CN101818213B - Gene chip and kit for detecting human papillomavirus (HPV) - Google Patents

Gene chip and kit for detecting human papillomavirus (HPV) Download PDF

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Publication number
CN101818213B
CN101818213B CN2010101519826A CN201010151982A CN101818213B CN 101818213 B CN101818213 B CN 101818213B CN 2010101519826 A CN2010101519826 A CN 2010101519826A CN 201010151982 A CN201010151982 A CN 201010151982A CN 101818213 B CN101818213 B CN 101818213B
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seq
hpv
human papillomavirus
detection
gene chip
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CN101818213A (en
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郭兴中
石慧
董正伟
方国伟
郭尧
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JINAN ADICON MEDICAL EXAMINATION CENTER Co Ltd
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JINAN ADICON MEDICAL EXAMINATION CENTER Co Ltd
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Abstract

The invention discloses a gene chip for detecting human papillomavirus (HPV), comprising a solid carrier and a human papillomavirus detecting probes fixed on the solid carrier. The detecting probes comprise nucleotide sequences in SEQ ID No.9-37, and the 27 types of HVP subtype specific probes in the invention correspondingly comprise 22 kinds of high-risk and mediate-risk HPV, and 5 kinds of low-risk HPV and two kinds of high-risk HPV integration (HPV16/HPV18). The invention also discloses a detecting kit for detecting various subtypes of HPV in a sample with high speed and high flux, and the kit comprises the gene chip, a primer sequence for detection, a human GAPDH gene, special HPV lysing solution, PCR reaction liquid and a color reagent, wherein the detecting probe fixed on the gene chip has the nucleotide sequence in the SEQ ID No.9-37; the primer sequence for detection is used for amplifying the DNA sequence of the HPV in a clinical sample, and the human GAPDH gene is used for amplifying the clinical sample. The HPV detection has important significance for the clinical diagnosis of HPV as well as the early prevention, the diagnosis, the treatment and the postoperation tracking of cervical cancer.

Description

Detect the gene chip and the test kit of human papillomavirus
Technical field
The invention belongs to life science and biological technical field, particularly a kind of gene chip that contains each hypotype probe of human papillomavirus (HPV) the invention still further relates to that a kind of HPV of being used for detects and the test kit of somatotype.
Background technology
The whole world has 510,000 women to be diagnosed as cervical cancer every year approximately, and it is the human second largest gynecologic malignant tumor that is only second to mammary cancer, and its morbidity is rejuvenation trend now.At home, annual newly-increased cases of cervical cancer is about 13.5 ten thousand, accounts for 1/3 of whole world morbidity quantity, has 80,000 people therefore to die of illness approximately and dies.Discover that (human papillomaviruses HPV) infects with human papillomavirus for cervical cancer patient more than 90%.Cervical cancer and precancerous lesion thereof be the synergistic result of multiple factor, the initiating agent that cervical cancer developed when high-risk HPV infected, the integration of HPV and host chromosome then is to promote the critical event that cervical carcinogenesis makes progress.Therefore detect HPV infection and integration situation in the cervical lesions, help early discovery, early diagnosis cervical cancer and precancerous lesion; The HPV of treatment control in time infects, and can prevent in the uterine neck knurl to become and take place, and can effectively reduce the M & M of cervical cancer, and the control of cervical cancer is had great clinical value.
HPV be a kind of have a species specificity have a liking for epithelium virus, belong to the small DNA virus of double-stranded closed loop.The mankind are unique hosts of HPV, in the stratified squamous epithelium of its directed infection human body skin and mucous membrane, have the host specific avidity of height.
IARC (IARC) symposium (nineteen ninety-five) clearly proposes, HPV infect be cervical cancer main diseases because of.Identify kind surplus the HPV hypotype 100 at present; Wherein kind infects relevant with pathology with uterine neck surplus in the of 30; Be divided into two kinds of high-risk-type and low risks according to the size of its virulence: HPV6,11,40,42 etc. is classified as low risk, mainly causes outer reproducibility condyloma class pathology, condyloma latum class pathology and the low cervical intraepithelial neoplasia (CIN I) of reproductive tract, anal skin and vagina bottom; High-risk-type is mainly HPV16,18,31,33,35,39,45,51,52,56,58,59,68,73,82 etc., mainly causes generation, especially HPV16 and 18 types of height cervical intraepithelial neoplasia (CIN II, CIN III) and cervical cancer.Therefore, the concrete HPV hypotype that detects in the sample has important directive significance for the control of cervical cancer.
HPV virus can't can not be induced the immunoreation that is easy to detect in vivo in vitro culture, therefore can't adopt SD method that it is diagnosed and somatotype.The diagnosis of early stage HPV mainly is according to typical clinical manifestation and macroscopic pointed condyloma; Or sexually revise according to cytology or pathological characteristics and to judge; Comprise that Pap smear (Pap Smear) and liquid based thin-layer cell detect (TCT); But a kind of ASCUS (ASCUS) of not confirming meaning appears in regular meeting; Often can cover a part of significant histopathology and occur false negative result unusually, need the binding molecule biology techniques to make a definite diagnosis.
Various in recent years Protocols in Molecular Biology widespread uses are for detecting virus genomic diagnostic techniques; Wherein common and fluorescence PCR method has advantages such as special, responsive, easy, quick; But because its highly sensitive; Can not satisfy clinical needs easily because of false positive appears in non-specific amplification, and owing to detect the limitation of flux.HC2 then is present unique acquisition drugs approved by FDA, can be applied to clinical diagnostic method.But this method can only detect the infection whether HPV is arranged in the sample, can not identify concrete HPV virus subtype, is unfavorable for clinical trail inspection and treatment.
High-risk HPV DNA is incorporated into host genome and will causes the host cell generation to comprise a series of irreversible Kettenreaktion such as cancer suppressor gene functional defect, activated oncogene, genomic instability and cell immortalityization; It is one of important mechanisms of cervical carcinogenesis; Its caution is worth and is higher than present general HPV-DNA infection detection, but the present commercially available probe that test kit adopted all lacks the detection of the situation of integrating to HPV, and present in addition existing HPV detects the not clear and definite subregion detection of film bar HPV; For the easy mistaken diagnosis of common clinician; The present invention is directed to above 2 kinds clinical significant index detected and improve, make that clinical HPV INFECTION IN DETECTION is abundanter, more accurate; More practical, more valuable.
Summary of the invention
In order to overcome the above-mentioned defective of prior art, the invention provides a kind of gene chip that can be used for detecting 27 kinds of HPV hypotypes and human chromosome integrated state:
A kind of gene chip that detects human papillomavirus comprises solid phase carrier and is fixed on the human papillomavirus detection probes on this solid phase carrier, it is characterized in that said detection probes comprises the nucleotide sequence of SEQ ID No.9-37:
HPV6:5’-AACTACATCTTCCACATACAC-3’(SEQ?ID?No.9)
HPV11:5’-GTCTAAATCTGCTACATACAC-3’(SEQ?ID?No.10)
HPV16:5’-ATTATGTGCTGCCATATCTACTT-3’(SEQ?ID?No.11)
HPV18:5’-ACAGTCTCCTGTACCTGGG-3’(SEQ?ID?No.12)
HPV31:5’-CCAATATGTCTGTTTGTGCTGC-3’(SEQ?ID?No.13)
HPV33:5’-GTACTAATATGACTTTATGC-3’(SEQ?ID?No.14)
HPV35:5’-GTGTTCTGCTGTGTCTTCTAGT-3’(SEQ?ID?No.15)
HPV39:5’-TATAGAGTCTTCCATACCT-3’(SEQ?ID?No.16)
HPV40:5’-CCCCACACCAACCCCATATAA-3’(SEQ?ID?No.17)
HPV42:5’-CATGACTTTGTGTGCCACTG-3’(SEQ?ID?No.18)
HPV43:5’-CGTTATGTGCCTCTACTGACC-3’(SEQ?ID?No.19)
HPV44:5’-CTACACAGTCCCCTCC-3’(SEQ?ID?No.20)
HPV45:5’-CTCTACACAAAATCCTGTG-3’(SEQ?ID?No.21)
HPV51:5’-CTGCTGCGGTTTCC-3’(SEQ?ID?No.22)
HPV52:5’-TTTATGTGCTGAGGTTAAAAAG-3(SEQ?ID?No.23)
HPV53:5’-CGCAACCACACAGTCTATG-3’(SEQ?ID?No.24)
HPV54:5’-ACAGCATCCACGCAGG-3’(SEQ?ID?No.25)
HPV56:5’-CAGAACAGTTAAGTAAATATGAT-3’(SEQ?ID?No.26)
HPV58:5’-CACTGAAGTAACTAAGG-3’(SEQ?ID?No.27)
HPV59:5’-TTCTACTACTTCTTCTATTCCTAA-3’(SEQ?ID?No.28)
HPV66:5’-TAATGCAGCTAAAAGC-3’(SEQ?ID?No.29)
HPV68:5’-TTTGTCTACTACTACTGAATCA-3’(SEQ?ID?No.30)
HPV70:5’-AACGGCCATACCTGCTGTATAT-3’(SEQ?ID?No.31)
HPV73:5’-TAGGTACACAGGCTAGTAG-3’(SEQ?ID?No.32)
HPV83:5’-GCTACACAGGCTAATGAATACACA-3’(SEQ?ID?No.33)
HPVmm4:5’-CACTGCTGTTACTCAATCTG-3’(SEQ?ID?No.34)
HPVCP8304:5’-GCTACATCTGCTGCT-3’(SEQ?ID?No.35)
GP:5’-GGAGCCAAAAGGGTCATCATCT-3’(SEQ?ID?No.36)
ALU:5’-AGCTACTCGGGAGGCTGAGGC-3’(SEQ?ID?No.37)
Further, said solid phase carrier is preferably nylon membrane; 3 ' end of said detection probes has amino labeled.
The design of the specific probe of the common hypotype of HPV of the present invention is according to HPV L1 zone, to different hypotypes design with detection probes (SEQ ID No.9-35) HPV DNA complementary nucleotide sequence.27 kinds of above-mentioned HPV hypospecificity probes, correspondence have comprised that 22 kinds high are jeopardized middle danger type HPV, and 5 kinds of low risk HPV and 2 kinds of high-risk HPVs are integrated (HPV16/HPV18).
SEQ ID No.36 is the probe to people GAPDH gene, because such primer has improved the accuracy that HPV detects to the detection of HPV, particularly relatively responsive to many hypotypes INFECTION IN DETECTION.
Middle probe of the present invention is a 3 ' amido modified probe (C7), can obtain better crossbreeding effect than 5 ' the amido modified probe.
The Tm of 27 kinds of probes is between 42 ℃-55 ℃ among the present invention; Homogeneous relatively; The optimal temperature conditions basically identical helped under same hybridization temperature, combining synchronously with close efficient when promptly 27 kinds of hypotype probes were hybridized with corresponding PCR product, and the accuracy of inspection is increased greatly.
In embodiments of the invention, can use a narrow line to replace the mode of point probe of the initial point of general employing, make big the increasing that contain much information that is loaded with on the unit surface.
Gene chip of the present invention is prepared from order to the below method:
(1) preparation of dna probe: synthetic terminal through amidized dna fragmentation with HPV DNA complementary 3 '; From the L1 zone of HPV DNA, pick out specific sequence,, design and synthesize out the amidized dna fragmentation of 3 ' terminal process according to the base complementrity characteristics;
(2) stationary probe: with above-mentioned probe stationary on the good nylon membrane of activation treatment; Earlier nylon membrane is carried out activation treatment, then probe is drawn on film, through the amino and the formation of the carboxyl on the activation film covalent attachment of probe end, firm with probe stationary on film;
(3) preparation gene chip: utilize the NaOH stopped reaction, seal the not surface negative charge group of bonding probes, make gene chip.
The present invention also provides the detection kit of each hypotype of HPV in a kind of quick, high-throughout detection sample, comprising:
(i) gene chip, fixing detection probes on it is the nucleotide sequence of SEQ ID No.9-37;
(ii) detect and use primer sequence, the human papillomavirus HPV DNA sequence of the clinical sample that is used for increasing, described primer sequence is:
G1:5’-CARGGACATAAYAATGGYATTTGCTG-3’(SEQ?ID?No.1)
G2:5’-CARGGACATAAYAATGGYATTTGTTG-3’(SEQ?ID?No.2)
G3:5’-GAAAAAYAAACTGYAAATCATAYTCCTC-3’(SEQ?ID?No.3)
G4:5’-GAAAAAYAAACTGYAAATCATAYTCTTC-3’(SEQ?ID?No.4)
16:5’-CATGCGGGTGGTCAGGTAATAT-3’(SEQ?ID?No.5)
18:5’-CATTTTGGGAATAATGTAATTGATTGT-3’(SEQ?ID?No.6)
(iii) be used for the increasing people GAPDH gene of clinical sample, end mark has vitamin H, and its primer sequence is:
GP1:5’-GCTTCTCTGCTGTAGGCTCATT-3’(SEQ?ID?No.7)
GP2:5’-GTCCTTCCACGATACCAAAGTT-3’(SEQ?ID?No.8)
The (iv) special-purpose lysate of human papillomavirus, its composition is 20mmol/Tris.HCL pH8.0,0.5%Triton-X-100,10%chelex-100;
(v) PCR reaction solution;
(vi) colouring reagents.
Further, said detection all has biotin labeling with 5 ' and 3 ' end of primer sequence; Said PCR reaction solution comprises: 2X PCR Mix, 20mM Tris-HCl (pH8.9), 50mM KCl, 3mM MgCl 2, 0.4mM dNTPs, 1mM DTT, 10%glycerol, 0.16%NP-40,0.1mM Tween-20,50U/mlTaq DNA polymerase.
In the HPV detection kit of the present invention, the primer of HPV16/18 and chromosomal integration amplification is SEQ IDNo.5-6, can detect 2 kinds of high-risk HPVs and integrate situation.
Positive control behaviour GAPDH of the present invention, its amplimer is SEQ ID No.7-8, increases simultaneously with HPV, detects simultaneously.
Utilize HPV detection kit of the present invention to detect HPV and infect, concrete steps are following:
(1) amplification sample: the DNA that extracts in the clinical sample is increased through the HPV gene parting detecting reagent, and 5 ' and 3 ' end of the primer all is marked with vitamin H, and amplification obtains 5 ' and 3 ' end and all has biotin labeled DNA product;
(2) hybridization: the dna probe that distributes on DNA that above-mentioned amplification is obtained and the gene chip reacts;
(3) colour developing: drip colouring reagents, naked eyes direct viewing result.
The test kit that is used to detect HPV of the present invention can accurate detection goes out HPV to be infected and identifies concrete hypotype, simple to operate, highly sensitive, follows the tracks of being significant for early diagnosis, prevention, treatment and the postoperative of cervical cancer.
Description of drawings
Fig. 1 is to use HPV detection kit of the present invention to detect the figure as a result of clinical sample.
Embodiment
Embodiment 1: the preparation of gene chip
According to worldwide HPV infection research result and domestic actual HPV infection conditions, select 27 kinds of HPV hypotypes, comprise 22 kinds of high-risk-types and middle danger type HPV, 5 kinds of low risk HPV and 2 kinds integrated (16/18 type).To every kind of HPV hypotype, the synthetic 3 ' end of design has amino specific probe (SEQID No.9-37).
With the cutting on request of film bar; Be soaked in 30min in the freshly prepared EDAC solution; Use distillation washing film 3 times, 2min/ time, on filter paper, dry, diaphragm is fixed on the filter paper; Draw probe 3 times according to the every in order lattice of the grid on the film; The film that point is good is placed 20min in room temperature and is dried; Soak film bar 5min with 0.5N NaOH; Discard NaOH, with distilled water wash 3 times, 2min/ time; After fully drying, preserve subsequent use in the drying bottle.
Embodiment 2: specimen preparation
Adopt the DNA in boiling method preparation and the purifying clinical sample.
The PCR reaction system is 20ul, the concrete prescription as follows:
2X?PCR?Mix 10μl
Plus?solution 2μl
SeqNo.1-2(100uM) 0.03μl
SeqNo.2-4(100uM) 0.03μl
SeqNo.5-6(100uM) 0.03μ1
Deionized water 5.91 μ l
Template DNA 2ul
A negative control is set up in each experiment, is template with the 2ul sterilized water promptly.
Increase by following condition:
Stage1:94℃?3min
Stage2:94℃?20s
51℃?1min
72℃?30s
40cycles
Stage3:72℃?2min
Embodiment 3:HPV DNA detection
The DNA sample that amplification among the embodiment 2 is obtained carries out hybridization with the gene chip for preparing among the embodiment 1, carries out interpretation according to the colour developing situation at last, has the position of colour developing to represent corresponding HPV hypotype.
1, hybridization
Get the 5ml centrifuge tube, indicate that the patient numbers, put into the film bar that indicates patient's numbering equally, add 3ml hybridization solution (0.3mol/L NaCl, 10mmol/L NaH 2PO 4, 2mmol/L EDTA, 0.1%SDS, pH7.4) and the PCR product, boiling water bath 10min; 51 ℃ of hybridization 1h.
Get the 50ml centrifuge tube, add 40ml B liquid and be preheated to 51 ℃.
Contrast: get in the hybrid pipe that 10ul PC adds negative control and hybridize, method is the same.
2, wash film
Take out the film bar, move to preheating film washing liquid (75mmol/L NaCl, 2.5mmol/L NaH are housed 2PO 4, 0.5mmol/L EDTA, 0.1%SDS is in 50ml centrifuge tube pH7.4), in 51 ℃ of jog washing 15min (every pipe 40ml solution can wash 5 films at most simultaneously).
3, colour developing
With 1: 2000 POD (px) solution of hybridization solution preparation (five the available 6ul POD of film bar mother liquors are mixed with 12ml and use liquid), the room temperature jog soaks 30min, discards POD solution.With hybridization solution room temperature jog washing 2 times, 5min/ time.Wash film 1-2min with 0.1mol/L Trisodium Citrate room temperature, the liquid of fresh colour developing simultaneously (19ml 0.1mol/L Trisodium Citrate, 1ml TMB, 10ul 3%H 2O 2).The film bar is soaked in the colour developing liquid visible spot manifests about lucifuge colour developing 5min, the film bar is soaked in finishes coupling reaction in the clear water, and in 4 ℃ of preservations.
4, interpretation as a result
As contrast, blue spot can appear in the positive quality control PC position of film bar, and point out this hybridization, colour developing in proper working order, interpretation as a result this time is regarded as effectively.
The result sees shown in Figure 1,
Positive quality control: PC is normal
High-risk-type: HPV16/HPV33/
Low risk: HPV42
Integrated: HPV16
Sequence table
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Claims (6)

1. a gene chip that detects human papillomavirus comprises solid phase carrier and is fixed on the human papillomavirus detection probes on this solid phase carrier, it is characterized in that said detection probes is made up of the nucleotide sequence of SEQ ID No.9-37:
HPV6:5’-AACTACATCTTCCACATACAC-3’ (SEQ?ID?No.9)
HPV11:5’-GTCTAAATCTGCTACATACAC-3’ (SEQ?ID?No.10)
HPV16:5’-ATTATGTGCTGCCATATCTACTT-3’?(SEQ?ID?No.11)
HPV18:5’-ACAGTCTCCTGTACCTGGG-3’?(SEQ?ID?No.12)
HPV31:5’-CCAATATGTCTGTTTGTGCTGC-3’?(SEQ?ID?No.13)
HPV33:5’-GTACTAATATGACTTTATGC-3’ (SEQ?ID?No.14)
HPV35:5’-GTGTTCTGCTGTGTCTTCTAGT-3’(SEQ?ID?No.15)
HPV39:5’-TATAGAGTCTTCCATACCT-3’?(SEQ?ID?No.16)
HPV40:5’-CCCCACACCAACCCCATATAA-3’?(SEQ?ID?No.17)
HPV42:5’-CATGACTTTGTGTGCCACTG-3’?(SEQ?ID?No.18)
HPV43:5’-CGTTATGTGCCTCTACTGACC-3’?(SEQ?ID?No.19)
HPV44:5’-CTACACAGTCCCCTCC-3’?(SEQ?ID?No.20)
HPV45:5’-CTCTACACAAAATCCTGTG-3’?(SEQ?ID?No.21)
HPV51:5’-CTGCTGCGGTTTCC-3’(SEQ?ID?No.22)
HPV52:5’-TTTATGTGCTGAGGTTAAAAAG-3(SEQ?ID?No.23)
HPV53:5’-CGCAACCACACAGTCTATG-3’?(SEQ?ID?No.24)
HPV54:5’-ACAGCATCCACGCAGG-3’?(SEQ?ID?No.25)
HPV56:5’-CAGAACAGTTAAGTAAATATGAT-3’?(SEQ?ID?No.26)
HPV58:5’-CACTGAAGTAACTAAGG-3’?(SEQ?ID?No.27)
HPV59:5’-TTCTACTACTTCTTCTATTCCTAA-3’(SEQ?ID?No.28)
HPV66:5’-TAATGCAGCTAAAAGC-3’ (SEQ?ID?No.29)
HPV68:5’-TTTGTCTACTACTACTGAATCA-3’(SEQ?ID?No.30)
HPV70:?5’-AACGGCCATACCTGCTGTATAT-3’?(SEQ?ID?No.31)
HPV73:5’-TAGGTACACAGGCTAGTAG-3’?(SEQ?ID?No.32)
HPV83:5’-GCTACACAGGCTAATGAATACACA-3’(SEQ?ID?No.33)
HPVmm4:5’-CACTGCTGTTACTCAATCTG-3’?(SEQ?ID?No.34)
HPVCP8304:5’-GCTACATCTGCTGCT-3’ (SEQ?ID?No.35)
GP:?5’-GGAGCCAAAAGGGTCATCATCT-3’?(SEQ?ID?No.36)
ALU:?5’-AGCTACTCGGGAGGCTGAGGC-3’?(SEQ?ID?No.37)
2. the gene chip of detection human papillomavirus as claimed in claim 1 is characterized in that, said solid phase carrier is a nylon membrane.
3. the gene chip of detection human papillomavirus as claimed in claim 2 is characterized in that, 3 ' end of said detection probes has amino labeled.
4. a test kit that is used to detect human papillomavirus is characterized in that, comprising:
(i) like the described gene chip of one of claim 1-3;
(ii) detect and use primer sequence, the human papillomavirus HPV DNA sequence of the clinical sample that is used for increasing, described primer sequence is:
G1:?5’-CARGGACATAAYAATGGYATTTGCTG-3’?(SEQ?ID?No.1)
G2:?5’-CARGGACATAAYAATGGYATTTGTTG-3’ (SEQ?ID?No.?2)
G3:?5’-GAAAAAYAAACTGYAAATCATAYTCCTC-3’?(SEQ?ID?No.3)
G4:?5’-GAAAAAYAAACTGYAAATCATAYTCTTC-3’?(SEQ?ID?No.4)
16:5’-CATGCGGGTGGTCAGGTAATAT-3’?(SEQ?ID?No.5)
18:?5’-CATTTTGGGAATAATGTAATTGATTGT-3’?(SEQ?ID?No.6)
(iii) be used for the increasing people GAPDH gene of clinical sample, end mark has vitamin H, and its primer sequence is:
GP1:5’-GCTTCTCTGCTGTAGGCTCATT-3’?(SEQ?ID?No.7)
GP2:5’-?GTCCTTCCACGATACCAAAGTT-3’?(SEQ?ID?No.8)
The (iv) special-purpose lysate of human papillomavirus, its composition is 20mmol Tris.HCl pH8.0,0.5%Triton-X-100,10%chelex-100;
(v) PCR reaction solution;
(vi) colouring reagents.
5. the test kit that is used to detect human papillomavirus as claimed in claim 4 is characterized in that, said detection all has biotin labeling with 5 ' and 3 ' end of primer sequence.
6. the test kit that is used to detect human papillomavirus as claimed in claim 4 is characterized in that, said PCR reaction solution comprises: 2 X PCR Mix, 20 mM Tris-HCl, pH8.9,50 mM KCl, 3 mM MgCl 2, 0.4 mM dNTPs, 1 mM DTT, 10 % glycerol, 0.16% NP-40,0.1mM Tween-20,50U/ml Taq DNA polymerase.
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CN102703606B (en) * 2012-05-16 2014-07-23 王新宇 Solid phase chip, probe and detection kit of HR-HPV E6/E7 gene single nucleotide polymorphism (SNP) detection
CN104630384A (en) * 2013-11-08 2015-05-20 江苏默乐生物科技有限公司 Human papilloma virus detection method
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CN108676797B (en) * 2018-06-07 2019-04-26 迈基诺(重庆)基因科技有限责任公司 For detecting the reagent set and method of human papilloma virus
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