CN103173543A - Detection chip for predicating mutation of radiation adverse reaction relevant gene - Google Patents

Detection chip for predicating mutation of radiation adverse reaction relevant gene Download PDF

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CN103173543A
CN103173543A CN2013100629894A CN201310062989A CN103173543A CN 103173543 A CN103173543 A CN 103173543A CN 2013100629894 A CN2013100629894 A CN 2013100629894A CN 201310062989 A CN201310062989 A CN 201310062989A CN 103173543 A CN103173543 A CN 103173543A
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probe
chip
gene
wild
mutant
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郭成贤
尹继业
裴奇
周伯庭
孟祥光
王瑛
陈娟
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Central South University
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Central South University
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Abstract

The invention discloses a detection chip for predicating mutation of a radiation adverse reaction relevant gene. The detection chip comprises a bearing substrate and a plurality of types of gene probes in array distribution on the substrate, wherein the gene probes comprise a plurality of complementary oligonucleotide sequences of genetic mutation sites relevant to the radiation adverse reaction. A wild type probe and a mutant type probe are designed targeted at each mutation site, and the probes with the lengths of 17-22bp are designed. By virtue of the chip disclosed by the invention, only 2ml of blood of a patient is needed, a result can be fast obtained in 3-4 hours, and a definite advice can be provided to a clinical doctor by using dedicated software in cooperation. By adopting the novel detection chip, the doctor can regulate a radiation therapy plan before the radiation therapy on a patient to greatly reduce unnecessary pain and economic burden of the patient.

Description

A kind of prediction radiation untoward reaction associated gene mutation detection chip
Technical field
The invention belongs to technical field of molecular biology, relate to a kind of radiation untoward reaction associated gene mutation detection chip.
Background technology
Malignant tumour is the great chronic disease that threatens human health.The tumour patient that surpasses half need to carry out radiotherapy, but tumour patient radiotherapy untoward reaction individual difference is larger.Solve in the past tumor radiotherapy untoward reaction individual difference, concentrate on the raising of radiotherapy means or technology.Along with completing of molecular biological development and the Human Genome Project, the especially development of pharmacogenomics and radiation genomics, making from the reason of the level of molecule and gene searching tumor radiotherapy untoward reaction individual difference becomes study hotspot.Research finds that some genes or albumen and tumor radiotherapy untoward reaction are closely related, comprises oncogene, cancer suppressor gene, cyclin, apoptosis gene, somatomedin, DNA-repair gene etc.Detect the knubble biological genetic marker of radiotherapy untoward reaction individual difference, in order to before radiotherapy, predicting and evaluating is carried out in untoward reaction, will be conducive to the individualized treatment scheme that the clinician formulates radiotherapy.
Biochip technology starts from the reverse south point hybrid experiment of the end of the eighties in last century and south point hybridization at beginning of the nineties contriver Dr.Sountern research and development.The biochip industrial technology is mainly concerned with the aspects such as biochip preparation, biochip applications, biochip information process analysis.Biochip technology has become efficiently, has obtained on a large scale the important means of relevant information.Biochip technology has been widely used in preventive assessment and the numerous areas such as treatment, new drug development, judicial expertise, environmental pollution monitoring and Food Hygiene Surveillance of molecular biology research, disease at present.
The present invention adopts biochip technology to detect the gene mutation site relevant to the radiotherapy untoward reaction, and the untoward reaction that the look-ahead radiotherapy may cause will be conducive to clinician's individuation and select the radiotherapy scheme, and the patient treatment interests are maximized.
Summary of the invention
The present invention is intended to the prediction to radiotherapy untoward reaction individual difference occur at present in the tumour radiotherapy process.Provide a kind of assist clinicians easily and efficiently to formulate individuation radiotherapy genes involved type diagnosing chip.
In order to achieve the above object, technical scheme provided by the invention is:
A kind of prediction radiation untoward reaction associated gene mutation detection chip comprises that solid phase substrate and point are loaded in the on-chip gene probe array of solid phase; Described gene probe contains the complementary oligonucleotide sequence with radiation untoward reaction associated gene mutation site; Described untoward reaction associated gene mutation site is TGFB1 rs1800469, SOD2 rs4880, XRCC1rs25487, XRCC3 rs861539, ATM rs1801673, TP53 rs1042522 and NOS3 rs1799983.Described TGFB1, SOD2, XRCC1, XRCC3, ATM, the sequence of TP53 and NOS3 is as shown in SEQ ID NO.1-7.
Wherein, described gene probe comprises wild type gene probe and mutated genes probe, and gene probe length is 17-22bp; Particularly, described gene probe comprises:
TGFB1 rs1800469 wild-type probe 5 '-CAGGGTCAGTGCCGTAAT-3 '
(SEQ?ID?NO.8)
TGFB1 rs1800469 mutant probe 5 '-TACTGTCAAAATGCCGCT-3 '
(SEQ?ID?NO.9)
SOD2 rs4880 wild-type probe 5 '-GTCCTCGGGGTAATACATCCAA-3 '
(SEQ?ID?NO.10)
SOD2 rs4880 mutant probe 5 '-GAAGGTTTTCGGCAGACGTGAC-3 '
(SEQ?ID?NO.11)
XRCC1 rs25487 wild-type probe 5 '-CTTGTCAACATAGGATCAT-3 '
(SEQ?ID?NO.12)
XRCC1 rs25487 mutant probe 5 '-TGGCTGCAAAATGCGATCT-3 '
(SEQ?ID?NO.13)
XRCC3 rs861539 wild-type probe 5 '-ATGGGCCCACTGTGTTATTT-3 '
(SEQ?ID?NO.14)
XRCC3 rs861539 mutant probe 5 '-CCCTGAGATTACGGCTTAAA-3 '
(SEQ?IDNO.15)
ATM rs1801673 wild-type probe 5 '-TTGAGCTCCATTGGTCAT-3 '
(SEQ?ID?NO.16)
ATM rs1801673 mutant probe 5 '-TCAGACTGGTTCTCTAGT-3 '
(SEQ?ID?NO.17)
TP53 rs1042522 wild-type probe 5 '-ACATACGTGTGCGAGGA-3 '
(SEQ?ID?NO.18)
TP53 rs1042522 mutant probe 5 '-ATATGAACGATGCAACA-3 '
(SEQ?ID?NO.19)
NOS3 rs1799983 wild-type probe 5 '-AATCAACTTACTGTAAACTTG-3 '
(SEQ?ID?NO.20)
NOS3 rs1799983 mutant probe 5 '-AATGAGTCGCCTCCTACTAGC-3 '
(SEQ?ID?NO.21)
Described gene probe also comprise positive with reference to probe 5 '-ACTCTAAGTGCTATGCC-3 ' (SEQ ID NO.22).
Described solid phase substrate material is a kind of in silicon chip, sheet glass, plastic sheet or nylon membrane or their arbitrary combination.
The coated poly-lysine of described gene probe and solid phase substrate surface or agarose.
Described gene probe and solid phase substrate surface are modified with amino or aldehyde radical.
The invention will be further described below in conjunction with principle and using method:
Prediction radiotherapy untoward reaction chip of the present invention comprises carrying substrates and be the several genes probe that array distributes on substrate, gene probe contains the complementary oligonucleotide sequence in radiotherapy untoward reaction prediction associated gene mutation site, result of study according to pharmacogenomics and/or radiation genomics, the incidence of these mutational sites in the crowd is higher, and reaction has a significant effect to tumor radiotherapy.In addition, for the control chip quality, also can arrange positive in probe on chip in gene probe array.Each mutational site design wild type gene probe array and two kinds of probes of mutated genes probe array, its probe length is 17-22bp.It is a plurality of point samples zones that a plurality of gene probe arrays can be set on each carrying substrates.Carrying substrates can adopt the solid-phase medias such as silicon chip, sheet glass, plastic sheet, nylon membrane, and chemically modified can be passed through in its surface.
The present invention predicts that radiation untoward reaction genes involved manufacturing method of chip is: according near the base sequence the gene locus of required detection, each mutational site design wild-type and two kinds of probes of mutant, design length is the probe of 17-22bp, use DNA sequence dna synthesizer synthesising probing needle, with spot sample device, probe is selected on substrate by certain spacing, the point sample area can be adjusted according to the factors such as size of number of probes, probe spacing, point, after point sample, chip is pressed the different of probe and substrate combination, taked appropriate means to be cured.Then use immediately or to be stored in 4 ° of C standby.
Carrying substrates can adopt the solid-phase medias such as silicon chip, sheet glass, plastic sheet, nylon membrane.Efficient and the detection sensitivity of being combined with substrate for improving probe, probe and substrate can be done further to modify and be coated.As its substrate surface treatment mode can be that poly-lysine is coated, agarose coated, amino or aldehyde radical modification.
The present invention predicts that the using method of radiation untoward reaction associated gene mutation chip is:
(1) sampling
From patient blood sampling 2ml;
(2) sample process
Use the genome DNA extraction test kit to extract DNA;
The operation steps that below relates to fluorescent dye primer and product thereof all (has in the darkroom of red light) under the lucifuge condition carries out.
(3) PCR reaction amplification
Use the gene mutation site Auele Specific Primer to react the amplification of DNA sample by PCR, use fluorescent substance or isotropic substance to carry out mark to primer or dNTP;
(4) hybridization
Get PCR product mixed solution, add positive hybridization solution with reference to solution and preheating, mixing, 3 minutes postposition of sex change are on ice, all transfer to the point sample zone (contrast point sample matrix positioning chip) of radiation untoward reaction associated gene mutation detection chip, add cover glass (noting not having bubble); Hybridization adds several dripping in the cabin, to keep humidity; Chip is put into hybridized the cabin, the cabin is hybridized in sealing, then puts thermostat container or water bath heat preservation one hour into;
(5) develop a film
Open and hybridize the cabin, take out chip, wash out cover glass with elutriant, then chip is put into elutriant, room temperature (25 ° of C ± 10 ° C) was placed 5 minutes, and is with sterilization distilled water flushing two times, dry under room temperature;
(6) read sheet
Recommendation ScanArray4000 scanner scans under 60-85 scanning intensity;
(7) interpretation of result
Adopt artificial interpretation or use the software kit analysis.Judge that according to the gene type assay result tumour patient is to radiocurable untoward reaction.
Utilize chip of the present invention, only need 2 milliliters of blood of patient, just obtain rapidly result in 3-4 hour again, and coordinate special software, provide clear and definite suggestion to the clinician.Adopt this new detection chip, the doctor can frontly before patient's radiotherapy adjust the radiotherapy scheme, has greatly reduced unnecessary misery and the economical load of patient.And, adopt biochip technology, can detect simultaneously a plurality of variant sites, once judging patient may be to untoward reaction or the tolerance of radiotherapy, and detected result can instruct its radiotherapy in the treatment throughout one's life.
Embodiment
Below constructed in accordance to be used for prediction radiotherapy untoward reaction associated gene mutation chip be that example is described in further detail the present invention.
According to selecting clinically the closely-related gene mutation site of tumour patient radiotherapy untoward reaction, and be chosen in 7 gene mutation sites that occurrence frequency in Chinese is higher, using value is arranged, make the genotype detecting chip that detects these mutational sites.The gene chip that is used for tumour patient prediction radiation untoward reaction contains the probe that detects 7 gene mutation sites, these 7 gene mutation sites are: TGFB1 rs1800469, SOD2 rs4880, XRCC1 rs25487, XRCC3rs861539, ATM rs1801673, TP53 rs1042522, NOS3 rs1799983.
Substrate is processed: substrate adopts glass medium, and its surface treatment mode adopts amination to modify.Concrete steps are:
(1) after cleaning slide 2h, use distilled water flushing 5 times in 2mol/L NaOH---70% ethanolic soln, 110 ° of C dry and are cooled to room temperature;
(2) slide is placed in 1% 3-aminopropyl trimethyl silane-95% acetone soln and soaks 2min;
(3) take out rear acetone rinsing 10 times of using, each 5min;
(4) 110 ° of dry 45min of C;
(5) process 2h in the Isosorbide-5-Nitrae of 1g/L-benzene diisothiocyanic acid salts solution;
(6) use washed with methanol 5min, acetone rinsing 5min, drying at room temperature.
The probe preparation:
(1) oligonucleotide of synthetic required sequence (polyT that comprises 10 ~ 15 bases of 5 ' end) on DNA synthesizer;
(2) on the DNA sequence dna synthesizer, oligonucleotide poly (T) molecular arm is introduced active aliphatic amino arm.
(3) with HOLC purifying 5 ' amido modified oligonucleotide of end, after centrifugal drying, be dissolved in 100mmol/LNa 2CO 3/ NaHCO 3Solution (PH9.0), concentration are 2mmol/L.
the making of gene chip: be divided into two gene probe point samples zones on the substrate of a glass medium, the area in each point sample zone is 10mm * 8mm, in the gene probe array that array in each point sample zone distributes, the probe of the probe of the 1st row and the 1st row is positive with reference to probe, the 2nd behavior catastrophe point TGFB1 rs1800469 gene probe, the 3rd behavior mutational site SOD2 rs4880 gene probe, the 4th behavior mutational site XRCC1 rs25487 gene probe, the 5th behavior mutational site XRCC3 rs861539 gene probe, the 6th behavior mutational site ATM rs1801673 gene probe, the 7th behavior mutational site TP53 rs1042522 gene probe, eighth row is mutational site NOS3 rs1799983 gene probe.Gene probe array comprises wild type gene probe and mutated genes probe.
Gene probe is as shown in table 1:
Table 1
Figure BDA00002868506400051
Figure BDA00002868506400061
Print and print aftertreatment:
(1) probe solution is respectively got 2ul, presses above-mentioned format print to the substrate of processing with point sample instrument;
(2) 37 ° of C sealing treatment 1h;
(3) with 1% ammonia soln washing 5min, then with distilled water washing 3 times;
(4) use immediately after drying at room temperature or to be stored in 4 ° of C standby.
Application method:
(1) first chip and other detection reagent are made into test kit, become to be grouped into as shown in table 2 in test kit:
Table 2
Figure BDA00002868506400062
Figure BDA00002868506400071
In table 2, listed reagent composition is described as follows:
Primer mixture 1: contain and be useful on amplification TGFB1 rs1800469, SOD2 rs4880, XRCC1 rs25487, XRCC3 rs861539, the fluorescent dye primer of the multiplex PCR of 5 gene mutation sites of ATM rs1801673;
Primer mixture 2: contain and be useful on amplification, TP53 rs1042522, the fluorescent dye primer of the multiplex PCR of a NOS3 rs17999832 gene mutation site;
Positive in solution (being called for short sun ginseng solution): the synthetic positive is with reference to the probe complementary sequence, through fluorescent mark;
Above-mentioned primer or complementary sequence are as shown in table 3:
Table 3
Figure BDA00002868506400072
Figure BDA00002868506400081
Hybridization solution: 0.2%SDS;
50 * elutriant: 10%SDS.
(2) experimental implementation step
1. adopt: from patient blood sampling 2ml;
2. sample process
Use Takara genome DNA extraction test kit to extract DNA;
The operation steps that below relates to primer and product thereof must (have in the darkroom of red light) under the lucifuge condition carries out.
3. PCR reaction
All primers that containing the test kit of the listed reagent of table 1 provides are primer mixture, please be first before using abundant mixing.
(A) contain primer mixture 1 (reagent 2) 2.5ul, template 50-100ng, 1 * PCR damping fluid, MgCl in the reaction system of 25ul 22.0mM, dNTPs0.2mM and 2U Taq enzyme.
PCR program: 94 ° of C denaturations 3 minutes; Then 94 ° of C sex change are 30 seconds, 56 ° of C renaturation 30 seconds, and 72 ° of C extended 40 seconds, 35 circulations like this; 72 ° of C extended 5 minutes again.
(B) contain primer mixture 2 (reagent 3) 2.5ul, template 50-100ng, 1 * PCR GCBuffer II, MgCl in the reaction system of 25ul 21.5mM, dNTPs0.2mM and 2U LATaq enzyme.
PCR program: 94 ° of C denaturations 3 minutes; Then 94 ° of C sex change are 30 seconds, 60 ° of C renaturation 1 minute, and 72 ° of C extended 1 minute, 30 circulations like this; 72 ° of C extended 7 minutes again.
Attention: the abundant mixing of mentioned component, add at last Taq enzyme and mixing, but can not thermal agitation; Place the PCR pipe on the PCR instrument, with PCR conversion zone on aluminium-foil paper parcel PCR instrument.
4. hybridization
With (A) and (B) PCR product mixing, mixing, get 7 μ l PCR product mixed solutions, add positive with reference to solution (reagent 4) 1 μ l and through hybridization solution (reagent 5) the 6 μ l of 48 ° of C preheatings, mixing, 3 minutes postposition of 94 ° of C sex change are all transferred to the point sample zone (contrast point sample matrix positioning chip) of chip on ice, add cover glass (noting not having bubble); Hybridization adds several dripping in the cabin, to keep humidity; Chip is put into hybridized the cabin, the cabin is hybridized in sealing, then puts 94 ° of C (± 1 ° of C) thermostat container or water bath heat preservation one hour into.
5. develop a film
Open and hybridize the cabin, take out chip, wash out cover glass with 1X elutriant (reagent 6), then chip is put into the staining jar that fills elutriant (reagent 6), room temperature (25 ° of C ± 10 ° C) was placed 5 minutes, rinsed two times with the sterilization distilled water, and is dry under room temperature;
6. read sheet
Use the ScanArray4000 scanner to scan under 60-85 scanning intensity;
(7) interpretation of result
Adopt artificial interpretation or use the software kit analysis.Provide radiotherapy untoward reaction prediction suggestion (seeing Table 4) according to gene type assay result and related data:
Table 4
Sequence Gene No. RS Clinical meaning
1 TGFB1 rs1800469 The sudden change patient, the subcutaneous fibrosis risk occurs to be increased
2 SOD2 rs4880 The sudden change patient, the subcutaneous fibrosis risk occurs to be increased
3 XRCC1 rs25487 The sudden change patient, the telangiectasis risk occurs to be increased
4 XRCC3 rs861539 The sudden change patient, subcutaneous fibrosis and telangiectasis risk occur to be increased
5 ATM rs1801673 The sudden change patient, telangiectatic risk occurs to be increased
6 TP53 rs1042522 The sudden change patient, telangiectatic risk occurs to be increased
7 NOS3 rs1799983 The sudden change patient, the untoward reaction risk increases
The present invention predicts radiation untoward reaction associated gene mutation chip index:
Recall rate (number of samples that has detected/sample sum)〉95%;
Accuracy (the sample sum of the number of samples/sample that correctly detects)〉99%;
Repeatability (number of times that same sample correctly detects/always detect number of times)〉99%.
Figure IDA00002868507000011
Figure IDA00002868507000021
Figure IDA00002868507000031
Figure IDA00002868507000051
Figure IDA00002868507000061
Figure IDA00002868507000071
Figure IDA00002868507000091
Figure IDA00002868507000101

Claims (7)

1. untoward reaction associated gene mutation detection chip is radiated in a prediction, comprise that solid phase substrate and point are loaded in the on-chip gene probe array of solid phase, it is characterized in that, described gene probe contains the complementary oligonucleotide sequence with radiation untoward reaction associated gene mutation site; Described untoward reaction associated gene mutation site is TGFB1 rs1800469, SOD2 rs4880, XRCC1 rs25487, XRCC3 rs861539, ATM rs1801673, TP53 rs1042522 and NOS3rs1799983.
2. chip as claimed in claim 1, is characterized in that, described gene probe comprises wild type gene probe and mutated genes probe, and gene probe length is 17-22bp.
3. chip as claimed in claim 1, is characterized in that, described gene probe comprises:
TGFB1 rs1800469 wild-type probe 5 '-CAGGGTCAGTGCCGTAAT-3 '
TGFB1 rs1800469 mutant probe 5 '-TACTGTCAAAATGCCGCT-3 '
SOD2 rs4880 wild-type probe 5 '-GTCCTCGGGGTAATACATCCAA-3 '
SOD2 rs4880 mutant probe 5 '-GAAGGTTTTCGGCAGACGTGAC-3 '
XRCC1 rs25487 wild-type probe 5 '-CTTGTCAACATAGGATCAT-3 '
XRCC1 rs25487 mutant probe 5 '-TGGCTGCAAAATGCGATCT-3 '
XRCC3 rs861539 wild-type probe 5 '-ATGGGCCCACTGTGTTATTT-3 '
XRCC3 rs861539 mutant probe 5 '-CCCTGAGATTACGGCTTAAA-3 '
ATM rs1801673 wild-type probe 5 '-TTGAGCTCCATTGGTCAT-3 '
ATM rs1801673 mutant probe 5 '-TCAGACTGGTTCTCTAGT-3 '
TP53 rs1042522 wild-type probe 5 '-ACATACGTGTGCGAGGA-3 '
TP53 rs1042522 mutant probe 5 '-ATATGAACGATGCAACA-3 '
NOS3 rs1799983 wild-type probe 5 '-AATCAACTTACTGTAAACTTG-3 '
NOS3 rs1799983 mutant probe 5 '-AATGAGTCGCCTCCTACTAGC-3 '
4. chip as claimed in claim 3, is characterized in that, described gene probe also comprise positive with reference to probe 5 '-ACTCTAAGTGCTATGCC-3 '.
5. chip as claimed in claim 1, is characterized in that, described solid phase substrate material is a kind of in silicon chip, sheet glass, plastic sheet or nylon membrane or their arbitrary combination.
6. chip as claimed in claim 1, is characterized in that, the coated poly-lysine of described gene probe and solid phase substrate surface or agarose.
7. chip as claimed in claim 1, is characterized in that, described gene probe and solid phase substrate surface are modified with amino or aldehyde radical.
CN2013100629894A 2013-02-28 2013-02-28 Detection chip for predicating mutation of radiation adverse reaction relevant gene Pending CN103173543A (en)

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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105018338A (en) * 2014-04-28 2015-11-04 郑州大学 Gene mutation detection chip for predicting curative effect and safety performance of statin drugs
CN105132415A (en) * 2015-08-19 2015-12-09 天津市康婷生物工程有限公司 In-vitro molecular detection method for manganese SOD2 and primer
CN112195229A (en) * 2020-09-07 2021-01-08 中国人民解放军火箭军特色医学中心 Kit for simultaneously detecting multiple SNP sites related to radiosensitivity

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
CHRISTIAN N.A.ET AL.: "TGFB1 polymorphisms are associated with risk of late normal tissue complications in the breast after radiotherapy for early breast cancer", 《RADIOTHERAPY AND ONCOLOGY》 *
SALVATORE TERRAZZINO ET AL.: "Common variants of eNOS and XRCC1 genes may predict acute skin toxicity in breast cancer patients receiving radiotherapy after breast conserving surgery", 《RADIOTHERAPY AND ONCOLOGY》 *
胡凯骞等: "基因芯片技术及其在放射治疗中的应用", 《原子核物理评论》 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105018338A (en) * 2014-04-28 2015-11-04 郑州大学 Gene mutation detection chip for predicting curative effect and safety performance of statin drugs
CN105132415A (en) * 2015-08-19 2015-12-09 天津市康婷生物工程有限公司 In-vitro molecular detection method for manganese SOD2 and primer
CN112195229A (en) * 2020-09-07 2021-01-08 中国人民解放军火箭军特色医学中心 Kit for simultaneously detecting multiple SNP sites related to radiosensitivity
CN112195229B (en) * 2020-09-07 2022-07-12 中国人民解放军火箭军特色医学中心 Kit for simultaneously detecting multiple SNP sites related to radiosensitivity

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