CN114561462A - Cervical cancer gene methylation detection primer probe combination and kit and application thereof - Google Patents
Cervical cancer gene methylation detection primer probe combination and kit and application thereof Download PDFInfo
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Abstract
The invention provides a primer probe combination for detecting methylation of cervical cancer genes, a kit and application thereof, wherein a nucleic acid sample of the cervical cancer to be detected is subjected to bisulfite conversion by a bisulfite modification method, a fluorescence quantitative PCR technology is combined, a literature research result, a TCGA methylation chip database and a transcriptome sequencing expression profile are comprehensively analyzed, screening candidate genes for hypermethylation of cervical cancer by multiple data filtration analysis, designing specific gene methylation detection primers and probes aiming at a plurality of methylation detection sites on the candidate genes for hypermethylation of cervical cancer, covering more than 10 methylation CpG sites, amplifying the DNA sample to be detected modified by the bisulfite by a multiplex PCR amplification technology, and determining the methylation condition of the target gene in the sample to be detected according to the PCR amplification result, and improving the sensitivity and specificity of the kit through multiple ways to realize early screening and diagnosis of cervical cancer.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to a primer probe combination for detecting methylation of cervical cancer genes, a kit and application thereof.
Background
Cervical cancer (cervical cancer) is one of the most common reproductive system malignant tumors of women, is the second place among the female malignant tumors in the world, has the morbidity and mortality rate second to breast cancer, and seriously threatens the physical and psychological health of women. The cervical cancer is almost related to high-risk human papilloma virus (HR-HPV) infection, the onset age is 40 to 50 years at most, and the onset of the cervical cancer is younger in recent years. Cervical cancer occurs in the cervical region, mostly is squamous carcinoma, secondly is adenocarcinoma and adenosquamous carcinoma, and rarely is small cell carcinoma, clear cell carcinoma, etc. The occurrence and development of cervical cancer is a slow and gradual process, and usually the continuous development process of cervical intraepithelial neoplasia (CINI → II → III) → carcinoma in situ → early stage invasive carcinoma → invasive carcinoma, wherein the CINI is developed into invasive carcinoma about 10-15 years, and the in situ carcinoma is developed into invasive carcinoma about 3-4 years, and is discovered only by active screening. The treatment effect of the cervical cancer is closely related to clinical stages, early cancer cervical cancer usually has better prognosis, the early discovery of the cervical cancer can increase the chance of retaining the uterus by operation, the overall survival rate is improved, early diagnosis and early treatment are the key for improving the cure rate, and the cervical cancer has the possibility of relapse, so the prognosis monitoring also needs to pay attention, and the clinical significance is very important on how to discover the cervical cancer as early as possible and how to detect the relapse of the cervical cancer in time after the operation.
The current cervical cancer diagnosis technology comprises the following steps: 1) cytological examination of cervical scrape: the method is easily influenced by subjective factors, has a certain false negative rate, and is easy to miss diagnosis; 2) imaging technology: MRI examination, B-ultrasonic examination and CT examination, but the small tumor is not sensitive enough and can not be diagnosed clearly; 3) colposcopy: the naked eyes can not observe whether the cancer is changed or not, and the medicine is not suitable for patients with vaginal stenosis, cervical surface necrosis and hemorrhage; 4) examination of cervical biopsy: the method belongs to invasive examination, is complex to operate, causes discomfort to patients needing long-term tracking and observation, and has heavy economic burden. Therefore, there is a need to develop a non-invasive reliable cervical cancer marker and detection technology, which can improve the detection rate of early cancer of cervical cancer, improve the treatment effect of cervical cancer and reduce the death rate of cervical cancer.
Epigenetics refers to the fact that the nucleotide sequence of a gene is not changed, but the gene expression is genetically changed, and is a hot spot of tumor research in recent years, and epigenetic changes such as DNA methylation, histone modification, chromatin remodeling, non-coding RNA regulation and the like are considered to be closely related to the occurrence of tumors, wherein the DNA methylation is the most common epigenetic change which can regulate cell proliferation, apoptosis and differentiation, and the level of the epigenetic change is closely related to the biological characteristics of tumors. The current research shows that the cervical cancer is the same as other cancers and is the result of long-term action of various carcinogenic factors, the pathological process is a complex process of multigene variation accumulation, and the abnormal methylation of various oncogenes and cancer suppressor genes is involved, wherein most abnormal methylation is the hypermethylation of the cancer suppressor genes, and the hypermethylation often leads to the transcriptional silencing of the cancer suppressor genes. DNA methylation abnormality usually occurs in early cancer, and the methylation state of the DNA methylation abnormality changes once the DNA methylation abnormality is formed and needs to be continuously stimulated by external environment for a long time through the occurrence and development processes of the cancer, so that the detection of the DNA methylation index can be used as an important biological index for cancer diagnosis, early screening and prognosis.
Detection methods for DNA methylation can be broadly divided into two categories: whole genome methylation analysis and specific site methylation detection. The whole genome methylation analysis has higher detection cost and is often used as a high-throughput means for screening and discovering target genes; the specific site methylation detection method comprises a sodium bisulfite-combined restriction endonuclease analysis method (COBRA), a methylation specificity PCR Method (MSP), a methylation sensitivity high-resolution melting curve analysis method (MethyLight), and the like, wherein the restriction endonuclease analysis method can only obtain the methylation condition of a special enzyme cutting site, the methylation specificity PCR method is based on common PCR and electrophoresis analysis, has complicated operation and is easy to cause sample pollution, the methylation sensitivity high-resolution melting curve analysis method has higher requirements on the instrument, a fluorescence quantitative PCR instrument with a high-resolution melting (HRM) module is required, and the methylation fluorescence quantitative method is based on high flux and high sensitivity, does not need electrophoresis, hybridization and other operations after PCR, reduces pollution and operation errors, and is widely applied to DNA methylation detection. The existing method for detecting the DNA methylation of the cervical cancer based on the methylation fluorescence quantitative method has the defects of poor detection precision aiming at a single gene and limited diagnosis effect, researchers often improve the detection sensitivity by combining combined detection of a plurality of genes, but the specificity may be reduced due to the combined detection of the plurality of genes, and meanwhile, if the detection is carried out by adopting a single-tube single-gene test mode, more reagents are required to be consumed, the operation of experimenters is increased, and the experiment cost is higher.
Therefore, the market urgently needs to develop a stable and reliable noninvasive cervical cancer detection method with high sensitivity and specificity.
Disclosure of Invention
In view of the above, the invention provides a primer probe combination for methylation detection of cervical cancer genes and a kit and application thereof, wherein a nucleic acid sample of cervical cancer to be detected is subjected to bisulfite conversion by a bisulfite modification method, a fluorescence quantitative PCR technology is combined, a literature research result, a TCGA methylation chip database and a transcriptome sequencing expression profile are comprehensively analyzed, a candidate gene for hypermethylation of cervical cancer is screened by multiple data filtration analysis, a specific gene methylation detection primer and a probe are designed for a plurality of methylation detection sites on the candidate gene for hypermethylation of cervical cancer, more than 10 methylation CpG sites are covered, a DNA sample to be detected modified by bisulfite is amplified by a multiple PCR amplification technology, the methylation condition of a target gene in the sample to be detected is determined according to the PCR amplification result, and the sensitivity and the specificity of the kit are improved by a plurality of ways, early screening and diagnosis of cervical cancer are realized.
In order to achieve the above objects, the present invention provides, in a first aspect, a methylation detection site for a cervical cancer gene, wherein the methylation detection site for the gene comprises one or more of SOX1, AJAP1, ZNF 671.
The second aspect of the invention provides a PCR primer probe combination for detecting methylation of cervical cancer genes, which comprises one or more of the following nucleic acid sequence combinations shown in 1) to 3):
1) the PCR primer and probe for detecting the methylation of SOX1 comprise one or more of a primer probe combination 1, a primer probe combination 2 and a primer probe combination 3, wherein the primer probe combination 1 comprises an upstream primer shown as SEQ ID NO.1, a downstream primer shown as SEQ ID NO.2 and a fluorescent probe shown as SEQ ID NO.3, the primer probe combination 2 comprises an upstream primer shown as SEQ ID NO.4, a downstream primer shown as SEQ ID NO.5 and a fluorescent probe shown as SEQ ID NO.6, and the primer probe combination 3 comprises an upstream primer shown as SEQ ID NO.7, a downstream primer shown as SEQ ID NO.8 and a fluorescent probe shown as SEQ ID NO. 9;
2) PCR primers and probes for methylation detection of AJAP1, comprising one or more of a primer probe combination 4, a primer probe combination 5 and a primer probe combination 6, wherein the primer probe combination 4 comprises an upstream primer shown as SEQ ID No.10, a downstream primer shown as SEQ ID No.11 and a fluorescent probe shown as SEQ ID No.12, the primer probe combination 5 comprises an upstream primer shown as SEQ ID No.13, a downstream primer shown as SEQ ID No.14 and a fluorescent probe shown as SEQ ID No.15, and the primer probe combination 6 comprises an upstream primer shown as SEQ ID No.16, a downstream primer shown as SEQ ID No.17 and a fluorescent probe shown as SEQ ID No. 18;
3) ZNF671 methylation detection PCR primer and probe comprise one or more of a primer probe combination 7, a primer probe combination 8 and a primer probe combination 9, wherein the primer probe combination 7 comprises an upstream primer shown as SEQ ID NO.19, a downstream primer shown as SEQ ID NO.20 and a fluorescent probe shown as SEQ ID NO.21, the primer probe combination 8 comprises an upstream primer shown as SEQ ID NO.22, a downstream primer shown as SEQ ID NO.23 and a fluorescent probe shown as SEQ ID NO.24, and the primer probe combination 9 comprises an upstream primer shown as SEQ ID NO.25, a downstream primer shown as SEQ ID NO.26 and a fluorescent probe shown as SEQ ID NO. 27.
In an embodiment of the present invention, the PCR primer probe combination for detecting methylation of a cervical cancer gene further includes a PCR primer and a probe for detecting an internal reference gene GAPDH, the primer includes an upstream primer shown in SEQ ID No.28 and a downstream primer shown in SEQ ID No.29, and the probe includes a fluorescent probe shown in SEQ ID No. 30.
In one embodiment of the invention, the 5' end of the fluorescent probe comprises a fluorescent reporter group, including any one of FAM, HEX, NED, ROX, TET, JOE, TAMRA, CY3, CY 5.
In one embodiment of the invention, the 3' end of the fluorescent probe comprises a fluorescence quenching group, including any one of MGB, BHQ-1, BHQ-2 and BHQ-3.
In a preferred embodiment of the present invention, the fluorescence quenching group is MGB.
The third aspect of the invention provides a kit for detecting methylation of cervical cancer genes, which comprises the PCR primer probe combination as described in the second aspect of the invention, and further comprises a positive quality control product and a negative quality control product.
In one embodiment of the invention, the positive quality control material is cervical cancer tissue DNA.
In one embodiment of the present invention, the negative quality control material is leukocyte DNA.
In an embodiment of the present invention, the final concentration composition of the reaction system of the cervical cancer gene methylation detection kit comprises: 0.1-1 μ M PCR primer, 0.1-1 μ M probe.
In a preferred embodiment of the present invention, the final concentration composition of the reaction system of the cervical cancer gene methylation detection kit comprises: 0.1-0.5 mu MPCR primer and 0.1-0.5 mu M probe.
In one embodiment of the invention, the fluorescence quantitative PCR reaction conditions of the kit for detecting methylation of cervical cancer genes are as follows:
in a preferred embodiment of the invention, the fluorescence quantitative PCR reaction conditions of the kit for detecting methylation of cervical cancer genes are as follows:
the fourth aspect of the present invention provides a method for detecting methylation of a cervical cancer gene, comprising the steps of:
1) separating nucleic acid of a target gene in a biological sample to be detected;
2) subjecting the nucleic acid obtained in step 1) to bisulfite conversion treatment to obtain bisulfite converted DNA (Bis-DNA);
3) detecting the methylation state of the Bis-DNA obtained in the step 2) by adopting a methylation fluorescent quantitative PCR technology.
In an embodiment of the present invention, the biological sample in step 1) includes one of tissue and cell.
In a preferred embodiment of the present invention, the biological sample of step 1) comprises exfoliated cervical cells.
In the fifth aspect, the invention provides the cervical cancer gene methylation detection site according to the first aspect, the PCR primer probe combination for cervical cancer gene methylation detection according to the second aspect, the cervical cancer gene methylation detection kit according to the third aspect, or the cervical cancer gene methylation detection method according to the fourth aspect, in the preparation of the cervical cancer detection kit.
The invention has the following beneficial effects:
1) can be used as an important index for early screening, process monitoring and prognosis evaluation of cervical cancer: the kit for detecting the methylation of the cervical cancer gene takes DNA methylation abnormality as a detection object, the DNA methylation abnormality usually occurs in the early stage of cancer and runs through the occurrence and development processes of the cancer, and the methylation state of the DNA methylation abnormality changes once the DNA methylation abnormality is formed and needs to be continuously stimulated by external environment for a long time, so that the detection of the DNA methylation index can be used as an important biological index for early screening, process monitoring and prognosis evaluation of the cervical cancer;
2) non-invasive detection: the kit for detecting the methylation of the cervical cancer gene can assist in diagnosing the cervical cancer by detecting the methylation state of the cervical cancer related gene in the exfoliated cervical cell, so that noninvasive detection is realized;
3) single-tube multiple gene methylation detection: the joint inspection of the single-tube multiple gene methylation detection sites is established, so that the reagent consumption is reduced, the material consumption cost is reduced, the operation steps of experimenters are reduced, and the labor cost is reduced.
4) The accuracy is high: the cervical cancer gene methylation detection kit provided by the invention screens cervical cancer hypermethylation candidate genes through multiple data analysis, designs specific gene methylation detection primers and probes aiming at a plurality of methylation detection sites on the cervical cancer hypermethylation candidate genes, covers more than 10 methylation CpG sites, amplifies a DNA sample to be detected modified by bisulfite by adopting a multiple PCR amplification technology, performs joint detection by combining the methylation conditions of different genes or improves the sensitivity and specificity of the kit through multiple ways by detecting a plurality of different methylation detection areas of a single gene, thereby realizing accurate detection of early screening and diagnosis of cervical cancer.
Drawings
FIG. 1 is a positive diagram of typical detection results of cervical cancer gene methylation detection provided in an embodiment of the present invention, wherein the CT value of a gene methylation detection site is less than or equal to 25 and less than the CT value of an internal reference gene, and the detection result is determined to be positive;
FIG. 2 is a positive diagram of another typical detection result of the methylation detection of cervical cancer genes, wherein the CT value of the methylation detection site of the gene is less than or equal to 25 and greater than the CT value of the amplified reference gene, the Delta CT value is less than or equal to 5, and the result is determined to be positive;
FIG. 3 is a negative diagram of typical detection results of methylation detection of cervical cancer genes, wherein the CT value of the methylation detection site of the gene is greater than the CT value of an internal reference gene and the Delta CT value is greater than 5, and the result is determined to be negative.
Detailed Description
The present invention is described in detail below with reference to specific examples so that those skilled in the art can easily practice the present invention in light of the disclosure of the present specification. The embodiments described below are only a part of the embodiments of the present invention, and not all of them. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention. Unless otherwise indicated, the reagents, methods and apparatus used in the present invention are conventional in the art, and experimental methods without specific conditions being indicated are generally performed according to conventional conditions or conditions recommended by the manufacturer.
According to the invention, a bisulfite modification method is adopted to carry out bisulfite conversion on a cervical cancer nucleic acid sample to be detected, a fluorescence quantitative PCR technology is combined, a literature research result, a TCGA methylation chip database and a transcriptome sequencing expression profile are comprehensively analyzed, a cervical cancer hypermethylation candidate gene is screened through multiple data filtration analysis, a specific gene methylation detection primer and a specific probe are designed, a DNA sample to be detected modified by bisulfite is amplified, the methylation condition of a target gene in the sample to be detected is determined according to a PCR amplification result, and early screening and diagnosis of the cervical cancer are realized.
The gene methylation detection site of the cervical cancer gene methylation detection kit provided by the invention comprises one or more of SOX1, AJAP1 and ZNF 671.
The PCR primer probe combination of the cervical cancer gene methylation detection kit provided by the invention comprises one or more of the following nucleic acid sequence combinations shown in 1) -3):
1) the PCR primer and probe for detecting the methylation of SOX1 comprise one or more of a primer probe combination 1, a primer probe combination 2 and a primer probe combination 3, wherein the primer probe combination 1 comprises an upstream primer shown as SEQ ID NO.1, a downstream primer shown as SEQ ID NO.2 and a fluorescent probe shown as SEQ ID NO.3, the primer probe combination 2 comprises an upstream primer shown as SEQ ID NO.4, a downstream primer shown as SEQ ID NO.5 and a fluorescent probe shown as SEQ ID NO.6, and the primer probe combination 3 comprises an upstream primer shown as SEQ ID NO.7, a downstream primer shown as SEQ ID NO.8 and a fluorescent probe shown as SEQ ID NO. 9;
2) PCR primers and probes for methylation detection of AJAP1, comprising one or more of a primer probe combination 4, a primer probe combination 5 and a primer probe combination 6, wherein the primer probe combination 4 comprises an upstream primer shown as SEQ ID No.10, a downstream primer shown as SEQ ID No.11 and a fluorescent probe shown as SEQ ID No.12, the primer probe combination 5 comprises an upstream primer shown as SEQ ID No.13, a downstream primer shown as SEQ ID No.14 and a fluorescent probe shown as SEQ ID No.15, and the primer probe combination 6 comprises an upstream primer shown as SEQ ID No.16, a downstream primer shown as SEQ ID No.17 and a fluorescent probe shown as SEQ ID No. 18;
3) ZNF671 methylation detection PCR primer and probe comprise one or more of a primer probe combination 7, a primer probe combination 8 and a primer probe combination 9, wherein the primer probe combination 7 comprises an upstream primer shown as SEQ ID NO.19, a downstream primer shown as SEQ ID NO.20 and a fluorescent probe shown as SEQ ID NO.21, the primer probe combination 8 comprises an upstream primer shown as SEQ ID NO.22, a downstream primer shown as SEQ ID NO.23 and a fluorescent probe shown as SEQ ID NO.24, and the primer probe combination 9 comprises an upstream primer shown as SEQ ID NO.25, a downstream primer shown as SEQ ID NO.26 and a fluorescent probe shown as SEQ ID NO. 27.
The PCR primer probe combination of the kit for detecting the methylation of the cervical cancer gene further comprises a PCR primer and a probe for detecting an internal reference gene GAPDH, wherein the primer comprises an upstream primer shown as SEQ ID NO.28 and a downstream primer shown as SEQ ID NO.29, and the probe comprises a fluorescent probe shown as SEQ ID NO. 30.
Preferably, the 5' end of the fluorescent probe comprises a fluorescent reporter group, including any one of FAM, HEX, NED, ROX, TET, JOE, TAMRA, CY3 and CY 5.
Preferably, the 3' end of the fluorescent probe comprises a fluorescence quenching group, including any one of MGB, BHQ-1, BHQ-2 and BHQ-3.
Further preferably, the fluorescence quenching group is MGB.
The cervical cancer gene methylation detection kit provided by the invention can be used for detecting one of tissues and cells.
The interpretation of the detection result of the cervical cancer gene methylation detection kit provided by the invention comprises the following steps:
1) setting a threshold value: the baseline can be adjusted either automatically per instrument or manually according to the instructions for use of the instrument, the threshold is set in the linear portion of the log plot of fluorescence values, data is derived from the software and CT values are read.
2) And (3) judging the effectiveness of the kit:
the negative quality control product has the reference gene amplified and the CT value is less than or equal to 25, and the gene methylation detection site is not amplified; the reference gene and the gene methylation detection site of the positive quality control product are amplified, and the CT value is less than or equal to 25.
3) And (3) judging the effectiveness of the sample:
a) if the internal reference gene is amplified and the CT value is less than or equal to 25, the analysis can be continued;
b) if the CT value of the reference gene is more than or equal to 25 or no amplification exists, but the methylation detection site of the gene is amplified and the CT value is less than or equal to 25, the analysis can be continued;
c) if the CT value of the internal reference gene is greater than 25 or no amplification exists, if the CT value of the gene methylation detection site is greater than 25 or no amplification exists, the analysis cannot be continued, repeated detection is needed, and if the CT value of the internal reference gene is greater than 25 or no amplification exists, the sampling detection needs to be carried out again.
4) Determination of methylation detection result
a) If the gene methylation detection site is amplified but the CT value is more than 20, judging that the detection result is negative;
b) the gene methylation detection site is amplified, the CT value is less than or equal to 20, the delta CT value (the CT value of the gene methylation detection site-the CT value of the reference gene) is less than or equal to 10, the detection result is judged to be positive, the delta CT value is more than 10, and the detection result is judged to be negative.
In order to show the technical scheme of the invention more clearly, the invention is further illustrated by combining specific examples.
Example 1: sample DNA extraction and bisulfite conversion
1. Treatment of cervical exfoliated cell samples and extraction of DNA
1) Collecting samples:
the collection operation of the cervical exfoliated cell sample is as follows: the medical staff firstly uses the vaginal speculum to expose the cervix, and uses the cotton swab to wipe off the excessive secretion of the cervix. Placing a cervical brush at the cervical orifice, rotating for 5 circles in a single direction to obtain a sufficient epithelial cell sample, then placing the head of the cervical brush into a sample tube filled with cell preservation solution, breaking the cervical brush handle along the crease of the brush handle, leaving the brush head in the sample tube, screwing a tube cover, and making a sample mark
2) DNA extraction:
the method for extracting the DNA of the cervical exfoliated cells by using a nucleic acid extraction or purification reagent (universal type) produced by Anhudajian medical science and technology limited comprises the following specific steps:
(a) centrifuging a to-be-detected cervical exfoliated cell preservation solution sample at 4000rpm for 15min, sucking waste supernate by using a sample adding gun, and then adding 500 mu L of cell preservation solution;
(b) b, taking the cell sample obtained in the step a, adding 500 mu L of lysate A and 30 mu L of protease K into each tube, and performing lysis at 70 ℃ for 40 min;
(c) centrifuging for a short time, adding 200 μ L isopropanol into each tube, mixing well, and centrifuging for a short time;
(d) c, adding all the liquid in the step c into an adsorption column, and centrifuging at full speed for 30 s;
(e) washing once with 600 microliter of rinsing liquid I, and centrifuging at full speed for 30 s;
(f) rinsing with 600 μ L of rinsing solution II once, and centrifuging at full speed for 30 s;
(g) rinsing with 600 μ L of rinsing solution II once, and centrifuging at full speed for 2 min;
(h) air drying the centrifugal column in an air draft cabinet for 3min, suspending, adding 60 μ L of 70 deg.C preheated eluent, standing at room temperature for 5min, centrifuging at 13000rpm for 2min, collecting DNA, and storing at-20 deg.C.
2. Bisulfite conversion:
the genomic DNA obtained in the step was subjected to bisulfite conversion by using a nucleic acid extraction or purification reagent (centrifugal column type) produced by Anhudajian medical science and technology, Inc., having the following steps:
(a) taking 45 mu L of DNA sample to be detected, putting the sample into a new 1.5mL centrifuge tube, adding 5 mu L of transformation buffer solution, and placing the sample in a metal bath for incubation for 15min at the constant temperature of 37 ℃;
(b) after incubation is finished, adding 100 mu L of conversion solution prepared in advance into each sample, uniformly mixing and centrifuging for a short time, and incubating for 12-16 hours in a metal bath at 50 ℃ in a dark place;
(c) putting the sample on ice (0-4 ℃) and incubating for 10 min;
(d) placing the adsorption column in a collecting tube, and adding 400 μ L binding solution into the adsorption column;
(e) adding the sample in the step c into an adsorption column (containing binding liquid), covering a tube cover tightly, turning upside down, uniformly mixing for several times, centrifuging for 30s at full speed (14000rpm), and discarding waste liquid;
(f) adding 100 mu L of rinsing liquid into the adsorption column, centrifuging at full speed for 30s, and discarding the waste liquid;
(g) adding 200 mu L of desulfonation liquid into the adsorption column, incubating for 20min at room temperature (20-30 ℃), then centrifuging for 30s at full speed, and removing waste liquid;
(h) adding 200 mu L of rinsing liquid into the adsorption column, centrifuging at full speed for 30s, repeatedly adding 200 mu L of rinsing liquid, centrifuging at full speed for 30s, and discarding the waste liquid and the collecting pipe;
(i) placing the adsorption column into a 1.5mL sterile centrifuge tube, suspending and dropwise adding 30 mu L eluent into the middle part of the adsorption membrane, eluting the converted DNA, centrifuging at full speed for 1min, collecting Bis-DNA, and storing at-20 ℃.
Example 2: cervical cancer hypermethylation candidate gene, specific primer and probe screening
1. Screening of cervical exfoliated cell hypermethylation candidate genes of cervical cancer patients
Comprehensively analyzing the research results of the literature, a TCGA methylation chip database and a transcriptome sequencing expression profile, screening methylation sites with significant differences, and finally screening and determining SOX1, AJAP1 and ZNF671 as high methylation candidate genes of cervical cancer through multiple data filtering analysis.
2. Primer probe combination screening for cervical cancer methylation detection
1) Screening of specific primers and probes:
designing methylation primers and probes on Methyl primer Express v1.0 software according to the nucleic acid sequences of the SOX1, AJAP1 and ZNF671, repeatedly designing and knocking by an applicant, screening to obtain PCR probes and primers for related gene methylation, and synthesizing the designed primers and probes by Beijing Rui Boxing biological technology company Limited, wherein the specific sequences are shown in the following table:
specific primers and probes for an internal reference gene GAPDH are arranged at the same time, and the specific sequences are as follows:
| name (R) | Sequence (5 '-3') |
| Methy-GAPDH-F | AAGTTAGGTTAGTTTGGTAGGGAAGTT(SEQ ID NO.28) |
| Methy-GAPDH-R | AACCCTAAACCACCTCCCC(SEQ ID NO.29) |
| Methy-GAPDH-P | TTTGGGTTTTTTTGGGGGTAAGGAGATGT(SEQ ID NO.30) |
Wherein the 5 'end of the probe sequence is modified with a fluorescent group selected from any one of FAM, HEX, NED, ROX, TET, JOE, TAMRA, CY3 and CY5, and the 3' end is marked with a fluorescence quenching group selected from any one of MGB, BHQ-1, BHQ-2 and BHQ-3.
Example 3: methylation fluorescent quantitative PCR amplification detection of cervical cancer hypermethylation candidate genes
1. The reaction system of the methylation fluorescent quantitative PCR is as follows: 7.5. mu.L of 2 XPCR reaction premix, 0.1. mu.L of each 10. mu.M GAPDH primer and probe, 0.5. mu.L of each 10. mu.M primer probe combination, 0.2. mu.L of each probe, 3. mu.L of Bis-DNA, and up to 15. mu.L of water.
2. Reaction conditions of methylation fluorescent quantitative PCR
3. Interpretation of detection results of methylation fluorescent quantitative PCR
1) Setting a threshold value: the baseline can be adjusted either automatically per instrument or manually according to the instructions for use of the instrument, the threshold is set in the linear portion of the log plot of fluorescence values, data is derived from the software and CT values are read.
2) And (3) judging the effectiveness of the kit:
the negative quality control product has the reference gene amplified and the CT value is less than or equal to 25, and the gene methylation detection site is not amplified; the reference gene and the gene methylation detection site of the positive quality control product are amplified, and the CT value is less than or equal to 25.
3) And (3) judging the effectiveness of the sample:
a) if the internal reference gene is amplified and the CT value is less than or equal to 25, the analysis can be continued;
b) if the CT value of the reference gene is more than or equal to 25 or no amplification exists, but the methylation detection site of the gene is amplified and the CT value is less than or equal to 25, the analysis can be continued;
c) if the CT value of the internal reference gene is greater than 25 or no amplification exists, if the CT value of the gene methylation detection site is greater than 25 or no amplification exists, the analysis cannot be continued, repeated detection is needed, and if the CT value of the internal reference gene is greater than 25 or no amplification exists, the sampling detection needs to be carried out again.
4) Determination of methylation detection result (CT value of gene methylation detection site-CT value of reference gene)
a) If the CT value of the gene methylation detection site is less than or equal to 25, the result is judged to be positive if the CT value of the gene methylation detection site is less than the CT value of the reference gene or the reference gene is not amplified; if the CT value of the gene methylation detection site is greater than the CT value of the reference gene and the delta CT value is less than or equal to 5, judging that the result is positive;
b) the gene methylation detection site is not amplified, or the CT value of the gene methylation detection site is greater than the CT value of the reference gene and the Delta CT value is greater than 5, and the result is judged to be negative.
Example 4: clinical sample detection and verification kit effect
1. Cervical exfoliated cell sample detection
The test and verification kit effect is performed on clinical cervical exfoliated cell samples according to the experimental procedures described in the above examples 1, 2 and 3, in order to verify the test effect of the primer probe combination for methylation detection of cervical cancer genes, the primer probe combination in the above example 2 is used to test 24 cervical exfoliated cell samples for cervical cancer and 6 normal female cervical exfoliated cell samples for normal female, wherein the numbers 1-24 are cervical exfoliated cell samples for cervical cancer, and the numbers 25-30 are normal female cervical exfoliated cell samples for cervical cancer, under the condition that the negative quality control product and the positive quality control product meet the validity judgment of the kit, typical methylation detection result amplification graphs are shown in fig. 1, fig. 2 and fig. 3, the detailed results are shown in the following tables, "+" represents positive detection, and "-" represents negative detection:
from the above results, the statistical analysis was as follows:
from the results, the detection sensitivity of the single primer probe combination in the cervical cancer gene methylation detection kit provided by the invention is 70.8-87.5%, and the specificity is 83.3-100%.
In order to further improve the performance of the kit, the combination of the primer and probe is expected to improve the detection effect of the kit in a multiple joint detection mode, wherein the detection sensitivity and specificity of the following combinations are both more than 90 percent:
the above results are obtained based on single-tube detection analysis of single-gene single-detection-site of cervical cancer, the detection mode needs to consume more reagents and simultaneously increases the operation of experimenters, the experiment cost is higher, and the joint inspection of single-tube multiple-gene methylation detection sites can reduce the reagent consumption to a greater extent, reduce the material cost, simultaneously reduce the operation of experimenters and reduce the labor cost. Therefore, the invention establishes the optimal combination of the single-tube multiple gene methylation detection site joint inspection and further screens the cervical cancer gene methylation detection kit, takes the DNA samples of the cervical cancer cervical exfoliated cell sample and the normal female cervical exfoliated cell sample as templates, and tests the detection effect of the single-tube multiple gene methylation detection site joint inspection, and the result is as follows:
the results show that the detection sensitivity and specificity of the joint detection of partial single-tube multiple gene methylation detection sites are reduced to a certain extent, so that the primer probe combinations 1, 6 and 8, the primer probe combinations 3, 4 and 8, the primer probe combinations 3, 5 and 7 and the primer probe combinations 3, 6 and 8 are preferably used for further verification.
2. Tissue sample testing
By testing the tissue samples with the above preferred combination, the effect of testing the tissue samples was tested, with the following results:
the result shows that the detection sensitivity of the cervical cancer gene methylation detection kit provided by the invention is between 94.7% and 100%, the specificity is between 88.9% and 100%, and the kit has higher detection sensitivity and detection specificity when detecting the gene methylation of the cervical cancer tissue sample.
In conclusion, the cervical cancer gene methylation detection kit provided by the invention has higher detection sensitivity and detection specificity, becomes an ideal choice for cervical cancer diagnosis and early screening, and assists in early diagnosis and early treatment of cervical cancer.
While the foregoing description shows and describes several preferred embodiments of the invention, it is to be understood, as noted above, that the invention is not limited to the forms disclosed herein, but is not to be construed as excluding other embodiments and is capable of use in various other combinations, modifications, and environments and is capable of changes within the scope of the inventive concept as expressed herein, commensurate with the above teachings, or the skill or knowledge of the relevant art. And that modifications and variations may be effected by those skilled in the art without departing from the spirit and scope of the invention as defined by the appended claims.
Sequence listing
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Anhui Dajian medicine science and technology Limited
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Claims (10)
1. The cervical cancer gene methylation detection site is characterized by comprising one or more of SOX1, AJAP1 and ZNF 671.
2. The PCR primer probe combination for detecting the methylation of the cervical cancer genes is characterized by comprising one or more of the following nucleic acid sequence combinations shown in 1) to 3):
1) the PCR primer and probe for detecting the methylation of SOX1 comprise one or more of a primer probe combination 1, a primer probe combination 2 and a primer probe combination 3, wherein the primer probe combination 1 comprises an upstream primer shown as SEQ ID NO.1, a downstream primer shown as SEQ ID NO.2 and a fluorescent probe shown as SEQ ID NO.3, the primer probe combination 2 comprises an upstream primer shown as SEQ ID NO.4, a downstream primer shown as SEQ ID NO.5 and a fluorescent probe shown as SEQ ID NO.6, and the primer probe combination 3 comprises an upstream primer shown as SEQ ID NO.7, a downstream primer shown as SEQ ID NO.8 and a fluorescent probe shown as SEQ ID NO. 9;
2) PCR primers and probes for methylation detection of AJAP1, comprising one or more of a primer probe combination 4, a primer probe combination 5 and a primer probe combination 6, wherein the primer probe combination 4 comprises an upstream primer shown as SEQ ID No.10, a downstream primer shown as SEQ ID No.11 and a fluorescent probe shown as SEQ ID No.12, the primer probe combination 5 comprises an upstream primer shown as SEQ ID No.13, a downstream primer shown as SEQ ID No.14 and a fluorescent probe shown as SEQ ID No.15, and the primer probe combination 6 comprises an upstream primer shown as SEQ ID No.16, a downstream primer shown as SEQ ID No.17 and a fluorescent probe shown as SEQ ID No. 18;
3) ZNF671 methylation detection PCR primer and probe comprise one or more of a primer probe combination 7, a primer probe combination 8 and a primer probe combination 9, wherein the primer probe combination 7 comprises an upstream primer shown as SEQ ID NO.19, a downstream primer shown as SEQ ID NO.20 and a fluorescent probe shown as SEQ ID NO.21, the primer probe combination 8 comprises an upstream primer shown as SEQ ID NO.22, a downstream primer shown as SEQ ID NO.23 and a fluorescent probe shown as SEQ ID NO.24, and the primer probe combination 9 comprises an upstream primer shown as SEQ ID NO.25, a downstream primer shown as SEQ ID NO.26 and a fluorescent probe shown as SEQ ID NO. 27.
3. The PCR primer probe combination for detecting the methylation of the cervical cancer gene as claimed in claim 2, further comprising a PCR primer and a probe for detecting the internal reference gene GAPDH, wherein the primer comprises an upstream primer shown as SEQ ID No.28 and a downstream primer shown as SEQ ID No.29, and the probe comprises a fluorescent probe shown as SEQ ID No. 30.
4. The PCR primer probe combination for detecting the methylation of the cervical cancer gene as claimed in claim 2 or claim 3, wherein the 5' end of the fluorescent probe comprises a fluorescent reporter group, and the fluorescent reporter group comprises any one of FAM, HEX, NED, ROX, TET, JOE, TAMRA, CY3 and CY 5.
5. The PCR primer probe combination for the methylation detection of the cervical cancer gene according to claim 2 or claim 3, wherein the 3' end of the fluorescent probe comprises a fluorescence quenching group, and the fluorescence quenching group comprises any one of MGB, BHQ-1, BHQ-2 and BHQ-3.
6. A kit for detecting methylation of cervical cancer genes, which is characterized by comprising the PCR primer probe combination as claimed in claim 2 or claim 3, and further comprising a positive quality control substance and a negative quality control substance.
7. The kit for detecting methylation of a cervical cancer gene according to claim 6, wherein the final concentration composition of the reaction system of the kit for detecting methylation of a cervical cancer gene comprises: 0.1-1 μ M PCR primer, 0.1-1 μ M probe.
8. The kit for detecting methylation of a cervical cancer gene according to claim 6, wherein the PCR reaction conditions of the kit are as follows:
9. the detection method for detecting the methylation of the cervical cancer gene is characterized by comprising the following steps:
1) separating nucleic acid of a target gene in a biological sample to be detected;
2) subjecting the nucleic acid obtained in the step 1) to bisulfite conversion treatment to obtain bisulfite converted DNA, namely Bis-DNA;
3) detecting the methylation state of the Bis-DNA obtained in the step 2) by adopting a methylation fluorescent quantitative PCR technology.
10. The use of the methylation detection site of the cervical cancer gene according to claim 1, the PCR primer probe combination for the methylation detection of the cervical cancer gene according to claim 2, the methylation detection kit of the cervical cancer gene according to claim 6, or the methylation detection method of the cervical cancer gene according to claim 9 for preparing the kit for detecting the cervical cancer.
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| CN202011362758.1A CN114561462B (en) | 2020-11-27 | 2020-11-27 | Cervical cancer gene methylation detection primer probe combination, kit and application thereof |
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| CN117701721A (en) * | 2024-02-05 | 2024-03-15 | 广州迈景基因医学科技有限公司 | Detection reagent and kit for methylation of SOX1-SEPTIN9-TAC1 gene of cervical cancer |
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