CN114438202B - SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers - Google Patents

SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers Download PDF

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CN114438202B
CN114438202B CN202111538750.0A CN202111538750A CN114438202B CN 114438202 B CN114438202 B CN 114438202B CN 202111538750 A CN202111538750 A CN 202111538750A CN 114438202 B CN114438202 B CN 114438202B
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周其伟
马强
李明
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Guangzhou Ruixi Biotechnology Co ltd
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Abstract

The invention provides a SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers, which comprises a SNORD57 reverse transcription primer for detecting SNORD57 and/or a primer probe composition for detecting SNORD57, wherein the primer probe composition for detecting SNORD57 comprises a SNORD57 forward primer, a SNORD57 reverse primer and a SNORD57 probe. The invention provides a specific reverse transcription primer and a primer group aiming at the small finger-nucleus RNA SNORD57, and has the advantages of high amplification efficiency, good specificity and the like. The invention realizes the semi-automatic detection of SNORD57, and has the advantages of high speed, high sensitivity and wide applicable sample range.

Description

SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers
Technical Field
The invention relates to the technical field of molecular detection, in particular to a SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers.
Background
Nucleolar RNA (snorRNA) is a small molecular non-coding RNA which is widely existed in nucleolus of eukaryotic cells, has the length of 60-300 nt, is mainly existed in nucleolus, and plays a role in modifying ribosome RNA and some spliceosome RNA after transcription by RNAs. Expression of snoRNA may be regulated by host genes, CNV and DNA methylation. There is a large body of evidence that suggests the importance of snoRNA in the development of cancer, e.g., SNORD78 is overexpressed in non-small cell lung and prostate cancers, and the SNORDSOA/B, which can directly bind to and inhibit K-Ras, is deleted in a variety of cancer types; SNORA42 expression is an independent prognostic factor for increased overall survival in cancer patients. SNORA55 silencing in prostate cancer cell lines significantly inhibited cell proliferation and migration. The dysfunction of snoRNA plays an important role in the development of cancer, invasion and metastasis, and more studies prove that snoRNA plays an important role in the development and progression of diseases, especially tumors.
SNORD57 is a kind of nucleolus RNA, and researches have found that SNORD57 has close relation with colorectal cancer, and may be an important tumor marker of intestinal cancer. Therefore, SNORD57 is expected to become a new target for diagnosing and treating colorectal cancer, and the development of a kit for detecting the SNORD57 gene has important clinical significance. The research shows that the expression level of the SNORD57 is high in a plasma/serum sample of polyps, adenomas and intestinal cancers, and is low in a sample with normal enteroscopy, and the SNORD57 can be used as a marker for diagnosing and screening the polyps, the adenomas and the intestinal cancers.
Few reports about the detection of SNORD57 are reported at home and abroad, and corresponding primers and probes are directly designed aiming at the SNORD57, so that non-specific amplification can be caused. At present, no quick, simple and effective SNORD57 detection method exists.
Disclosure of Invention
The invention aims to overcome the defects in the prior art and provide a SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers.
The first purpose of the invention is to provide a SNORD57 reverse transcription primer for detecting SNORD 57.
The second purpose of the invention is to provide a primer probe composition for detecting SNORD 57.
The third purpose of the invention is to provide the SNORD57 reverse transcription primer for detecting SNORD57 and/or the primer probe composition for detecting SNORD57, and the application of the primer probe composition in preparing products for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers.
The fourth purpose of the invention is to provide a detection kit for detecting the SNORD 57.
In order to achieve the purpose, the invention is realized by the following scheme:
in the actual preparation process, the SNORD57 sequence is obtained according to GenBank, wherein the SNORD57 refers to nucleolar RNA and is named as SNORD57 or C/D box 57. The SNORD57 effective sequence is an original sequence or a reverse complementary sequence of the original sequence, and the nucleotide sequences are respectively shown as SEQ ID NO.1 and SEQ ID NO. 2. The sequence is found to have certain homology with the human genome through BLAST functional analysis of NCBI, which indicates that corresponding primers and probes cannot be directly designed aiming at the SNORD57 and non-specific amplification can be caused, and in order to avoid the situation, the invention designs a unique reverse transcription primer, wherein the reverse transcription primer contains the SNORD57 sequence and cannot cause non-specificity of subsequent PCR.
Forward and reverse primers and probes are designed according to the designed target sequence, and the specificity of the forward and reverse primers and probes is preliminarily identified through the BLAST function of NCBI. Under the action of the mixed solution containing the primer and the probe, the RT-PCR reaction solution and the mixed solution containing the reaction enzyme, the circulating amplification of the in vitro nucleic acid is realized through a PCR instrument, and the real-time fluorescence PCR detection is carried out. Based on the detection, the SNORD57 detection kit capable of realizing screening and diagnosis of intestinal polyps, intestinal adenomas and/or intestinal cancers, which is semi-automatic in detection, high in speed and sensitivity and wide in sample application range, is developed.
A SNORD57 reverse transcription primer for detecting SNORD57 is disclosed, the nucleotide sequence of SNORD57 is shown in SEQ ID NO.1 or SEQ ID NO.2, the SNORD57 reverse transcription primer is a sequence 1 and a sequence 2 from 5' end to 3' end in sequence, the sequence 1 is a sequence of 18-25 bases which has no homology with human genome and microorganism, and the sequence 2 is a sequence (namely a reverse transcription primer binding site) of 6-12 bases which is completely complementary with the 3' end sequence of SNORD57 gene.
Preferably, the nucleotide sequence of the sequence 1 is shown as SEQ ID NO. 5.
Preferably, the sequence 2 is a 9-base sequence that is completely complementary to the sequence at the 3' end of the SNORD57 gene.
Preferably, the nucleotide sequence of the SNORD57 reverse transcription primer is shown as SEQ ID NO. 3.
A primer probe composition for detecting SNORD57, wherein the nucleotide sequence of the SNORD57 is shown in SEQ ID No.1 or SEQ ID No.2, and the primer probe composition for detecting SNORD57 comprises a SNORD57 forward primer, a SNORD57 reverse primer and a SNORD57 probe; the SNORD57 forward primer is 18-25 basic groups at the most upstream of the 5' end of the SNORD 57; the SNORD57 reverse primer is the sequence 1 of claim 1 or 2; the nucleotide sequence of the SNORD57 probe is shown in any one of SEQ ID NO.6, SEQ ID NO.7 or SEQ ID NO. 8.
Preferably, the SNORD57 forward primer is the 20 bases most upstream of the 5' end of the SNORD 57.
Preferably, the primer probe composition for detecting SNORD57 comprises a SNORD57 forward primer with a nucleotide sequence shown in SEQ ID No.4, a SNORD57 reverse primer with a nucleotide sequence shown in SEQ ID No.5 and a SNORD57 probe with a nucleotide sequence shown in SEQ ID No. 6.
Preferably, the 5 'end of the SNORD57 probe is labeled with any one of FAM, VIC, HEX, texas Red or CY5 fluorophores, and the 3' end of the probe is labeled with an MGB group, so that the melting temperature (Tm) of the probe can be increased and the probe/target hybridization can be stabilized.
More preferably, the 5' end of the probe is labeled with FAM fluorophore.
The SNORD57 reverse transcription primer for detecting SNORD57 and/or the primer probe composition for detecting SNORD57 are applied to preparation of products for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers.
A detection kit for detecting SNORD57 can be used for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers.
A detection kit for detecting SNORD57, which comprises the SNORD57 reverse transcription primer for detecting SNORD57 and/or the primer probe composition for detecting SNORD 57.
The primer probe composition is present in the kit in the form of a mixed solution.
Preferably, the detection kit also contains a SNORD57 positive quality control substance and/or a SNORD57 negative quality control substance.
More preferably, the SNORD57 positive quality control product is an artificially synthesized pseudovirus or RNA sequence.
Most preferably, the SNORD57 positive quality control product is RNA containing a SNORD57 target sequence, and the nucleotide sequence of the SNORD57 positive quality control product is shown in SEQ ID NO.1 or SEQ ID NO.2, so that the storage is convenient, the quality is stable, and the storage and the transportation of the kit are convenient.
More preferably, the negative quality control substance is physiological saline.
Preferably, the detection kit also contains a reverse transcription reaction reagent and/or a PCR reaction reagent.
More preferably, the reverse transcription reaction reagent contains a reverse transcription buffer, a reverse transcriptase, an rnase inhibitor and/or dNTPs.
More preferably, the PCR reaction reagent contains Taq enzyme, UNG enzyme, dNTPs and/or PCR buffer.
More preferably, the final concentration of the reaction system of the forward primer and the reverse primer in the detection kit is 0.1-0.6. Mu. Mol/L.
Most preferably, the final reaction system concentration of the forward primer and the reverse primer in the SNORD57 primer set is 0.2. Mu. Mol/L.
Compared with the prior art, the invention has the following beneficial effects:
the invention provides a SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers, which comprises a SNORD57 reverse transcription primer for detecting SNORD57 and/or a primer probe composition for detecting SNORD57, wherein the primer probe composition for detecting SNORD57 comprises a SNORD57 forward primer, a SNORD57 reverse primer and a SNORD57 probe. The invention provides specific reverse transcription primers and primer probe compositions for the first time for the finger nucleolus RNA SNORD 57. And verifies that the primer has the advantages of high amplification efficiency, good specificity and the like. Wherein, the 3 'end of the SNORD57 reverse transcription primer has 9 bases which are complementary with the 3' end of the SNORD57 and can be used for specific reverse transcription, and the probe of the invention is an MGB probe, which can improve the TM value of the probe and increase the specificity of the reaction.
The invention can clone trace mRNA by using RT-PCR, and the constructed cDNA library has the advantages of reducing pollution chance, reducing RNA secondary structure, reducing mismatching rate of PCR reaction and the like, shielding the interference of genome DNA to the maximum extent, improving the amplification efficiency of PCR reaction and improving the detection sensitivity. The invention can realize the semi-automatic detection of SNORD57, has high speed, high sensitivity and wide applicable sample range, and is suitable for the detection of sample types such as serum, plasma and the like.
Drawings
Fig. 1 is a schematic diagram of the principle of the present invention.
FIG. 2 is a graph showing the negative quality control product of example 1.
FIG. 3 is a graph showing the positive control in example 1.
FIG. 4 is a graph of the standard amplification curve of example 2.
FIG. 5 is a standard curve of example 2.
Detailed Description
The present invention will be described in further detail with reference to the drawings and specific examples, which are provided for illustration only and are not intended to limit the scope of the present invention. The test methods used in the following examples are all conventional methods unless otherwise specified; the materials, reagents and the like used are, unless otherwise specified, commercially available reagents and materials.
Example 1 primer and Probe design
The nucleotide sequence of SNORD57 is obtained according to GenBank, and is shown as SEQ ID NO.1, and the reverse complementary sequence is shown as SEQ ID NO. 2. The SNORD57 refers to nucleolar RNA and is named as SNORD57 or C/D box 57. The sequence of SNORD57 has certain homology with the human genome through BLAST functional analysis of NCBI, which shows that corresponding primers and probes cannot be directly designed aiming at the SNORD57, and non-specific amplification can be caused. To avoid this, unique reverse transcription primers were designed whose reverse transcription products contained both the SNORD57 sequence and did not contribute to non-specificity of subsequent PCR. FIG. 1 is a schematic diagram of the principle of primer design.
1. Reverse transcription primer
The 3 'end of the SNORD57 reverse transcription primer has 9 bases which are complementary with the 3' end sequence of the SNORD57 gene, and the primer can be used for the specific reverse transcription of the SNORD57 gene. The nucleotide sequence of the SNORD57 reverse transcription primer is shown as SEQ ID NO. 3.
2. Forward primer and reverse primer
The 1 st to 20 th basic groups from the 5 'end to the 3' end of the reverse transcription primer are SNORD57 reverse primer sequences, the nucleotide sequence of the forward primer is shown as SEQ ID NO.4, and the nucleotide sequence of the reverse primer is shown as SEQ ID NO. 5.
3. Specific probe
The length of the specific probe is 20-24 bp, and the nucleotide sequence of the specific probe is shown as SEQ ID NO.6, SEQ ID NO.7 or SEQ ID NO. 8. Marking FAM fluorescent group at 5' end of the specific probe; the 3' end is labeled with an MGB group, which can increase the melting temperature (Tm) of the probe and stabilize probe/target hybridization. The primer and probe sequence listing is shown in table 1.
TABLE 1 sequence listing
Figure BDA0003413699420000051
Figure BDA0003413699420000061
4. Identification of specificity
The designed primers and probes were bioinformatically aligned by the BLAST function of NCBI, and the homology of the designed primer and probe sequences was analyzed.
Through comparison and analysis, the related primers and probes have no homology with other human genomes or microbial genomes, and the designed primers and probes are proved to have better specificity.
Example 2 SNORD57 detection kit for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers
1. Composition of
Reverse transcription reaction solution 1 tube: comprises a reverse transcription buffer solution and a reverse transcription primer with the nucleotide sequence shown in SEQ ID NO.3 and obtained by the design in the embodiment 1, wherein the final concentration of a reaction system of the reverse transcription primer is 0.1 mu mol/L.
Reverse transcriptase mix 1 tube: contains reverse transcriptase, RNase inhibitor and dNTPs.
1 tube of PCR reaction solution: contains Taq enzyme, UNG enzyme, dNTPs (containing dUTP) and PCR buffer;
the kit also comprises a PCR primer group obtained by the design in the embodiment 1, namely a forward primer with a nucleotide sequence shown as SEQ ID NO.4, a reverse primer with a nucleotide sequence shown as SEQ ID NO.5 and a specific probe with a nucleotide sequence shown as SEQ ID NO.6, wherein the 5 'end of the probe is marked with FAM fluorescent group, and the 3' end of the probe is marked with an MGB group;
the final concentration of the amplification system of the primer is 0.2 mu mol/L, and the final concentration of the amplification system of the probe is 0.1 mu mol/L.
1 tube of positive quality control product: the RNA containing the SNORD57 target sequence has a nucleotide sequence shown as SEQID NO.1, and is convenient to store, stable in quality and convenient to store and transport.
Negative quality control 1 tube: physiological saline.
2. Application method
1. Reverse transcription reaction
(1) Preparation of reagents: 8 mu L of reverse transcription reaction liquid and 2 mu L of reverse transcription reaction enzyme mixed liquid are fully and evenly mixed for later use.
(2) Sample adding: and respectively adding 10 mu L of sample RNA to be detected, a negative quality control product and a positive quality control product into the PCR reaction tube, tightly covering a tube cover, and placing the tube cover into an instrument sample groove.
(3) Reverse transcription: placing the PCR reaction tube in a PCR instrument, and setting a reaction program: 5min at 25 ℃ and 15min at 50 ℃; 5min at 85 ℃.
2. PCR amplification
(1) Preparing a reagent: to the PCR reaction tube, 20. Mu.L of the PCR reaction solution was added.
(2) Sample adding: to the PCR reaction tube, 5. Mu.L each of the reverse transcription products was added, and the tube cap was closed for use.
(3) And (3) PCR reaction: the PCR reaction tube was placed in a PCR instrument, and a reaction program was set, as shown in Table 2:
TABLE 2PCR reaction procedure
Figure BDA0003413699420000071
Note: * Indicating the collection of fluorescent signals
3. Analysis of results
And storing the detection data file after the reaction is finished. The Amplification Plot window is opened under Results. The location of the sample of interest to be analyzed is selected. Changing the Baseline value to start:3, stop:10, and opens the manual setting Threshold:2-6e +3. And (3) double clicking numerical values on Rn coordinates to open a Graph Settings window, changing Log in Post Run Settings into Linear, opening an Analysis preferences window after OK, and selecting an Analysis automatic Analysis result under an Analysis menu.
4. Interpretation of results
FAM channels of negative quality control products have no obvious S-type amplification curve (see figure 2); the amplification curve of the FA M channel of the positive quality control substance is an obvious S-shaped curve (see figure 3), and the Ct value of the positive quality control substance is less than 38.
Example 3 detection of amplification efficiency of kit
1. Experimental method
Selecting SNORD57 RNA with a given value, diluting with 10-fold gradient of nuclease-free water to 4 gradients to prepare quantitative standard substance (concentration is 1 × 10 respectively) 6 copies/mL、1×10 5 copies/mL、1×10 4 copies/mL、1×10 3 copies/mL) was detected using the kit of example 2, and quality control was performed using negative and positive quality controls.
2. Results of the experiment
FAM of negative quality control products has no S-type amplification curve; the amplification curves of the FAM channels of the positive quality control substances are all obvious S-shaped curves, and the Ct value of the positive quality control substances is 28.56. The negative and positive quality control products meet the quality control requirements of the kit, so the detection result of the sample to be detected is effective.
The FAM detection channel amplification curve of the SNORD57 quantitative standard substance is S-shaped (see figure 4), the correlation coefficient of the standard curve is 0.998, the slope is-3.34 (see figure 5), the amplification efficiency of the kit is calculated to be 0.94, and the sensitivity of the kit can reach 1 x 10 3 copies/mL, which indicates that the kit has better amplification efficiency and higher sensitivity.
EXAMPLE 4 specificity of the kit detection
1. Experimental methods
Clinical samples were selected, all samples were subjected to nucleic acid extraction, detection was performed using the kit of example 2, and quality control was performed using negative and positive quality controls.
Wherein the clinical samples are: 1 esophageal cancer patient sample, 1 gastric cancer patient sample, 1 gastritis patient sample, 1 enteritis patient sample, 1 appendicitis patient sample, 1 colitis patient sample, 1 peptic ulcer patient sample, 1 liver cancer patient sample, 1 pancreatic cancer patient sample, 1 cholangiocarcinoma patient sample, 1 oral cancer patient sample, and 5 colorectal cancer negative (normal person) samples.
2. Results of the experiment
FAM of negative quality control products has no S-type amplification curve; the amplification curves of the FAM channels of the positive quality control substances are all obvious S-shaped curves, and the Ct value of the positive quality control substances is 25.23. The negative and positive quality control products meet the quality control requirements of the kit, so the detection result of the sample to be detected is effective. As can be seen from the detection results of the samples to be detected, the Ct values of the kit for samples to be detected, such as esophageal cancer patient samples, gastric cancer patient samples, gastritis patient samples, enteritis patient samples, appendicitis patient samples, colitis patient samples, peptic ulcer patient samples, liver cancer patient samples, pancreatic cancer patient samples, bile duct cancer patient samples, oral cancer patient samples, colorectal cancer negative samples (normal persons) and the like, are all greater than 38 or have no Ct values (see Table 3).
TABLE 3 specific sample test results
Figure BDA0003413699420000081
Figure BDA0003413699420000091
In the test, the detection results of 16 samples are all negative and are completely consistent with the enteroscope result, which shows that the kit is feasible in detecting specificity and has good specificity.
EXAMPLE 5 detection of clinical samples of colorectal cancer
1. Experimental methods
20 samples (containing polypide, adenoma and tumor) which are clinically detected by enteroscopy are selected, 30 samples (containing colorectal cancer) are selected, nucleic acid extraction is carried out on all samples, the kit of the embodiment 2 is used for detection, and meanwhile, detection of negative and positive quality control products is carried out.
2. Results of the experiment
The negative and positive quality control products meet the quality control requirements of the kit, so the detection result of the sample to be detected is effective. The Ct value of one of 20 negative samples is less than 38, the kit is judged to be positive and is inconsistent with the clinical result, and the detection results of the other 19 negative samples are completely consistent with the clinical result; in 30 positive samples, 1 sample has no Ct value, the kit is judged to be negative, and the other detection results are consistent with clinical results, and the detection results are shown in Table 4.
TABLE 4 detection results of clinical specimens of colorectal cancer
Figure BDA0003413699420000092
Figure BDA0003413699420000101
Figure BDA0003413699420000111
The detection results of 50 clinical specimens are completely consistent with the clinical results of 48 specimens, which indicates that the kit can be used for detecting the SNORD57 gene in the colorectal cancer sample. The kit is simple and convenient to operate, short in detection time, capable of realizing high-throughput detection, low in price, mainly applied to detection of the SNORD57 gene, and capable of being used for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers.
Example 6 detection of polyp and adenoma samples
1. Experimental methods
20 samples (without polyps, adenomas and tumors) which are clinically detected as negative by an enteroscope, 20 samples of intestinal polyps and 10 samples of intestinal adenomas are selected, all samples are subjected to nucleic acid extraction, the kit of the embodiment 2 is used for detection, and the detection of negative and positive quality control products is carried out at the same time.
2. Results of the experiment
The negative and positive quality control products meet the quality control requirements of the kit, so the detection result of the sample to be detected is effective. Ct values of 20 negative samples are all larger than 38, the judgment results of the kit are all negative, and the coincidence rate with clinical results is 100%; the Ct value of 4 samples in 20 intestinal polyp samples is more than 38 or no Ct value, the kit is judged to be negative, the Ct values of the other 16 samples are all less than 38, and the kit is judged to be positive; the Ct value of 1 sample in 10 intestinal adenoma samples is more than 38, the kit is judged to be negative, the Ct values of the other 9 samples are all less than 38, and the kit is judged to be positive. The detailed results are shown in Table 5.
TABLE 5 detection results of polyp and adenoma samples
Figure BDA0003413699420000121
Figure BDA0003413699420000131
Figure BDA0003413699420000141
The detection shows that the kit has good detection rate for hyperplastic polyp and adenoma and higher accuracy. Polyps and adenomas have a certain correlation with the occurrence of intestinal cancer, and studies have reported that nearly 80% of large intestine cancers are converted from intestinal polyps. The invention has important clinical significance in early screening and early diagnosis of intestinal cancer, and can be used as the basis for early diagnosis or definite diagnosis of tumor.
It should be finally noted that the above examples are only intended to illustrate the technical solutions of the present invention, and not to limit the scope of the present invention, and that other variations and modifications based on the above description and thought may be made by those skilled in the art, and that all embodiments need not be exhaustive. Any modification, equivalent replacement, and improvement made within the spirit and principle of the present invention should be included in the protection scope of the claims of the present invention.
Sequence listing
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Claims (4)

1. A primer probe composition for detecting SNORD57, wherein the nucleotide sequence of the SNORD57 is shown as SEQ ID No.1 or SEQ ID No.2, and the primer probe composition for detecting SNORD57 comprises a SNORD57 forward primer, a SNORD57 reverse primer, a reverse transcription primer and a SNORD57 probe;
the SNORD57 reverse transcription primer is a sequence 1 and a sequence 2 from the 5 'end to the 3' end in sequence, the sequence 1 is a sequence which has no homology with human genome and microorganism and has 18 to 25 basic groups, and the nucleotide sequence of the sequence 1 is shown as SEQ ID NO. 5; the sequence 2 is a sequence of which 9 bases are completely complementary with the 3' end sequence of the SNORD57 gene, and the nucleotide sequence of the SNORD57 reverse transcription primer is shown as SEQ ID NO. 3;
the SNORD57 forward primer is 20 basic groups at the most upstream of the 5' end of the SNORD57, and the nucleotide sequence is shown as SEQ ID NO. 4; the SNORD57 reverse primer is the sequence 1; the nucleotide sequence of the SNORD57 probe is shown in SEQ ID NO. 6.
2. The primer-probe composition for detecting SNORD57 as claimed in claim 1, wherein the 5 'end of the SNORD57 probe is labeled with any one of FAM, VIC, HEX, texas Red or CY5 fluorophore, and the 3' end of the probe is labeled with one MGB group.
3. The primer probe composition for detecting SNORD57 as claimed in claim 1, for use in preparing products for screening and diagnosing intestinal polyps, intestinal adenomas and/or intestinal cancers.
4. A detection kit for detecting SNORD57, which is characterized by comprising the primer probe composition for detecting SNORD57 according to claim 1.
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