18:69402761、Chr18:69402778、Chr18:69402792、Chr18:69402876、Chr18:69402884和Chr18:69402896至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域10正链上的Chr18:69469702、Chr18:69469711、Chr18:69469740、Chr18:69469887和Chr18:69469905至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域11负链上的Chr18:69401866、Chr18:69401848、Chr18:69401828、Chr18:69401822、Chr18:69401819、Chr18:69401813、Chr18:69401754和Chr18:69401736至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域12负链上的Chr18:69401754、Chr18:69401736、Chr18:69401705、Chr18:69401703、Chr18:69401699、Chr18:69401607和Chr18:69401600至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域13负链上的Chr18:6940562、Chr18:6940558、Chr18:6940554、Chr18:6940543、Chr18:6940534、Chr18:6940516、Chr18:6940443和Chr18:6940434至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域14负链上的Chr18:69401238、Chr18:69401222、Chr18:69401217、Chr18:69401215、Chr18:69401210、Chr18:69401160、Chr18:69401150、Chr18:69401146和Chr18:69401143至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域15负链上的Chr18:69401083、Chr18:69401071、Chr18:69401068、Chr18:69401042、Chr18:69401040、Chr18:69401035、Chr18:69401033、Chr18:69400995、Chr18:69400992、Chr18:69400990和Chr18:69400981至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域16负链上的Chr18:69400933、Chr18:69400927、Chr18:69400915、Chr18:69400898、Chr18:69400895、Chr18:69400892、Chr18:69400880、Chr18:69400765、Chr18:69400761、Chr18:69400754和Chr18:69400752至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域17负链上的Chr18:69400723、Chr18:69400717、Chr18:69400714、Chr18:69400711、Chr18:69400676、Chr18:69400665、Chr18:69400658、Chr18:69400635和Chr18:69400632至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域18负链上的Chr18:69400559、Chr18:69400557、Chr18:69400546、Chr18:69400540、Chr18:69400486、Chr18:69400484和Chr18:69400480至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域19负链上的Chr18:69402897、Chr18:69402885、Chr18:69402810、Chr18:69402793、Chr18:69402756和Chr18:69402752至少一个位置上胞嘧啶的甲基化；
诊断或辅助诊断试剂用于检测DOK6基因上的区域20负链上的Chr18:69469985、Chr18:69469971、Chr18:69469963、Chr18:69469947和Chr18:69469888至少一个位置上胞嘧啶的甲基化。
在一种或多种实施方式中，上述试剂选自如下核酸组合中的至少一种：
用于检测区域1的核酸组合1、用于检测区域2的核酸组合2、用于检测区域3的核酸组合3、用于检测区域4的核酸组合4、用于检测区域5的核酸组合5、用于检测区域6的核酸组合6、用于检测区域7的核酸组合7、用于检测区域8的核酸组合8、用于检测区域9的核酸组合9、用于检测区域10的核酸组合10、用于检测区域11的核酸组合11、用于检测区域12的核酸组合12、用于检测区域13的核酸组合13、用于检测区域14的核酸组合14、用于检测区域15的核酸组合15、用于检测区域16的核酸组合16、用于检测区域17的核酸组合17、用于检测区域18的核酸组合18、用于检测区域19的核酸组合19和用于检测区域20的核酸组合20；
核酸组合1的碱基序列如SEQ ID NO.1-3所示，核酸组合2的碱基序列如SEQ ID NO.4-6所示，核酸组合3的碱基序列如SEQ ID NO.7-9所示，核酸组合4的碱基序列如SEQ ID NO.10-12所示，核酸组合5的碱基序列如SEQ ID NO.13-15所示，核酸组合6的碱基序列如SEQ ID NO.16-18所示，核酸组合7的碱基序列如SEQ ID NO.19-21所示，核酸组合8的碱基序列如SEQ ID NO.22-24所示，核酸组合9的碱基序列如SEQ ID NO.25-27所示，核酸组合10的碱基序列如SEQ ID NO.28-30所示，核酸组合11 的碱基序列如SEQ ID NO.31-33所示，核酸组合12的碱基序列如SEQ ID NO.34-36所示，核酸组合13的碱基序列如SEQ ID NO.37-39所示，核酸组合14的碱基序列如SEQ ID NO.40-42所示，核酸组合15的碱基序列如SEQ ID NO.43-45所示，核酸组合16的碱基序列如SEQ ID NO.46-48所示，核酸组合17的碱基序列如SEQ ID NO.49-51所示，核酸组合18的碱基序列如SEQ ID NO.52-54所示，核酸组合19的碱基序列如SEQ ID NO.55-57所示，核酸组合20的碱基序列如SEQ ID NO.58-60所示。
在一种或多种实施方式中，试剂选自如下核酸组合中的至少一种：
用于检测区域2的核酸组合2、用于检测区域4的核酸组合4、用于检测区域9的核酸组合9、用于检测区域13的核酸组合13、用于检测区域14的核酸组合14、用于检测区域18的核酸组合18和用于检测区域19的核酸组合19。
在一种或多种实施方式中，上述结直肠癌或癌前病变的诊断或辅助诊断产品选自如下产品中的至少一种：试剂盒、芯片和测序文库。需要说明的是，上述结直肠癌或癌前病变的诊断或辅助诊断产品可以是任意一种的体外诊断产品形式，并不限于上述的试剂盒、芯片和测序文库的产品类型，只要能满足结直肠癌或癌前病变的诊断或辅助诊断的需求均在本公开的保护范围内。
本公开提供了一种检测DOK6基因CpG岛的甲基化水平的核酸组合，检测DOK6基因CpG岛的核酸组合选自如下核酸组合中的至少一种：核酸组合1、核酸组合2、核酸组合3、核酸组合4、核酸组合5、核酸组合6、核酸组合7、核酸组合8、核酸组合9、核酸组合10、核酸组合11、核酸组合12、核酸组合13、核酸组合14、核酸组合15、核酸组合16、核酸组合17、核酸组合18、核酸组合19和核酸组合20；
核酸组合1的碱基序列如SEQ ID NO.1-3所示，核酸组合2的碱基序列如SEQ ID NO.4-6所示，核酸组合3的碱基序列如SEQ ID NO.7-9所示，核酸组合4的碱基序列如SEQ ID NO.10-12所示，核酸组合5的碱基序列如SEQ ID NO.13-15所示，核酸组合6的碱基序列如SEQ ID NO.16-18所示，核酸组合7的碱基序列如SEQ ID NO.19-21所示，核酸组合8的碱基序列如SEQ ID NO.22-24所示，核酸组合9的碱基序列如SEQ ID NO.25-27所示，核酸组合10的碱基序列如SEQ ID NO.28-30所示，核酸组合11的碱基序列如SEQ ID NO.31-33所示，核酸组合12的碱基序列如SEQ ID NO.34-36所示，核酸组合13的碱基序列如SEQ ID NO.37-39所示，核酸组合14的碱基序列如SEQ ID NO.40-42所示，核酸组合15的碱基序列如SEQ ID NO.43-45所示，核酸组合16的碱基序列如SEQ ID NO.46-48所示，核酸组合17的碱基序列如SEQ ID NO.49-51所示，核酸组合18的碱基序列如SEQ ID NO.52-54所示，核酸组合19的碱基序列如SEQ ID NO.55-57所示，核酸组合20的碱基序列如SEQ ID NO.58-60所示。
需要说明的是，若一种核酸组合与上述核酸组合(核酸组合1-20)所示的碱基序列具有至少具有85％(例如85％、86％、87％、88％、89％、90％、91％、92％、93％、94％、95％、96％、97％、98％或99％等)以上的序列一致性，且该核酸组合同样具有一定的结直肠癌或癌前病变的诊断功能(特异性或灵敏度与本申请核酸组合1-20相比，相当或略有下降或略有提高或大幅提高等)，也在本公开的保护范围内。
需要说明的是，上述核酸组合1-20分别对应与区域1-20的检测。
本公开提供了一种结直肠癌或癌前病变的诊断或辅助诊断的检测试剂，其包括上述的检测DOK6基因CpG岛的甲基化水平的核酸组合。
在一种或多种实施方式中，上述检测试剂为检测DOK6基因的CpG岛的甲基化状态的试剂，甲基化状态的检测手段包括如下至少一种的方法：甲基化特异性PCR法、亚硫酸氢盐测序法、甲基化特异性微阵列法、全基因组甲基化测序法、焦磷酸测序法、甲基化特异性高效液相层析法、数字PCR法、 甲基化特异性高分辨率溶解曲线法、甲基化敏感性限制性内切酶法、荧光定量法和flap endonuclease法。
在一种或多种实施方式中，癌前病变为结直肠腺瘤，例如管状腺瘤、绒毛状腺瘤和绒毛管状腺瘤。在其他实施方式中，癌前病变还包括腺瘤病、炎症性肠病相关异型增生、传统锯齿状腺瘤和广基锯齿状腺瘤/息肉等。癌前病变包括不限于其他的肠道疾病。
本公开提供了一种结直肠癌或癌前病变的诊断或辅助诊断的检测试剂盒，其包括上述的检测DOK6基因CpG岛的甲基化水平的核酸组合或上述的结直肠癌或癌前病变的诊断或辅助诊断的检测试剂。
在一种或多种实施方式中，上述试剂盒的检测样本为血液样本、粪便样本或组织样本。
在一种或多种实施方式中，上述的检测试剂盒还包括PCR缓冲液，水，扩增酶等物质。
本公开提供一种诊断或辅助诊断受试者中结直肠癌或癌前病变的方法，其特征在于，所述方法包括
a)测定所述受试者的样品中DOK6基因上的靶区域的甲基化，所述靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：区域I、区域II和区域III；
其中，所述区域I选自Chr18:69400274-69401932正链或Chr18:69401932-69400274负链，所述区域II选自Chr18:69402698-69402935正链或Chr18:69402935-69402698负链，所述区域III选自Chr18：69469672-69470012正链或Chr18：69470012-69469672负链；以及
b)分析测定结果以确定结直肠癌或癌前病变。
在一种或多种实施方式中，所述步骤b)包括将受试者的样品的测定结果与未患结直肠癌或癌前病变的正常个体的样本中DOK6基因上的靶区域的甲基化水平进行比较，其中受试者的样品的测定结果高于未患结直肠癌或癌前病变的正常个体的样本中DOK6基因上的靶区域的甲基化水平指示所述受试者患有结直肠癌或癌前病变。
在一种或多种实施方式中，所述样本为血液样本、粪便样本或组织样本。
在一种或多种实施方式中，所述方法的a)步骤中的检测选自甲基化特异性PCR法、亚硫酸氢盐测序法、甲基化特异性微阵列法、全基因组甲基化测序法、焦磷酸测序法、甲基化特异性高效液相层析法、数字PCR法、甲基化特异性高分辨率溶解曲线法、甲基化敏感性限制性内切酶法、荧光定量法和flap endonuclease法。
在一种或多种实施方式中，在步骤a)中，使用权利要求6中所限定的核酸组合对所述样品进行测定。
具体实施方式
为使本公开实施例的目的、技术方案和优点更加清楚，下面将对本公开实施例中的技术方案进行清楚、完整地描述。实施例中未注明具体条件者，按照常规条件或制造商建议的条件进行。所用试剂或仪器未注明生产厂商者，均为可以通过市售购买获得的常规产品。
除非本文另有定义，否则结合本公开使用的科学和技术术语应具有本领域普通技术人员通常理解的含义。以下描述示例性方法和材料，但是与本文描述的那些类似或等同的方法和材料也可以用于本公开的实践或测试中。
以下结合实施例对本公开的特征和性能作进一步的详细描述。
本公开提供的结直肠癌或癌前病变的诊断或辅助诊断试剂、检测试剂盒以及核酸组合物是以人DOK6基因CpG岛的甲基化作为标志物，发明人发现，DOK6基因CpG岛在结直肠癌/癌前病变样本中的甲基化水平显著高于正常样本。通过检测样本中DOK6基因的CpG岛的甲基化水平的增加可以对结直肠癌或癌前病变进行诊断或辅助诊断，具有较高的灵敏度和特异性。采用本公开提供的检测试剂和试剂盒能有效地提高结直肠癌/癌前病变的检出率，从而满足结直肠癌/癌前病变早筛早诊的临床需求。本 公开提供的基因检测产品也可以为体检人群提供更好的肠道健康评估服务，实现对肠道病变的早发现、早诊断、早治疗，有利于节约家庭的医疗负担成本。
如本文所用，术语“正链”是指在基因的DNA双链中，携带有编码蛋白质氨基酸信息的核苷酸序列的链，又称编码链、正义链。正链的核苷酸与mRNA核苷酸序列相同。
如本文所用，术语“负链”是指在基因的DNA双链中，转录时作为mRNA合成模板的那条单链，也称作模板链或反义链。
如本文所用，术语“诊断”是指从医学角度对人们的精神和体质状态作出的判断。具体来说是一种确定那种疾病或病症可以解释受试者的症状和体征的过程。例如，通过使用本文所述的试剂盒或核苷酸组来确定直肠癌或腺瘤的存在。
实施例1
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合1，核酸组合1包括SEQ ID NO.1-3所示的核苷酸。该核苷酸组合1可检测DOK6基因上Chr18:69400290-69400480(区域1)正链的甲基化；
区域1正链碱基序列(5’-3’)如下：
Figure PCTCN2021142201-appb-000001
完全甲基化的区域1经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000002
SEQ ID NO.1-3所示的核苷酸可检测位于该区域正链上Chr18:69400301、Chr18:69400306、Chr18:69400310、Chr18:69400338、Chr18:69400341、Chr18:69400344、Chr18:69400348、Chr18:69400461和Chr18:69400479位置上胞嘧啶的甲基化。
实施例2
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合2，核酸组合2包括SEQ ID NO.4-6所示的核苷酸。该核苷酸组合2可检测DOK6基因上Chr18:69400531-69400649(区域2)正链的甲基化；
区域2正链碱基序列(5’-3’)如下：
Figure PCTCN2021142201-appb-000003
完全甲基化的区域2经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000004
SEQ ID NO.4-6所示的核苷酸可检测位于该区域正链上Chr18:69400539、Chr18:69400545、Chr18:69400587、Chr18:69400601、Chr18:69400631和Chr18:69400634位置上胞嘧啶的甲基化。
实施例3
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合3，核酸组合3 包括SEQ ID NO.7-9所示的核苷酸。该核苷酸组合3可检测DOK6基因上Chr18:69400739-69400893(区域3)正链的甲基化；
区域3正链碱基序列(5’-3’)如下：
Figure PCTCN2021142201-appb-000005
完全甲基化的区域3经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000006
SEQ ID NO.7-9所示的核苷酸可检测位于该区域正链上Chr18:69400751、Chr18:69400753、Chr18:69400787、Chr18:69400874、Chr18:69400879和Chr18:69400891位置上胞嘧啶的甲基化。
实施例4
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合4，核酸组合4包括SEQ ID NO.10-12所示的核苷酸。该核苷酸组合4可检测DOK6基因上Chr18:69400997-69401110(区域4)正链的甲基化；
区域4正链碱基序列(5’-3’)如下：
Figure PCTCN2021142201-appb-000007
完全甲基化的区域4经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000008
SEQ ID NO.10-12所示的核苷酸可检测位于该区域正链上Chr18:69401001、Chr18:69401011、Chr18:69401047、Chr18:69401054、Chr18:69401061、Chr18:69401099、Chr18:69401102和Chr18:69401110位置上胞嘧啶的甲基化。
实施例5
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合5，核酸组合5包括SEQ ID NO.13-15所示的核苷酸。该核苷酸组合5可检测DOK6基因上Chr18:69401156-69401286(区域5)正链的甲基化；
区域5正链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000009
完全甲基化的区域5经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000010
SEQ ID NO.13-15所示的核苷酸可检测位于该区域正链上Chr18:69401159、Chr18:69401166、Chr18:69401168、Chr18:69401176、Chr18:69401196、Chr18:69401202、Chr18:69401209、Chr18:69401262和Chr18:69401283位置上胞嘧啶的甲基化。
实施例6
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合6，核酸组合6包括SEQ ID NO.16-18所示的核苷酸。该核苷酸组合6可检测DOK6基因上Chr18:69401302-69401453(区域6)负链的甲基化；
区域6正链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000011
完全甲基化的区域6经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000012
SEQ ID NO.16-18所示的核苷酸可检测位于该区域正链上Chr18:69401321、Chr18:69401341、Chr18:69401344、Chr18:69401348、Chr18:69401352、Chr18:69401357、Chr18:69401433和Chr18:69401442位置上胞嘧啶的甲基化。
实施例7
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合7，核酸组合7包括SEQ ID NO.19-21所示的核苷酸。该核苷酸组合7可检测DOK6基因上Chr18:69401500-69401649(区域7)正链的甲基化；
区域7正链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000013
完全甲基化的区域7经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000014
SEQ ID NO.19-21所示的核苷酸可检测位于该区域正链上Chr18:69401518、Chr18:69401545、Chr18:69401556、Chr18:69401560、Chr18:69401633和Chr18:69401645位置上胞嘧啶的甲基化。
实施例8
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合8，核酸组合8包括SEQ ID NO.22-24所示的核苷酸。该核苷酸组合8可检测DOK6基因上Chr18:69401777-69401902(区域8)正链的甲基化；
区域8正链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000015
Figure PCTCN2021142201-appb-000016
完全甲基化的区域8经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000017
SEQ ID NO.22-24所示的核苷酸可检测位于该区域正链上Chr18:69401780、Chr18:69401783、Chr18:69401785、Chr18:69401787、Chr18:69401796、Chr18:69401818、Chr18:69401821、Chr18:69401827、Chr18:69401833和Chr18:69401902位置上胞嘧啶的甲基化。
实施例9本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合9，核酸组合13包括SEQ ID NO.25-27所示的核苷酸。该核苷酸组合9可检测DOK6基因上Chr18:69402740-69402896(区域9)正链的甲基化；
区域9正链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000018
完全甲基化的区域9经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000019
SEQ ID NO.25-27所示的核苷酸可检测位于该区域正链上Chr18:69402751、Chr18:69402755、Chr18:69402761、Chr18:69402778、Chr18:69402792、Chr18:69402876、Chr18:69402884和Chr18:69402896位置上胞嘧啶的甲基化。
实施例10
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合10，核酸组合10包括SEQ ID NO.28-30所示的核苷酸。该核苷酸组合10可检测DOK6基因上Chr18:69469693-69469908(区域10)正链的甲基化；
区域10正链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000020
完全甲基化的区域10经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000021
SEQ ID NO.28-30所示的核苷酸可检测位于该区域正链上Chr18:69469702、Chr18:69469711、Chr18:69469740、Chr18:69469887和Chr18:69469905位置上胞嘧啶的甲基化。
实施例11
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合11，核酸组合11包括SEQ ID NO.31-33所示的核苷酸。该核苷酸组合11可检测DOK6基因上Chr18:69401868-69401735(区域11)负链的甲基化；
区域11负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000022
完全甲基化的区域11经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000023
SEQ ID NO.31-33所示的核苷酸可检测位于该区域负链上Chr18:69401866、Chr18:69401848、Chr18:69401828、Chr18:69401822、Chr18:69401819、Chr18:69401813、Chr18:69401754和Chr18:69401736位置上胞嘧啶的甲基化。
实施例12
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合12，核酸组合12包括SEQ ID NO.34-36所示的核苷酸。该核苷酸组合12可检测DOK6基因上Chr18:69401755-69401590(区域12)负链的甲基化；
区域12负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000024
完全甲基化的区域12经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000025
SEQ ID NO.34-36所示的核苷酸可检测位于该区域负链上Chr18:69401754、Chr18:69401736、Chr18:69401705、Chr18:69401703、Chr18:69401699、Chr18:69401607和Chr18:69401600位置上胞嘧啶的甲基化。
实施例13
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合13，核酸组合13包括SEQ ID NO.37-39所示的核苷酸。该核苷酸组合13可检测DOK6基因上Chr18:69401564-69401424(区域13)负链的甲基化；
区域13负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000026
完全甲基化的区域13经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000027
SEQ ID NO.37-39所示的核苷酸可检测位于该区域负链上Chr18:6940562、Chr18:6940558、Chr18:6940554、Chr18:6940543、Chr18:6940534、Chr18:6940516、Chr18:6940443和Chr18:6940434位置上胞嘧啶的甲基化。
实施例14
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合14，核酸组合14包括SEQ ID NO.40-42所示的核苷酸。该核苷酸组合14可检测DOK6基因上Chr18:69401261-69401139(区域14)负链的甲基化；
区域14负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000028
完全甲基化的区域14经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000029
SEQ ID NO.40-42所示的核苷酸可检测位于该区域负链上Chr18:69401238、Chr18:69401222、Chr18:69401217、Chr18:69401215、Chr18:69401210、Chr18:69401160、Chr18:69401150、Chr18:69401146和Chr18:69401143位置上胞嘧啶的甲基化。
实施例15
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合15，核酸组合15包括SEQ ID NO.43-45所示的核苷酸。该核苷酸组合15可检测DOK6基因上Chr18:69401085-69400981(区域15)负链的甲基化；
区域15负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000030
完全甲基化的区域15经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000031
SEQ ID NO.43-45所示的核苷酸可检测位于该区域负链上Chr18:69401083、Chr18:69401071、Chr18:69401068、Chr18:69401042、Chr18:69401040、Chr18:69401035、Chr18:69401033、Chr18:69400995、Chr18:69400992、Chr18:69400990和Chr18:69400981位置上胞嘧啶的甲基化。
实施例16
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合16，核酸组合16包括SEQ ID NO.46-48所示的核苷酸。该核苷酸组合16可检测DOK6基因上Chr18:69400934-69400749(区域16)负链的甲基化；
区域16负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000032
Figure PCTCN2021142201-appb-000033
完全甲基化的区域16经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000034
SEQ ID NO.46-48所示的核苷酸可检测位于该区域负链上Chr18:69400933、Chr18:69400927、Chr18:69400915、Chr18:69400898、Chr18:69400895、Chr18:69400892、Chr18:69400880、Chr18:69400765、Chr18:69400761、Chr18:69400754和Chr18:69400752位置上胞嘧啶的甲基化。
实施例17
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合17，核酸组合17包括SEQ ID NO.49-51所示的核苷酸。该核苷酸组合17可检测DOK6基因上Chr18:69400729-69400630(区域17)负链的甲基化；
区域17负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000035
完全甲基化的区域17经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000036
SEQ ID NO.49-51所示的核苷酸可检测位于该区域负链上Chr18:69400723、Chr18:69400717、Chr18:69400714、Chr18:69400711、Chr18:69400676、Chr18:69400665、Chr18:69400658、Chr18:69400635和Chr18:69400632位置上胞嘧啶的甲基化。
实施例18
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合18，核酸组合18包括SEQ ID NO.52-54所示的核苷酸。该核苷酸组合18可检测DOK6基因上Chr18:69400577-69400468(区域18)负链的甲基化；
区域18负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000037
完全甲基化的区域18经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000038
SEQ ID NO.52-54所示的核苷酸可检测位于该区域负链上Chr18:69400559、Chr18:69400557、Chr18:69400546、Chr18:69400540、Chr18:69400486、Chr18:69400484和Chr18:69400480位置上胞嘧啶的甲基化。
实施例19
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合19，核酸组合19包括SEQ ID NO.55-57所示的核苷酸。该核苷酸组合19可检测DOK6基因上Chr18:69402905-69402736 (区域19)负链的甲基化；
区域19负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000039
完全甲基化的区域19经亚硫酸氢盐转化后的序列为(5’-3’)：
Figure PCTCN2021142201-appb-000040
SEQ ID NO.55-57所示的核苷酸可检测位于该区域负链上Chr18:69402897、Chr18:69402885、Chr18:69402810、Chr18:69402793、Chr18:69402756和Chr18:69402752位置上胞嘧啶的甲基化。
实施例20
本实施例提供用于结直肠癌或腺瘤的诊断或辅助诊断的试剂盒，其包括核苷酸组合20，核酸组合20包括SEQ ID NO.58-60所示的核苷酸。该核苷酸组合20可检测DOK6基因上Chr18:69469992-69469868(区域20)负链的甲基化；
区域20负链碱基序列如下(5’-3’)：
Figure PCTCN2021142201-appb-000041
完全甲基化的区域20经亚硫酸氢盐转化后的序列为(5’-3’)：
TATTTAGCGGGTAGGGGAGATCGGATATTCGGTTTAAGTAGGTTACGATGAGATAAGGTTGGAGTTTAGGTTGAAGAGTATTCGAGCGATTTAGAAGTAGATGTCGTTATTTTTTGGGGAAGGGT。
SEQ ID NO.58-60所示的核苷酸可检测位于该区域负链上Chr18:69469985、Chr18:69469971、Chr18:69469963、Chr18:69469947和Chr18:69469888位置上胞嘧啶的甲基化。
表1各核酸组合的序列表。
Figure PCTCN2021142201-appb-000042
Figure PCTCN2021142201-appb-000043
实施例21
本实施例提供使用实施例1-20任意一种试剂盒进行结直肠癌或腺瘤癌诊断的方法，其包括如下步骤：
1、DNA模板的提取：
结直肠癌患者粪便、结直肠腺瘤患者粪便和正常人粪便均由武汉大学中南医院收集，患者均签署知 情同意书，对每份样本进行匿名化处理。当所用样本是粪便样本时，采用武汉艾米森生命科技有限公司核酸提取试剂盒(鄂汉械备20200225号)提取粪便中的人源DOK6基因，该试剂盒采用捕获探针对粪便中的目的片段进行捕获，捕获探针上标记有生物素，正链区域和负链区域分开进行捕获提取，即提取正链基因组时加入正链捕获探针，提取负链区域时加入负链捕获探针。正链和负链的捕获探针序列参见表2，将10μM的不同区域的探针和10mg/mL的链霉亲和素磁珠按照等体积混合，形成捕获剂，提取时各区域的捕获探针替换试剂盒中原有的捕获探针，具体操作步骤参见试剂盒说明书。
表2探针序列表。
Figure PCTCN2021142201-appb-000044
所用样本是血液样本，采用天根生化科技(北京)有限公司的磁珠法血清/血浆游离DNA提取试剂盒(DP709)进行血浆cfDNA提取，具体操作参见试剂盒说明书。
2、亚硫酸盐的转化
将上述步骤1提取好的基因组进行亚硫酸氢盐转化，所用核酸转化试剂盒为武汉艾米森生命科技有限公司核酸纯化试剂(鄂汉械备20500843)，具体实验操作参见试剂盒说明书。
3、甲基化特异性PCR反应
将亚硫酸氢盐转化后的DNA进行甲基化特异性PCR反应以检测DOK6基因区域1-20的甲基化状态，每个区域单独进行检测，即一个PCR管中每次只加入一个区域的检测引物和探针，同时加入内参基因的检测探针。以ACTB作为内参基因，PCR反应体系如表3所示。ACTB作为内参基因，其中ACTB上游引物为：AAGGTGGTTGGGTGGTTGTTTTG(SEQ ID NO.75)；ACTB下游引物为：AATAACACCCCCACCCTGC(SEQ ID NO.76)；ACTB探针为：GGAGTGGTTTTTGGGTTTG(SEQ ID NO.77)。
检测目标区域的探针5’端的报告基团为FAM，3’端猝灭基团为MGB，ACTB探针5’端的报告基团为VIC，3’端猝灭基团为BHQ1。
表3 PCR反应体系。
组分 规格 体积(μL)
缓冲液 5× 5
dNTPs 各2.5mM 2
区域上游引物 10μM 0.5
区域下游引物 10μM 0.5
区域探针 10μM 0.5
ACTB上游引物 10μM 0.5
ACTB下游引物 10μM 0.5
ACTB探针 10μM 0.5
DNA聚合酶 5U/μL 0.3
待测样本DNA / 2
纯化水 / 补至25
如表3所示，在检测DOK6区域1-区域20任一区域在样本中的甲基化水平时，只需将某一区域对应的引物探针、ACTB引物探针、缓冲液、dNTP、DNA聚合酶和样本DNA等按照表中的体积加入到反应体系中，其中缓冲液、dNTP和DNA聚合酶为常规市售商品。
对于粪便样本，检测区域1-10时，加入的待测样本DNA是前述捕获提取到的正链DNA经亚硫酸氢盐转化而成，检测区域11-20时，加入的待检样本DNA是前述捕获提取到的负链DNA经亚硫酸氢转化而成；对于血液样本，检测区域1-20时，加入的待检样本DNA是提取到的cfDNA经转化而成。
PCR反应条件如下表4所示。
表4 PCR反应条件。
Figure PCTCN2021142201-appb-000045
Ct值读取：PCR完成后，调整基线，将一次PCR中样本最小Ct值提前1-2个循环前的荧光值设置为基线值，将阈值设置在S型扩增曲线的拐点处，得到样本各个基因的Ct值。
质量控制：在每次检测时对阴性对照和阳性对照进行同步检测。
阴性对照为纯化水。
阳性对照的制备方法为：将ACTB的扩增区域对应的经亚硫酸氢盐转化后的序列进行人工合成，并克隆至载体上，形成人工合成质粒。将完全甲基化的区域1-20对应的经亚硫酸氢盐转化后的序列进行人工合成，并克隆至人工合成质粒。区域1-20的阳性对照为10 3拷贝/微升的ACTB人工合成质粒和10 3拷贝/微升的区域1-20的人工合成质粒1：1混合而成，如区域1的阳性对照为10 3拷贝/微升的ACTB人工合成质粒和10 3拷贝/微升的区域1的人工合成质粒1：1混合而成。
阴性对照要无扩增，阳性对照Ct值应在26-30之间，待检样本的内参基因的Ct值应≤35，阴性对照、阳性对照及内参基因均满足上述要求后，表明本次实验有效，可进行下一步样本结果的判定。否则，当次实验无效，须重新进行检测。
结果分析和判读方法：若某一检测区域在样本上的Ct值≤38.5，则认为该样本在这一检测区域为甲基化阳性，若某一检测区域在样本上的Ct值>38.5，则认为该样本在这一检测区域为甲基化阴性。将样本的甲基化检测结果同病理结果进行对比，计算甲基化检测的敏感性和特异性。敏感性为病理结果为阳性的样本中甲基化阳性的比例，特异性为病理结果为阴性的样本中甲基化阴性的比例。
实施例22
本实施例提供了一种结直肠癌或癌前病变的诊断或辅助诊断试剂，其包括用于检测区域3的核酸组合3(同实施例3)和用于检测区域4的核酸组合4(同实施例4)。
实施例23
本实施例提供了一种结直肠癌或癌前病变的诊断或辅助诊断试剂，其包括用于检测区域9的核酸组 合9(同实施例9)、用于检测区域14的核酸组合14(同实施例14)。
实施例24
本实施例提供了一种结直肠癌或癌前病变的诊断或辅助诊断试剂，其包括用于检测区域13的核酸组合13(同实施例13)、用于检测区域18的核酸组合18(同实施例18)和用于检测区域19的核酸组合19(同实施例19)。
实验例1
于武汉大学中南医院收集经肠镜和组织活检确诊为结直肠癌患者、腺瘤患者和健康人的粪便样本，每人收集一份粪便，收集装置为武汉艾米森粪便标本采集保存管(鄂汉械备20191654号)，共收集到结直肠癌粪便样本78例、结直肠腺瘤样本104例、正常的粪便样本127例。按照实施例21提供的方法进行DNA提取提取和亚硫酸氢盐转化、选用实施例1-20中的针对DOK6基于20个区域的特异性引物和探针组合进行PCR检测，PCR检测结果如表5所示。
表5区域1-20在粪便样本中的检测灵敏度和特异性
Figure PCTCN2021142201-appb-000046
本文中，结直肠腺瘤灵敏度的计算方法为检测到的结直肠腺瘤PCR阳性数除以总结直肠腺瘤病例数；结直肠癌灵敏度的计算方法为检测到的结直肠癌PCR阳性数除以总结直肠癌病例数；特异性的计算方法为检测到的PCR阴性数除以无疾病的正常样本数。
由表5可以看出，在粪便样本中，区域1-20均能对结直肠腺瘤样本、结直肠癌症样本和正常样本实现较好区分，但各个区域的检测效果略有不同，整体来看，区域1-20对结直肠腺瘤的检测灵敏性均大于40％，对结直肠癌样本的检测灵敏性均大于80％，特异性均大于80％。区域2、区域4、区域9、区域13、区域14、区域18和区域19的检测灵敏度和特异性均显著优于其他区域，在粪便样本中，检测这几个区域的甲基化水平的增加对结直肠腺瘤的检测灵敏度均超过60％，对结直肠癌的检测灵敏度均超 过90％，特异性均大于90％。
实验例2
于武汉大学中南医院收集经肠镜和组织活检确诊为结直肠癌患者、腺瘤患者和健康人的血浆样本，每人收集5mL，共收集到结直肠癌血浆样本108例、结直肠腺瘤血浆样本130例、正常的血浆样本90例。按照实施例10提供的方法进行血浆DNA提取和重亚硫酸盐转化、选用实施例1-9中的针对DOK6基于20个区域的特异性引物和探针组合进行PCR检测，PCR检测结果如表6所示。
表6区域1-20在血浆样本中的检测灵敏度和特异性。
Figure PCTCN2021142201-appb-000047
由表6可以看出，在血浆样本中的检测结果与粪便检测的结果一致。区域1-20均能对结直肠腺瘤样本、结直肠癌症样本和正常样本实现较好区分，但各个区域的检测效果略有不同，整体来看，区域1-20对结直肠腺瘤的检测灵敏性均大于45％，对结直肠癌样本的检测灵敏性均大于80％，特异性均大于80％。区域2、区域4、区域9、区域13、区域14、区域18和区域9的检测灵敏度和特异性均显著优于其他区域，在血浆样本中，检测这几个区域的甲基化水平的增加对结直肠腺瘤的检测灵敏度均超过60％，对结直肠癌的检测灵敏度均超过90％，特异性均大于90％。
以上所述仅为本公开的优选实施例而已，并不用于限制本公开，对于本领域的技术人员来说，本公开可以有各种更改和变化。凡在本公开的精神和原则之内，所作的任何修改、等同替换、改进等，均应包含在本公开的保护范围之内。
工业实用性
本公开提供的结直肠癌或癌前病变的诊断或辅助诊断试剂、检测试剂盒以及核酸组合物是以人DOK6基因CpG岛的甲基化作为标志物，发明人发现，DOK6基因CpG岛在结直肠癌/癌前病变样本中的甲基化水平显著高于正常样本。通过检测样本中DOK6基因的CpG岛的甲基化水平的增加可以对结直肠癌或癌前病变进行诊断或辅助诊断，具有较高的灵敏度和特异性。采用本公开提供的检测试剂和试剂盒能有效地提高结直肠癌/癌前病变的检出率，从而满足结直肠癌/癌前病变早筛早诊的临床需求。本公开提供的基因检测产品也可以为体检人群提供更好的肠道健康评估服务，实现对肠道病变的早发现、早诊断、早治疗，有利于节约家庭的医疗负担成本。

Claims (15)

  1. 一种试剂在制备结直肠癌或癌前病变的诊断或辅助诊断产品中的应用，其特征在于，所述试剂为用于检测DOK6基因上的靶区域的甲基化的试剂，所述靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：区域I、区域II和区域III；
    其中，所述区域I选自Chr18:69400274-69401932正链或Chr18:69401932-69400274负链，所述区域II选自Chr18:69402698-69402935正链或Chr18:69402935-69402698负链，所述区域III选自Chr18：69469672-69470012正链或Chr18：69470012-69469672负链。
  2. 根据权利要求1所述的应用，其特征在于，所述靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：
    区域1、区域2、区域3、区域4、区域5、区域6、区域7、区域8、区域9、区域10、区域11、区域12、区域13、区域14、区域15、区域16、区域17、区域18、区域19和区域20；
    其中，所述区域1选自Chr18：69400290-69400480正链，所述区域2选自Chr18：69400531-69400649正链，所述区域3选自正链Chr18：69400739-69400839，所述区域4选自Chr18:69400997-69401110正链，所述区域5选自Chr18:69401156-69401286正链，所述区域6选自Chr18:69401302-69401453正链，所述区域7选自Chr18:69401500-69401649正链，所述区域8选自Chr18:69401777-69401902正链，所述区域9选自Chr18:69402740-69402896正链，所述区域10选自Chr18:69469693-69469908正链，所述区域11选自Chr18:69401868-69401735负链，所述区域12选自Chr18:69401755-69401590负链，所述区域13选自Chr18:69401564-69401424负链，所述区域14选自Chr18:69401261-69401139负链，所述区域15选自Chr18:69401085-69400981负链，所述区域16选自Chr18:69400934-69400749负链，所述区域17选自Chr18:69400729-69400630负链，所述区域18选自Chr18:69400577-69400468负链，所述区域19选自Chr18:69402905-69402736负链，所述区域20选自Chr18:69469992-69469868负链。
  3. 根据权利要求2所述的应用，其特征在于，所述靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：区域2、区域4、区域9、区域13、区域14、区域18和区域19；
    所述区域2选自Chr18:69400531-69400649正链，所述区域4选自Chr18:69400997-69401110正链，所述区域9选自Chr18:69402740-69402896正链，所述区域13选自Chr18:69401564-69401424负链，所述区域14选自Chr18:69401261-69401139负链，所述区域18选自Chr18:69400577-69400468负链，所述区域19选自Chr18:69402905-69402736负链。
  4. 根据权利要求2所述的应用，其特征在于，所述试剂用于检测DOK6基因上的区域1正链上的Chr18:69400301、Chr18:69400306、Chr18:69400310、Chr18:69400338、Chr18:69400341、Chr18:69400344、Chr18:69400348、Chr18:69400461和Chr18:69400479至少一个位置上胞嘧啶的甲基化；
    所述试剂试剂用于检测DOK6基因上的区域2正链上的Chr18:69400539、Chr18:69400545、Chr18:69400587、Chr18:69400601、Chr18:69400631和Chr18:69400634至少一个位置上胞嘧啶的甲基化；
    所述试剂试剂用于检测DOK6基因上的区域3正链上的Chr18:69400751、Chr18:69400753、Chr18:69400787、Chr18:69400874、Chr18:69400879和Chr18:69400891至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域4正链上的Chr18:69401001、Chr18:69401011、 Chr18:69401047、Chr18:69401054、Chr18:69401061、Chr18:69401099、Chr18:69401102和Chr18:69401110至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域5正链上的Chr18:69401159、Chr18:69401166、Chr18:69401168、Chr18:69401176、Chr18:69401196、Chr18:69401202、Chr18:69401209、Chr18:69401262和Chr18:69401283至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域6正链上的Chr18:69401321、Chr18:69401341、Chr18:69401344、Chr18:69401348、Chr18:69401352、Chr18:69401357、Chr18:69401433和Chr18:69401442至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域7正链上的Chr18:69401518、Chr18:69401545、Chr18:69401556、Chr18:69401560、Chr18:69401633和Chr18:69401645至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域8正链上的Chr18:69401780、Chr18:69401783、Chr18:69401785、Chr18:69401787、Chr18:69401796、Chr18:69401818、Chr18:69401821、Chr18:69401827、Chr18:69401833和Chr18:69401902至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域9正链上的Chr18:69402751、Chr18:69402755、Chr18:69402761、Chr18:69402778、Chr18:69402792、Chr18:69402876、Chr18:69402884和Chr18:69402896至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域10正链上的Chr18:69469702、Chr18:69469711、Chr18:69469740、Chr18:69469887和Chr18:69469905至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域11负链上的Chr18:69401866、Chr18:69401848、Chr18:69401828、Chr18:69401822、Chr18:69401819、Chr18:69401813、Chr18:69401754和Chr18:69401736至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域12负链上的Chr18:69401754、Chr18:69401736、Chr18:69401705、Chr18:69401703、Chr18:69401699、Chr18:69401607和Chr18:69401600至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域13负链上的Chr18:6940562、Chr18:6940558、Chr18:6940554、Chr18:6940543、Chr18:6940534、Chr18:6940516、Chr18:6940443和Chr18:6940434至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域14负链上的Chr18:69401238、Chr18:69401222、Chr18:69401217、Chr18:69401215、Chr18:69401210、Chr18:69401160、Chr18:69401150、Chr18:69401146和Chr18:69401143至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域15负链上的Chr18:69401083、Chr18:69401071、Chr18:69401068、Chr18:69401042、Chr18:69401040、Chr18:69401035、Chr18:69401033、Chr18:69400995、Chr18:69400992、Chr18:69400990和Chr18:69400981至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域16负链上的Chr18:69400933、Chr18:69400927、Chr18:69400915、Chr18:69400898、Chr18:69400895、Chr18:69400892、Chr18:69400880、Chr18:69400765、Chr18:69400761、Chr18:69400754和Chr18:69400752至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域17负链上的Chr18:69400723、Chr18:69400717、 Chr18:69400714、Chr18:69400711、Chr18:69400676、Chr18:69400665、Chr18:69400658、Chr18:69400635和Chr18:69400632至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域18负链上的Chr18:69400559、Chr18:69400557、Chr18:69400546、Chr18:69400540、Chr18:69400486、Chr18:69400484和Chr18:69400480至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域19负链上的Chr18:69402897、Chr18:69402885、Chr18:69402810、Chr18:69402793、Chr18:69402756和Chr18:69402752至少一个位置上胞嘧啶的甲基化；
    所述试剂用于检测DOK6基因上的区域20负链上的Chr18:69469985、Chr18:69469971、Chr18:69469963、Chr18:69469947和Chr18:69469888至少一个位置上胞嘧啶的甲基化。
  5. 根据权利要求2所述的应用，其特征在于，所述试剂选自如下核酸组合中的至少一种：
    用于检测所述区域1的核酸组合1、用于检测所述区域2的核酸组合2、用于检测所述区域3的核酸组合3、用于检测所述区域4的核酸组合4、用于检测所述区域5的核酸组合5、用于检测所述区域6的核酸组合6、用于检测所述区域7的核酸组合7、用于检测所述区域8的核酸组合8、用于检测所述区域9的核酸组合9、用于检测所述区域10的核酸组合10、用于检测所述区域11的核酸组合11、用于检测所述区域12的核酸组合12、用于检测所述区域13的核酸组合13、用于检测所述区域14的核酸组合14、用于检测所述区域15的核酸组合15、用于检测所述区域16的核酸组合16、用于检测所述区域17的核酸组合17、用于检测所述区域18的核酸组合18、用于检测所述区域19的核酸组合19和用于检测所述区域20的核酸组合20；
    所述核酸组合1的碱基序列如SEQ ID NO.1-3所示，所述核酸组合2的碱基序列如SEQ ID NO.4-6所示，所述核酸组合3的碱基序列如SEQ ID NO.7-9所示，所述核酸组合4的碱基序列如SEQ ID NO.10-12所示，所述核酸组合5的碱基序列如SEQ ID NO.13-15所示，所述核酸组合6的碱基序列如SEQ ID NO.16-18所示，所述核酸组合7的碱基序列如SEQ ID NO.19-21所示，所述核酸组合8的碱基序列如SEQ ID NO.22-24所示，所述核酸组合9的碱基序列如SEQ ID NO.25-27所示，所述核酸组合10的碱基序列如SEQ ID NO.28-30所示，所述核酸组合11的碱基序列如SEQ ID NO.31-33所示，所述核酸组合12的碱基序列如SEQ ID NO.34-36所示，所述核酸组合13的碱基序列如SEQ ID NO.37-39所示，所述核酸组合14的碱基序列如SEQ ID NO.40-42所示，所述核酸组合15的碱基序列如SEQ ID NO.43-45所示，所述核酸组合16的碱基序列如SEQ ID NO.46-48所示，所述核酸组合17的碱基序列如SEQ ID NO.49-51所示，所述核酸组合18的碱基序列如SEQ ID NO.52-54所示，所述核酸组合19的碱基序列如SEQ ID NO.55-57所示，所述核酸组合20的碱基序列如SEQ ID NO.58-60所示；
    优选地，所述试剂选自如下核酸组合中的至少一种：
    用于检测所述区域2的核酸组合2、用于检测所述区域4的核酸组合4、用于检测所述区域9的核酸组合9、用于检测所述区域13的核酸组合12、用于检测所述区域14的核酸组合14、用于检测所述区域18的核酸组合18和用于检测所述区域19的核酸组合19。
  6. 一种检测DOK6基因CpG岛的甲基化水平的核酸组合，其特征在于，所述检测DOK6基因CpG岛的核酸组合选自如下核酸组合中的至少一种：核酸组合1、核酸组合2、核酸组合3、核酸组合4、核酸组合5、核酸组合6、核酸组合7、核酸组合8、核酸组合9、核酸组合10、核酸组合11、核酸组合12、核酸组合13、核酸组合14、核酸组合15、核酸组合16、核酸组合17、核酸组合18、核酸组合19和核酸组合20；
    所述核酸组合1的碱基序列如SEQ ID NO.1-3所示，所述核酸组合2的碱基序列如SEQ ID NO.4-6所示，所述核酸组合3的碱基序列如SEQ ID NO.7-9所示，所述核酸组合4的碱基序列如SEQ ID NO.10-12所示，所述核酸组合5的碱基序列如SEQ ID NO.13-15所示，所述核酸组合6的碱基序列如SEQ ID NO.16-18所示，所述核酸组合7的碱基序列如SEQ ID NO.19-21所示，所述核酸组合8的碱基序列如SEQ ID NO.22-24所示，所述核酸组合9的碱基序列如SEQ ID NO.25-27所示，所述核酸组合10的碱基序列如SEQ ID NO.28-30所示，所述核酸组合11的碱基序列如SEQ ID NO.31-33所示，所述核酸组合12的碱基序列如SEQ ID NO.34-36所示，所述核酸组合13的碱基序列如SEQ ID NO.37-39所示，所述核酸组合14的碱基序列如SEQ ID NO.40-42所示，所述核酸组合15的碱基序列如SEQ ID NO.43-45所示，所述核酸组合16的碱基序列如SEQ ID NO.46-48所示，所述核酸组合17的碱基序列如SEQ ID NO.49-51所示，所述核酸组合18的碱基序列如SEQ ID NO.52-54所示，所述核酸组合19的碱基序列如SEQ ID NO.55-57所示，所述核酸组合20的碱基序列如SEQ ID NO.58-60所示。
  7. 一种结直肠癌或癌前病变的诊断或辅助诊断的检测试剂，其特征在于，其包括权利要求6所述的检测DOK6基因CpG岛的甲基化水平的核酸组合。
  8. 根据权利要求7所述的结直肠癌或癌前病变的诊断或辅助诊断的检测试剂，其特征在于，所述检测试剂为检测DOK6基因的CpG岛的甲基化状态的试剂，所述甲基化状态的检测手段包括如下至少一种的方法：甲基化特异性PCR法、亚硫酸氢盐测序法、甲基化特异性微阵列法、全基因组甲基化测序法、焦磷酸测序法、甲基化特异性高效液相层析法、数字PCR法、甲基化特异性高分辨率溶解曲线法、甲基化敏感性限制性内切酶法、荧光定量法和flap endonuclease法；
    优选地，所述癌前病变为结直肠腺瘤。
  9. 一种结直肠癌或癌前病变的诊断或辅助诊断的检测试剂盒，其特征在于，其包括权利要求6所述的检测DOK6基因CpG岛的甲基化水平的核酸组合或权利要求7-8任一项所述的结直肠癌或癌前病变的诊断或辅助诊断的检测试剂。
  10. 根据权利要求9所述的结直肠癌或癌前病变的诊断或辅助诊断的检测试剂盒，其特征在于，所述试剂盒的检测样本为血液样本、粪便样本或组织样本。
  11. 一种诊断或辅助诊断受试者中结直肠癌或癌前病变的方法，其特征在于，所述方法包括
    a)测定所述受试者的样品中DOK6基因上的靶区域的甲基化，所述靶区域选自DOK6基因的如下至少一种区域中的全长区域或部分区域：区域I、区域II和区域III；
    其中，所述区域I选自Chr18:69400274-69401932正链或Chr18:69401932-69400274负链，所述区域II选自Chr18:69402698-69402935正链或Chr18:69402935-69402698负链，所述区域III选自Chr18：69469672-69470012正链或Chr18：69470012-69469672负链；以及
    b)分析测定结果以确定结直肠癌或癌前病变。
  12. 根据权利要求11所述的方法，其特征在于，所述步骤b)包括将受试者的样品的测定结果与未患结直肠癌或癌前病变的正常个体的样本中DOK6基因上的靶区域的甲基化水平进行比较，其中受试者的样品的测定结果高于未患结直肠癌或癌前病变的正常个体的样本中DOK6基因上的靶区域的甲基化水平指示所述受试者患有结直肠癌或癌前病变。
  13. 根据权利要求12所述的方法，其特征在于，所述样本为血液样本、粪便样本或组织样本。
  14. 根据权利要求11-13中任一项所述的方法，其特征在于，所述方法的a)步骤中的检测选自甲基化特异性PCR法、亚硫酸氢盐测序法、甲基化特异性微阵列法、全基因组甲基化测序法、焦 磷酸测序法、甲基化特异性高效液相层析法、数字PCR法、甲基化特异性高分辨率溶解曲线法、甲基化敏感性限制性内切酶法、荧光定量法和flap endonuclease法。
  15. 根据权利要求11-14中任一项所述的方法，其特征在于，在步骤a)中，使用权利要求6中所限定的核酸组合对所述样品进行测定。
PCT/CN2021/142201 2021-06-30 2021-12-28 一种结直肠癌或癌前病变的诊断或辅助诊断试剂、核酸组合、试剂盒及应用 WO2023273257A1 (zh)

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