CN113502353A

CN113502353A - Application of integrated high-frequency gene locus of high-intermediate-risk HPV (human papilloma virus) related to cervical cancer occurrence

Info

Publication number: CN113502353A
Application number: CN202110769179.7A
Authority: CN
Inventors: 陈世民; 杨帆; 黄晓园
Original assignee: Wuhan Kaideweisi Biotechnology Co ltd
Current assignee: Wuhan Kaideweisi Biotechnology Co ltd
Priority date: 2021-07-07
Filing date: 2021-07-07
Publication date: 2021-10-15

Abstract

The invention discloses an application of an integrated high-frequency genetic locus of high-medium-risk HPV (human papilloma virus) related to cervical carcinoma occurrence, belonging to the technical field of molecular genetics; by aiming at integration sites CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND2 of high-risk HPV, corresponding PCR amplification upstream and downstream primers are designed and assembled to obtain a corresponding kit for detecting the high-risk population of cervical cancer.

Description

Application of integrated high-frequency gene locus of high-intermediate-risk HPV (human papilloma virus) related to cervical cancer occurrence

Technical Field

The invention belongs to the technical field of molecular genetics, and particularly relates to application of integration sites of high-intermediate-risk HPV (human papilloma virus) on a human genome in a kit for detecting high-risk cervical cancer.

Background

Human Papilloma Virus (HPV), a circular double-stranded small-molecule DNA virus without envelope coating, has a genome length of about 8000 base pairs (bp). According to research results of WHO International cancer research Institute (IARC) and other international organizations, 13 genotypes including HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59 and 68 are suggested to be classified as high-risk genotypes, and 5 genotypes including 26, 53, 66, 73 and 82 are suggested to be classified as medium-risk genotypes. Persistent infection with high-risk HPV types is the leading cause of cervical intraepithelial neoplasia and cervical cancer. Results of studies on a global scale show that the presence of high-risk HPV DNA is detected in 99.7% of cervical cancer patients. Nevertheless, not every patient infected with high-risk HPV develops cervical cancer. With the progress of molecular biology and cytogenetics, scientific research finds that the integration of HPV DNA with host chromosomes is an important step in the process of cervical cell immortalization. After HPV DNA integration, oncoprotein is continuously expressed, instability of host genome is increased, and normal cervical epithelium is induced to develop precancerous lesion and finally become carcinogenic. At present, HPV genome integration is a research result of important markers for malignant transformation of cervical intraepithelial neoplasia into cervical cancer, and is agreed in the industry. In benign lesions caused by HPV, the viral DNA inside the cell is usually located outside the host genome. In high-grade intratumoral and cervical cancers, HPV DNA is usually present in the host cell genome in an integrated form, and the integration rate increases significantly with the severity of cervical lesions. Therefore, the integration site of HPV and human genome can be used as a potential biomarker for cervical lesion and cervical cancer.

The existing methods for HPV integration detection include fluorescence in situ hybridization, Southern blot hybridization detection, multiplex real-time fluorescence PCR, amplification of papillomavirus oncogene transcripts, multiplex ligation-dependent probe amplification, ligation-mediated-PCR, and the like. Although these methods are all capable of detecting the HPV integration site, they all require the pre-design of a fixed targeted gene site or region to be detected. Because integration of HPV DNA into a human genome is random, the genetic locus to be detected cannot be estimated, the region to be detected needs to be sequenced, and then a reversible end termination sequencing method needs to be adopted. The method can be used for sequencing the HPV DNA integrated into the human genome segment, detecting the randomly integrated sites and finding unknown integrated regions, and compared with the traditional molecular biological method, the method can reduce the detection false negative and improve the detection rate.

The reversible end termination sequencing method has the advantages of accuracy, high sensitivity, rapidness and low cost, can simultaneously sequence a plurality of genes, can realize HPV typing detection and HPV integration detection. A capture probe is designed aiming at high-medium-risk HPV DNA, a liquid phase hybridization gene capture technology is utilized to enrich target region related gene segments, a reversible terminal termination sequencing technology is combined to obtain DNA sequence data, an integration site can be obtained by sequence comparison, and finally, a PCR sanger sequencing is used to verify the detected integration site. The method can greatly reduce the cost of human gene sequencing, genetic research and gene diagnosis, improve the sequencing depth and more accurately discover the variation information of the specific region.

Disclosure of Invention

In view of the above deficiencies of the prior art, the present invention utilizes reversible end-termination sequencing method to detect virus integration and PCR Sanger sequencing method to find eleven new HPV integration sites (CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6, CTNND2) related to the occurrence of cervical cancer; the kit for detecting the high risk group of cervical cancer is prepared by integrating the HPV to the locus, and has the advantages of rapidness, convenience, accuracy and the like; specifically, the following technique is used.

The upstream and downstream primer combinations are used for PCR amplification of integration sites of high-intermediate-risk HPV, wherein the integration sites of the high-intermediate-risk HPV are CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND 2; the 11 integration sites are integration gene sites formed by inserting partial or all sequences of HPV16, 18, 52 and 58 into human genome sequences.

The address of the sequence of HPV is as follows:

the website address of HPV16 is https:// www.ncbi.nlm.nih.gov/nuccore/NC _ 001526.2;

the website address of HPV18 is https:// www.ncbi.nlm.nih.gov/nuccore/AY 262282.1;

the website address of HPV52 is http:// www.ncbi.nlm.nih.gov/nuccore/GQ 472848.1;

the website address of HPV58 is http:// www.ncbi.nlm.nih.gov/nuccore/HQ 537777.1;

the insertion sites of the human genomic sequence include the following sites: chr 8: 127218387, respectively; chr 8: 112504554, respectively; chr 2: 145696795, respectively; chr 14: 68158022, respectively; chr 5: 167489837, respectively; chr 8: 2952780, respectively; and (2) ChrX: 122012948, respectively; chr 2: 114297012, respectively; chr 10: 107998046, respectively; chr 5: 31244804, respectively; chr 5: 12006626. of the above sites, the amino acid sequence identified by "chr 8: 127218387 "for example, indicates that HPV is integrated at position 127218387 on human chromosome 8.

The website corresponding to the human chromosome is as follows:

the website address of Chr2 is http:// www.ncbi.nlm.nih.gov/nuccore/NC _ 000002.11;

the website address of Chr5 is http:// www.ncbi.nlm.nih.gov/nuccore/NC _ 000005.9;

the website address of Chr8 is http:// www.ncbi.nlm.nih.gov/nuccore/NC _ 000008.10;

the website address of Chr10 is http:// www.ncbi.nlm.nih.gov/nuccore/NC _ 000006.11;

the website address of Chr14 is http:// www.ncbi.nlm.nih.gov/nuccore/NC _ 000014.9;

the website address of ChrX is http:// www.ncbi.nlm.nih.gov/nuccore/NW _004070891.1

The HPV site (or breakpoint) points include the following sites (or breakpoints): HPV 18: 5734; HPV 16: 5676 (f); HPV 16: 5942; HPV 18: 1740; HPV 58: 187; HPV 52: 3349; HPV 58: 5497; HPV 18: 6447; HPV 16: 3549; HPV 18: 3133; HPV 52: 7936. among the above breakpoints, the breakpoint expressed by "HPV 18: 5734 "for example, it means that the breakpoint at HPV integrated in the human genome is at base 5734.

Table 1 below is the site of integration of the genomic sequences of HPV16, 18, 52, 58 on the human genome. The "HPV sites" shown in the third column of Table 1 are inserted into the "sites on the human genome" shown in the second column of the "genes" shown in the first column, respectively.

TABLE 1 site of integration of the HPV genomic sequences on the human genome

Gene	Sites on the human genome	HPV sites
			CCAT1	Chr8：127218387	HPV18：5734
CSMD3	Chr8：112504554	HPV16：5676
			PABPC1P2	Chr2：145696795	HPV16：5942
RAD51B	Chr14：68158022	HPV18：1740
			TENM2	Chr5：167489837	HPV58：187
CSMD1	Chr8：2952780	HPV52：3349
			GRIA3	ChrX：122012948	HPV58：5497
DPP10	Chr2：114297012	HPV18：6447
			SLC25A51P1	Chr10：107998046	HPV16：3549
CDH6	Chr5：31244804	HPV18：3133
			CTNND2	Chr5：12006626	HPV52：7936

The sequences of the upstream primer and the downstream primer of the integration site CCAT1 are shown as SEQ ID NO.12 and SEQ ID NO.13 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CSMD3 are shown as SEQ ID NO.14 and SEQ ID NO.15 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site PABPC1P2 are shown as SEQ ID NO.16 and SEQ ID NO.17 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site RAD51B are shown as SEQ ID NO.18 and SEQ ID NO.19 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site TENM2 are shown as SEQ ID NO.20 and SEQ ID NO.21 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CSMD1 are shown as SEQ ID NO.22 and SEQ ID NO.23 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site GRIA3 are shown as SEQ ID NO.24 and SEQ ID NO.25 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site DPP10 are shown as SEQ ID NO.26 and SEQ ID NO.27 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site SLC25A51P1 are shown as SEQ ID NO.28 and SEQ ID NO.29 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CDH6 are shown as SEQ ID NO.30 and SEQ ID NO.31 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CTNND2 amplified by PCR are shown as SEQ ID NO.32 and SEQ ID NO. 33.

The PCR amplification upstream and downstream primer combinations for detecting HPV integration sites are shown in Table 2 below.

TABLE 2 PCR amplification of upstream and downstream primer combinations for detection of HPV integration sites

Those skilled in the art can appropriately add, reduce or change the length of the primer sequence shown in Table 2 above (delete part of the bases, retain only part or all of the 3' sequence) by adding different restriction enzyme site sequences, protecting bases, etc., and change the individual bases, based on the primer sequence shown in Table 2 above. The above operation is within the scope of the present invention as long as it does not affect PCR amplification.

Preferably, the sequence of the integration site CCAT1 is shown in SEQ ID NO. 1;

the sequence of the integration site CSMD3 is shown as SEQ ID NO. 2;

the sequence of the integration site PABPC1P2 is shown in SEQ ID NO. 3;

the sequence of the integration site RAD51B is shown as SEQ ID NO. 4;

the sequence of the integration site TENM2 is shown as SEQ ID NO. 5;

the sequence of the integration site CSMD1 is shown as SEQ ID NO. 6;

the sequence of the integration site GRIA3 is shown as SEQ ID NO. 7;

the sequence of the integration site DPP10 is shown in SEQ ID NO. 8;

the sequence of the integration site SLC25A51P1 is shown in SEQ ID NO. 9;

the sequence of the integration site CDH6 is shown as SEQ ID NO. 10;

the sequence of the integration site CTNND2 is shown in SEQ ID NO. 11.

The sequences of integration sites formed after insertion of the above HPV genomes into the human genome are shown in Table 3 below.

TABLE 3 integration sequences formed after insertion of the HPV genome into the human genome

Those skilled in the art can make appropriate additions, reductions or changes, for example, adding different restriction enzyme site sequences, protecting bases, etc., according to the sequences of the integration sites described in the above table 3, reducing the sequence length (e.g., deleting part of bases) of the integration sites described in the above table 3, and making changes for individual bases; such manipulations are within the scope of the present invention, as long as most of the bases of the sequence of the integration site described in Table 2 of the present invention are still retained.

The HPV integrated gene locus related to the occurrence of the cervical cancer, and the primers and reagents used in the detection process can be assembled into a kit for detecting the high risk group of the cervical cancer, and the kit is used for detecting the high risk group of the cervical cancer.

A kit for detecting high risk group of cervical cancer, comprising the upstream and downstream primer combination of the integration site of the amplified high intermediate risk HPV of claim 1, the sequence of which is shown as SEQ ID NO.12-SEQ ID NO. 33.

The method for extracting the DNA of the human cervical exfoliated cells is not particularly limited, and the method can be used as long as the integrity of the extracted DNA sample is ensured, a commercial DNA extraction kit can be purchased, and the DNA extraction reagent described in the fifth edition (F.M. Oseber et al) of the well-compiled molecular biology experimental guidelines can be referred to or can be properly adjusted to be used for extracting the DNA of the human cervical exfoliated cells.

Preferably, the kit for detecting the high risk group of cervical cancer further comprises a DNA extraction reagent, a PCR reagent and a plurality of sample storage tubes.

The invention has no special strict limitation on the manufacturers, concentrations and systems of the reagents used for PCR amplification, and can be premixed reagents for PCR amplification or singly packaged reagents for PCR amplification as long as the target bands can be amplified.

Preferably, in the kit for detecting a high risk group of cervical cancer, the DNA extraction reagent is: buffer ACL, RNaseA, protease K, Buffer ACL, Buffer WA, Buffer WB, and Elution Buffer;

the PCR reagent comprises DNA polymerase, an amplification buffer solution and double distilled water. When the kit is adopted, healthy normal cervical exfoliated cells (namely human cervical exfoliated cells which are not infected by HPV virus) can be selected as negative control, or liquid-based thin-layer cell preservation solution containing trace cervical cells can be selected as raw materials, DNA in the liquid-based thin-layer cell preservation solution is extracted, and a cell sample containing human cervical cell DNA is prepared by PCR amplification or clone transformation.

Preferably, in the kit for detecting a high risk group of cervical cancer, the sample storage tubes are 1.5ml EP tubes, and each sample storage tube contains 1 ml cell preservation solution.

Preferably, in the kit for detecting the high risk group of cervical cancer, the PCR reagent is

Master Mix, available from Nanjing Novowed Biotech, Inc., cat # P511-01.

The use method of the kit for detecting the high risk group of cervical cancer comprises the following steps:

(1) collecting human cervical exfoliated cells as a sample, and extracting exfoliated cell DNA by using a DNA extraction reagent;

(2) detecting and extracting a cervical exfoliated cell DNA sequence by using a reversible end termination sequencing method, and analyzing; filtering the joint sequence, the low-quality sequence and the repetitive sequence, evaluating the quality of the sequence before and after filtering, and ensuring that the sequence Q30 after filtering is more than 80 percent and the sequence length is more than 100 bp;

and (3) rapidly comparing the sequences of the preprocessed sequencing data to HPV virus and human genome reference sequences by adopting sequence comparison software. Based on the alignment, the sequence of the chimera is identified (i.e., one sequence, partially aligned with the HPV genome, and partially aligned with the human genome). Locally clustering the chimeric sequences according to positions on the human genome, locally aligning the clustered sequences with a reference genome, and determining whether the sample integrates a partial sequence of HPV and whether the partial sequence of HPV is integrated in the gene (such as CCAT1) according to the alignment result;

(3) using SEQ ID N0: 12 to SEQ ID NO.33, and performing PCR amplification on the integration site sequence obtained in the step (2) by using upstream and downstream primer sequences;

(4) and (4) analyzing results: sequencing the PCR product amplified in the step (3), and comparing the sequencing product with a human genome and an HPV genome. When a part of human genome and a part of HPV genome are aligned simultaneously, the integration of the gene by the HPV genome is shown, and the joint of the aligned human genome and HPV genome is the integration site of HPV; the detection of the integration site indicates that the result is positive, namely the cervical cancer high risk group is obtained; otherwise, the result is negative, i.e. not belonging to the high risk group of cervical cancer.

The PCR amplification method is not particularly limited, and the reagent operation can select proper amplification conditions according to the PCR amplification reagent as long as the target band can be amplified, wherein the PCR amplification method preferably comprises 25 cycles of 95 ℃ for 30s, 95 ℃ for 5s, 60 ℃ for 20s, 72 ℃ for 15s and 72 ℃ for 5min, and the parameters can be properly adjusted according to actual conditions.

The detection method of the HPV integrated gene locus related to the occurrence of cervical cancer, the HPV integrated gene locus related to the occurrence of cervical cancer and the primer for detecting the HPV integrated gene locus can be assembled into a kit for detecting the high risk group of cervical cancer, and can also be used for manufacturing DNA chips or other products, and the products can be used for detecting the high risk group of cervical cancer.

Compared with the prior art, the invention has the advantages that: the kit for detecting the high risk group of cervical cancer is prepared by obtaining HPV integration sites CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND2 related to the occurrence of cervical cancer by utilizing a reversible end termination sequencing method and PCRSanger sequencing, and integrating the HPV integration sites into the gene sites according to the DNA of cervical exfoliated cells. The kit assembled by HPV integration is applied to high risk groups for judging cervical cancer, has good innovation and is helpful for clinical diagnosis.

Drawings

FIG. 1 is a flow chart of the method of using the kit for detecting a high risk group of cervical cancer according to the present invention;

FIG. 2 shows the result of HPV integration positive rate analysis of all integration gene sites of different pathological stage samples;

FIG. 3 is a diagram showing HPV integration positivity of 11 high-frequency gene loci according to the present invention.

Detailed Description

The technical solutions of the present invention will be described clearly and completely below, and it should be understood that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. 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.

Example 1

The cervical exfoliated cells of 988 LSIL patients, 358 HSIL patients and 126 cervical cancer patients were selected as samples.

The LSIL of the invention refers to low-grade squamous intraepithelial lesion, and the HSIL refers to high-grade squamous intraepithelial lesion, which is different pathological stages of cervical intraepithelial neoplasia.

1. Centrifuging the cervical exfoliated cell sample for 5min to collect cells, and removing supernatant; sequentially adding 200 mul PBS and 20 mul protease K, and uniformly mixing by oscillation;

2. adding 200 μ l Buffer BCL, shaking, mixing, adding 56 deg.C water bath for 10min, reversing the above process, mixing for several times, and purifying with column; adding 150 μ l of anhydrous ethanol, shaking, mixing, and centrifuging for a short time to collect liquid on the inner wall of the tube cover;

3. placing FastPuggDNA Mini Columns II adsorption column in 2ml Collection tube, transferring the above mixed solution (including flocculent precipitate) to adsorption column; centrifuging at 12,000rpm (13,400 Xg) for 1 min; discarding the filtrate, and placing the adsorption column in a collection tube; add 500. mu.l Buffer WA to the adsorption column along the tube wall, centrifuge for 1min at 12,000rpm (13,400 Xg);

4. discarding the filtrate, and placing the adsorption column in a collection tube; add 600. mu.l Buffer WB along the tube wall, centrifuge at 12,000rpm (13,400 Xg) for 1min, discard the filtrate;

5. repeating the step 4;

6. placing the adsorption column in a collection tube; centrifuging the column at 12,000rpm (13,400 Xg) for 2 min;

7. transferring the adsorption column to a new 1.5ml centrifuge tube; dripping 50-200 μ l of Elution Buffer into the center of the adsorption column membrane, and standing at room temperature for 2-5 min; centrifuging at 12,000rpm (13,400 Xg) for 1 min;

8. the adsorption column was discarded and the DNA product was stored at-20 ℃ until use.

Example 2

The integration site of HPV in cervical tissue genome DNA is detected by reversible end-termination sequencing.

1. Viral integration detection of genomic DNA samples of cervical exfoliated cells: designing HPV full-length probes containing 18 subtypes (HPV16, HPV18, HPV26, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV53, HPV56, HPV58, HPV59, HPV66, HPV68, HPV73 and HPV82), wherein the sequence details of the probes are shown in the patent application CN112195287A of the applicant at 11, 12/2020 of 2020-A probe set for HPV typing and integration detection of human papillomavirus and a kit thereof;

constructing a DNA sequencing library according to the requirement of Illumina, carrying out enzyme digestion on sample genome DNA into small fragments by adopting an enzyme digestion mode, and then repairing and adding A to treat the tail ends of the small fragments; ensuring that the total amount of the constructed DNA library is more than or equal to 1500ng, and the main peak of the length of the library fragment is about 350-550 bp; according to a liquid phase probe hybridization capture technology, HPV probes containing 18 subtypes are applied to hybridize with a genomic DNA library for 16-24h at 65 ℃, and target products are captured to elute non-hybridized DNA fragments; the obtained fragments are amplified through 16 PCR cycles, purified and then captured by secondary hybridization, the obtained purified amplification product is a sequencing library, the concentration of the library is ensured to be more than or equal to 1 ng/mu l, and the main peak of the length of the library fragments is about 350-550 bp; adding the sequencing library into a gene sequencer Nextseq CN500 for sequencing;

2. analyzing the virus integration detection result:

firstly, removing sequences with low quality, repeated and polluted by adaptor primer, and simultaneously comparing the remaining sequences with human genome (NCBI build 37, HG) and HPV genome (HPV: NC _, HPV: AY, HPV: NC _, HPV: HQ, HPV: HQ, HPV: HQ, HPV: M HPV: EF202156, HPV: KF, HPV: GQ, HPV: NC _, HPV: EF, HPV: HQ, HPV EU: LR, HPV: EU, HPV: LR and HPV: LR);

second, sequences that are aligned completely to the human genome or the HPV viral genome are removed, leaving only chimeric sequences that are aligned partially to human and partially to the HPV genome at the same time. The assembly of the chimeric sequences by end pairing determines the exact integration site. The sequences assembled by end pairing are aligned again by using BWA v0.7.17, Samtools v1.9 and Picard v2.20.6 software, and the junction of the human genomic DNA and the HPV genomic DNA sequences is the integration site of HPV. From the alignment results, it can be determined whether the sample has integrated and whether there is integration in the CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6, CTNND2 gene loci.

Example 3

The HPV integration sites were verified using PCR amplification and Sanger sequencing.

1.PCR amplification

Designing upstream and downstream primers capable of amplifying the HPV integration sites, wherein the primers are shown in Table 2 and are prepared according to the system shown in the following Table 4:

TABLE 4 primer systems

Each tube was mixed well and amplified in a standard PCR instrument according to the procedure shown in table 5 below:

TABLE 5 PCR amplification procedure

2. And sending the PCR product obtained after amplification to Wuhan Pongziaceae biotechnology limited company for Sanger sequencing.

(1) PCR products (the content is more than 200ng, the volume is more than 20ul) obtained after amplification are sent to Wuhan Pongziaceae biotechnology limited company for Sanger sequencing;

(2) PCR samples were purified and the sequence of the PCR fragments was determined by adding ABI3730XL sequencer.

3. And (4) analyzing and detecting the integration sites of the HPV according to the sequencing result, and detecting a new integration site.

(1) Opening a sequencing result by applying the text document;

(2) performing sequencing result comparison by using NCBI BLAST;

open BLAST page: http: // www.ncbi.nlm.nih.gov/BLAST/o click on the nucleotide BLAST section's nucleotide BLAST link to a new page; inputting the Sequence in the Enter Query Sequence part or pasting the Sequence; the Job Title component may also call a name for this Job; select "others" in the Choose Search Set section, select NCBI chromosome in the drop-down dialog; selecting the accuracy of the comparison in the Program Selection part, and generally selecting high similarity sequences to click a BLAST button to obtain a comparison result;

(3) judging the comparison result;

the Description part indicates that one part of the sequence is from human genome DNA, and the other part of the sequence is from HPV genome DNA; wherein the higher the Max score, Total score, Max identity, the higher the degree of similarity; the lower the E value, the higher the degree of similarity; the alignment of the most similar human DNA and HPV viral DNA is selected.

(4) Counting results;

from the alignment results, it can be determined whether the sample has integration and integration of any one or more of CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND2 gene sites;

example 4

LSIL, HSIL and cervical cancer samples from HPV infection are extracted into genome DNA according to the method described in the embodiment 1, integration sites of HPV in cervical tissue genome DNA are detected by a reversible end termination sequencing method according to the method described in the embodiment 2, and all integrated gene sites are obtained after result analysis.

And (3) analyzing an experimental result:

FIG. 1 is a flow chart of the method of using the kit for detecting a high risk group of cervical cancer according to the present invention. The use method of the kit for detecting the high risk group of cervical cancer comprises the following steps: extracting cervical exfoliated cell genome DNA of a subject, detecting HPV integration sites by reversible end-termination sequencing virus integration detection and conventional PCR, and analyzing and judging the subject to belong to a high-risk group of cervical cancer according to detection results.

FIG. 2 analysis of HPV integration positivity of all integration gene sites of different pathological stage samples. The "all integration gene sites" described in the present invention refer to all HPV integration gene sites found in the process of detecting cervical exfoliated cell DNA by the inventors using the methods described in examples 1 and 2, and most of the HPV integration gene sites have low occurrence frequency. The integration sites of CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND2 have higher frequency. The sample is divided into LSIL, HSIL and cervical cancer samples, and the integration is positive, namely, part of the sample contains human genome sequence and part of the sample contains HPV genome sequence. According to the method for calculating the integration positive rate, the denominator is the total number of patients detected in a certain pathological stage, and the numerator is the number of the patients detected to be integration positive in the pathological stage. In 896 statistical LSIL samples, 339 HSIL samples and 114 cervical cancer samples, the detected HPV integration positive rate shows that the HPV integration positive rate is from 61.27% of LSIL to 68.14% of HSIL and then 92.98% of cervical cancer, and shows an increasing trend, and the result shows that the HPV integration positive rate is closely related to the malignancy degree of cervical lesions, and the higher the malignancy degree of cervical lesions, the higher the HPV integration positive rate is, so that HPV integration can be used as an index for evaluating the malignancy degree of cervical lesions and predicting the risk of cervical cancer;

FIG. 3 is a diagram showing HPV integration positive rate of 11 high-frequency gene loci, wherein the 11 gene loci of the invention are CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND 2. In 1472 samples, the HPV integration positive rate of 11 high-frequency gene loci (CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND2) is 9.25 percent, and the result shows that the high-frequency gene loci have higher detection positive rate, and the integration of the gene loci can be used as an index for evaluating the malignancy degree of cervical lesions and predicting the risk of cervical cancer;

the above description is only for the purpose of illustrating the preferred embodiments of the present invention and is not to be construed as limiting the invention, and any modifications, equivalents, improvements and the like that fall within the spirit and principle of the present invention are intended to be included therein.

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atttttctaa tttgtgtgtt taattgcaat gctgagacca tttacatatg taggtgttga 120

ggtaggtcgt ggtcagccat taggtgtggg cattagtggc catcctttat taaataaatt 180

ggatgacaca gaaaatgcta gtgcttatgc agcaaatgca ggtgtggata atagaga 237

<210> 4

<211> 821

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 4

gaatttgcca ttgtcaatgt cttatatgtt gtagaatgag aaagaaatga ctctttggag 60

tagatatctg caataaaatc tggattgatc tacttacagt cagtttcaga gtaggcagtc 120

tccagggcac tgggagtaac tagactctgg tctccaggcc taggttcagc tacattccct 180

acaaggcctt tggcgtgtac ctgttcagtt ggtcagtcac cctgtttcca aacaaaggac 240

atggccctga aaactataca caacagggca agatcctggc tctagtttgg gattcgtcat 300

gtctttttgt cttactatta tacaacatgg aatagatgat agcaattttg atttgtcaga 360

aatggtacaa tgggcatttg ataatgagct gacagatgaa agcgatatgg catttgaata 420

tgccttatta gcagacagca acagcaatgc agctgccttt ttaaaaagca attgccaagc 480

taaatattta aaagattgtg ccacaatgtg caaacattat aggcgagccc aaaaacgaca 540

aatgaatatg tcacagtgga tacgatttag atgttcaaaa atagatgaag ggggagattg 600

gagaccaata gtgcaattcc tgcgatacca acaaatagag tttataacat ttttaggagc 660

cttaaaatca tttttaaaag gaacccccaa aaaaaattgt ttagtatttt gtggaccagc 720

aaatacagga aaatcatatt ttggaatgag ttttatacac tttatacaag gagcagtaat 780

atcatttgtg aattccacta gtcatttttg gttggaaccg t 821

<210> 5

<211> 150

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 5

agtgggtgca gctcagattt gttgcctcta gaactgacag gaattaaatc cctgttgtct 60

taagtcatgc agtttgttgc catttgttat agcagtccca ggcaactgga ataggttgta 120

caaagggcgg aacgtgtgta gttctaaagt 150

<210> 6

<211> 150

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 6

ggtttcctgc cgcccactgg tctacacttg ttgtcccgcc taaactgact tgctgactca 60

cacgtcctgc agtgcagcta aacaatacat tgcctaacat tgcatgtttt aaactgcttt 120

taggcacata ttttatttaa actttcaatg 150

<210> 7

<211> 150

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 7

atgctaaaca tgtcagcagt tgtattatta tccatcccag aaatacccag caaacacttg 60

ctgagggatt aagcagattc agtacactgt actccatatc attaatacta tagggagaaa 120

cagaagtatt taaagattgt aattcaaatt 150

<210> 8

<211> 302

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 8

tcccaacgta ttagttgcca atactgtatt tggctgtcta tgtctttact gtcattttca 60

tagtggtcta tgattttgtc ctgcaacgca cttaaagttt ccagtcttta acttttttcc 120

tgtattacag atcttctcca gtcagatcct ctcccaacgt attagttgcc aatactgtat 180

ttggctgtct atgtctttac tgtcattttc atagtggtct atgattttgt cctgcaacgc 240

acttaaagtt tccagtcttt aacttttttc ctgtattaca gatcttctcc agtcagatcc 300

tc 302

<210> 9

<211> 225

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 9

cgtctggtcg tcgtcgtttc tgtggtggtt gtaggtgtgt gtctttggca cccacggaca 60

atgcggaggt cttggaggtt tcggtgcatt tcaaaatata ctgcaaagct atactaatta 120

aaatggcata ctactggcat aaaacagaga tatagaccaa tggaacagaa cagagccctc 180

agaaataatg ccacatatct acaaccatct gatctttgac aaacc 225

<210> 10

<211> 559

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 10

ttctgtttcc tctctcctag ccacagatcc ccatttatga ctttgtttcc tgctccatgt 60

cagtgtcaaa gttgctagta aggataaata gcaaggtcat gggactcttc tttatatttt 120

ctgggcctgg ctgttcaagc tgctgtttgt ggggggctca gtatatgatt agagtggaca 180

tttcctctct tggagaactt tgatggagtc ctcagaggtc gtctaactct ggaccctctt 240

ctcctatagt aagtaccttg ccccaggcaa gaaaaaaaat acagaaccta ctcactgctt 300

taaaaaaggt ggccaaacag tacaagtata ttttgatggc aacaaagaca attgtatgac 360

ctatgtagca tgggacagtg tgtattatat gactgatgca ggaacatggg acaaaacggc 420

tacctgtgta agtcacaggg gattgtatta tgtaaaggaa gggtacaaca cgttttatat 480

agaatttaaa agtgaatgtg aaaaatatgg gaacacaggt acgtgggaag tacattttgg 540

gaataatgta attgattgt 559

<210> 11

<211> 225

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 11

cgtctggtcg tcgtcgtttc tgtggtggtt gtaggtgtgt gtctttggca cccacggaca 60

atgcggaggt cttggaggtt tcggtgcatt tcaaaatata ctgcaaagct atactaatta 120

aaatggcata ctactggcat aaaacagaga tatagaccaa tggaacagaa cagagccctc 180

agaaataatg ccacatatct acaaccatct gatctttgac aaacc 225

<210> 12

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 12

cgtggtcagc ctttaggtgt 20

<210> 13

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 13

gaaacattag acgtggcggc 20

<210> 14

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 14

gtttgtaaca tcccaggcaa 20

<210> 15

<211> 25

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 15

tttaagggga tcttctttag gtgct 25

<210> 16

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 16

ggcattagtg gccatccttt 20

<210> 17

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 17

tatccacacc tgcatttgct 20

<210> 18

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 18

gcgagcccaa aaacgacaaa 20

<210> 19

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 19

ttggtctcca atctccccct 20

<210> 20

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 20

gggtgcagct cagatttgtt 20

<210> 21

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 21

ctacacacgt tccgcccttt 20

<210> 22

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 22

tctacacttg ttgtcccgcc 20

<210> 23

<211> 22

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 23

aggcaatgta ttgtttagct gc 22

<210> 24

<211> 23

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 24

atgctaaaca tgtcagcagt tgt 23

<210> 25

<211> 22

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 25

tctgcttaat ccctcagcaa gt 22

<210> 26

<211> 22

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 26

tcccaacgta ttagttgcca at 22

<210> 27

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 27

aagtgcgttg caggacaaaa 20

<210> 28

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 28

gtctggtcgt cgtcgtttct 20

<210> 29

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 29

ctccaagacc tccgcattgt 20

<210> 30

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 30

gaacatggga caaaacggct 20

<210> 31

<211> 21

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 31

acttcccacg tacctgtgtt c 21

<210> 32

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 32

gtctggtcgt cgtcgtttct 20

<210> 33

<211> 20

<212> DNA

<213> Artificial Sequence (Artificial Sequence)

<400> 33

ctccaagacc tccgcattgt 20

Claims

The upstream and downstream primer combination for PCR amplification of integration sites of high-intermediate-risk HPV is characterized in that the integration sites of the high-intermediate-risk HPV are CCAT1, CSMD3, PABPC1P2, RAD51B, TENM2, CSMD1, GRIA3, DPP10, SLC25A51P1, CDH6 and CTNND 2;

the sequences of the upstream primer and the downstream primer of the integration site CCAT1 are shown as SEQ ID NO.12 and SEQ ID NO.13 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CSMD3 are shown as SEQ ID NO.14 and SEQ ID NO.15 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site PABPC1P2 are shown as SEQ ID NO.16 and SEQ ID NO.17 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site RAD51B are shown as SEQ ID NO.18 and SEQ ID NO.19 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site TENM2 are shown as SEQ ID NO.20 and SEQ ID NO.21 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CSMD1 are shown as SEQ ID NO.22 and SEQ ID NO.23 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site GRIA3 are shown as SEQ ID NO.24 and SEQ ID NO.25 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site DPP10 are shown as SEQ ID NO.26 and SEQ ID NO.27 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site SLC25A51P1 are shown as SEQ ID NO.28 and SEQ ID NO.29 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CDH6 are shown as SEQ ID NO.30 and SEQ ID NO.31 through PCR amplification;

the sequences of the upstream primer and the downstream primer of the integration site CTNND2 amplified by PCR are shown as SEQ ID NO.32 and SEQ ID NO. 33.
2. The upstream and downstream primer combination for amplifying integration sites of high-and-medium-risk HPV according to claim 1, wherein the sequence of the integration site CCAT1 is shown as SEQ ID No. 1;

the sequence of the integration site CSMD3 is shown as SEQ ID NO. 2;

the sequence of the integration site PABPC1P2 is shown in SEQ ID NO. 3;

the sequence of the integration site RAD51B is shown as SEQ ID NO. 4;

the sequence of the integration site TENM2 is shown as SEQ ID NO. 5;

the sequence of the integration site CSMD1 is shown as SEQ ID NO. 6;

the sequence of the integration site GRIA3 is shown as SEQ ID NO. 7;

the sequence of the integration site DPP10 is shown in SEQ ID NO. 8;

the sequence of the integration site SLC25A51P1 is shown in SEQ ID NO. 9;

the sequence of the integration site CDH6 is shown as SEQ ID NO. 10;

the sequence of the integration site CTNND2 is shown in SEQ ID NO. 11. .
3. A kit for detecting a high risk group of cervical cancer, comprising the upstream and downstream primer combinations for amplifying integration sites of high intermediate risk HPV according to claim 1.
4. The kit for detecting the high risk group of cervical cancer according to claim 3, further comprising a DNA extraction reagent, a PCR reagent and a plurality of sample storage tubes.
5. The kit for detecting the high risk group of cervical cancer according to claim 4, wherein the DNA extraction reagent is: buffer ACL, RNaseA, protease K, Buffer ACL, Buffer WA, Buffer WB, and Elution Buffer;

the PCR reagent comprises DNA polymerase, an amplification buffer solution and double distilled water.
6. The kit for detecting the high risk group of cervical cancer according to claim 4 or 5, wherein the sample-holding tubes are 1.5ml EP tubes, and each of the sample-holding tubes contains 1 ml cell-preserving solution.
7. The kit for detecting the high risk group of cervical cancer according to claim 4 or 5, wherein the PCR reagent is
Master Mix。