CN102373288A - Method and kit for sequencing target areas - Google Patents
Method and kit for sequencing target areas Download PDFInfo
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- CN102373288A CN102373288A CN2011103919902A CN201110391990A CN102373288A CN 102373288 A CN102373288 A CN 102373288A CN 2011103919902 A CN2011103919902 A CN 2011103919902A CN 201110391990 A CN201110391990 A CN 201110391990A CN 102373288 A CN102373288 A CN 102373288A
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Abstract
The invention relates to the field of genetic engineering, and provides a method and a kit for sequencing target areas. The method comprises the following steps of: A, using a specificity primer to amplify a plurality of target areas in a sample to be detected, and establishing a sequencing library based on amplified products; B, subjecting the sequencing library to monomolecular amplification to obtain a plurality of monomolecular amplification products corresponding to the plurality of target areas; and C, subjecting the plurality of monomolecular amplification products to high-throughput gene sequencing at the same time so as to obtain sequence information of the plurality of target areas. The method and the corresponding kit are used for sequencing the plurality of areas at the same time by using a high-throughput sequencing technology; the sequence information including variation of known mutations and unknown mutations in the areas can be obtained accurately; the kit has high detection sensitivity, and can be used for further detecting mainly samples at the same time.
Description
Technical field
The present invention relates to the genetically engineered field, more particularly, relate to a kind of method and test kit that is checked order in the target area.
Background technology
Since human genome nucleotide sequence sketch and many other genome sketches appearances; And the discovery of SNPs (SNP) and little insertion/deletion polymorphism in a large number in human and the many other biological body genome sketches, people begin nucleic acid determination is become interested.Research shows that the variant nucleic acid sequence of some specific position has comprised a large amount of biological informations, maybe be relevant with the mankind or vegeto-animal some proterties, and these information will produce wide influence to the every aspect of medicine and agricultural etc.The development that for instance, can be contemplated that this field might realize personalized medicine.
At present; The common methods that target area (specific position) checked order is the Sanger PCR sequencing PCR; Can carry out the zone to the target area through the Sanger PCR sequencing PCR and detect, but the Sanger PCR sequencing PCR can only check order to a certain section zone of a sample at every turn, the order-checking cost is high; Sensitivity low (20%), and can not draw the precise information that morphs in each mutational site.
Therefore; Need a kind of novel method that can carry out the zone detection simultaneously to a plurality of target areas of testing sample; This method can accurately obtain these regional sequence informations; The variation situation that comprises each mutational site of known mutations and unknown mutation, detection sensitivity is high, can also further detect a large amount of samples simultaneously.
Summary of the invention
The object of the present invention is to provide a kind of method and test kit that is checked order in the target area; Can carry out the zone to a plurality of target areas of testing sample simultaneously detects; Accurately obtain these regional sequence informations; The variation situation that comprises each mutational site of known mutations and unknown mutation, detection sensitivity is high, can also further detect a large amount of samples simultaneously.
The present invention is achieved in that a kind of method that is checked order in the target area, may further comprise the steps:
A. utilize Auele Specific Primer, increased in a plurality of target areas in the testing sample, and make up the order-checking library based on amplified production;
B. the unit molecule amplification is carried out in the order-checking library, obtained a plurality of unit molecule amplified productions corresponding with said a plurality of target areas;
C. simultaneously said a plurality of unit molecule amplified productions are carried out the high-throughput gene sequencing, obtain the sequence information of said a plurality of target areas.
Wherein, said steps A may further comprise the steps:
A1. utilize Auele Specific Primer, increased in a plurality of target areas in the testing sample, obtain and the corresponding amplified production in said a plurality of target areas;
A2. utilize joint component, connect, obtain the library of checking order with the corresponding amplified production in said a plurality of target areas; Said joint component adopts at least a in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure.
Wherein, steps A 2 may further comprise the steps:
A21. the amplified production corresponding with said a plurality of target areas carried out fragmentation, obtain the fragmentation product;
A22. utilize joint component, be connected, make up the order-checking library with the fragmentation product.
The length in order-checking library, the described target area of steps A does not have particular restriction, is preferably 25bp～500bp.More preferably 50bp～200bp, more preferably 70bp～130bp.
Wherein, said steps A 22 may further comprise the steps:
A221. utilize first joint to be connected, the connection product of winning with the two ends of fragmentation product;
A222. cyclisation first connects product, gets cyclisation product;
A223.II s type digestion with restriction enzyme cyclisation product gets enzyme and cuts product;
A224. cut the product two ends at enzyme and connect second joint and the 3rd joint, the library of must checking order.
Wherein, said steps A 22 may further comprise the steps:
A221 '. utilize the 4th joint to be connected, get second and connect product with the fragmentation product;
A222 ' .II s type digestion with restriction enzyme second connects product, must have the endonuclease bamhi of the 4th joint;
A223 '. the endonuclease bamhi that has the 4th joint is connected with the 5th joint, forms the order-checking library.
Wherein, at least one joint in the steps A 2 said joint components includes first sequence label, is used in the library construction process, and mark is carried out in the order-checking library of different testing samples.Said first sequence label is preferably the nucleic acid molecule that has specific base sequence, and its base number is not limit.
Further, the said first sequence label base number is 3～20, more preferably 4～10.
Wherein, the complementary fully or part complementation in described Auele Specific Primer of steps A and target area.
Further; In the Auele Specific Primer of each target area correspondence; At least one primer and this target area part are complementary; 5 ' end of this part complementary primer includes second sequence label, is used in amplification target area process, and the target area amplified production of different testing samples is carried out mark.Said second sequence label is preferably the nucleic acid molecule that has specific base sequence, and its base number is not limit.
Further, the said second sequence label base number is 3～20, more preferably 4～10.
Wherein, the amplification of each target area of same sample in the said steps A is carried out simultaneously or part is carried out simultaneously or independently carried out respectively.
Wherein, the method for the described unit molecule of step B amplification is at least a among emulsion PCR, the bridge-type PCR.
Wherein, the described high throughput sequencing technologies of step C is based on the synthetic PCR sequencing PCR of polysaccharase or based on the connection PCR sequencing PCR of ligase enzyme.
Of the present invention a kind of test kit that can be used in any sequence measurement of the present invention is provided also, the present invention is achieved in that a kind of test kit that is checked order in the target area, comprising:
Auele Specific Primer is used for being increased in a plurality of target areas of testing sample;
Joint component is used for combining with amplified production making up the order-checking library.
Wherein, said joint component adopts at least a in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure.
Wherein, at least one joint in the said joint component includes first sequence label, is used in the library construction process, and mark is carried out in the order-checking library of different testing samples.Said first sequence label is preferably the nucleic acid molecule that has specific base sequence, and its base number is not limit, and is preferably 3～20.
Wherein, the complementary fully or part complementation in described Auele Specific Primer and target area.
Further; In the Auele Specific Primer of each target area correspondence; At least one primer and this target area part are complementary; 5 ' end of this part complementary primer includes second sequence label, is used in amplification target area process, and the target area amplified production of different testing samples is carried out mark.Said second sequence label is preferably the nucleic acid molecule that has specific base sequence, and its base number is not limit, and is preferably 3～20, and more preferably 4～10.
Compared with prior art; Method of the present invention and test kit carry out degree of depth order-checking through high throughput sequencing technologies to a plurality of target areas of testing sample simultaneously; Accurately draw the sequence information of these target areas, comprise the variation situation in each mutational site of known mutations and unknown mutation, accurately draw the frequency that morphs in each mutational site of each sample; Detection sensitivity is high, and can further carry out the multizone order-checking simultaneously to a large amount of samples.
Description of drawings
Fig. 1 be in the one embodiment of the invention to the target area check order method flow diagram;
Fig. 2 is the joint synoptic diagram of the single protruding terminus joint in the one embodiment of the invention;
Fig. 3 is the structural representation of the two protruding terminus joints in the one embodiment of the invention;
Fig. 4 is the structural representation of the joint of the band loop-stem structure in the one embodiment of the invention;
Fig. 5 is the structural representation of the y splice in the one embodiment of the invention;
Fig. 6 is the structural representation of the terminal y splice of T in the one embodiment of the invention;
Fig. 7 is the structural representation of the y splice in the another embodiment of the present invention;
Fig. 8 is the structural representation of the two deoxidation y splices in the one embodiment of the invention;
Fig. 9 utilizes fragmentation product and joint component to make up the method flow diagram in order-checking library in the one embodiment of the invention;
Figure 10 utilizes fragmentation product and joint component to make up the method flow diagram in order-checking library in the another embodiment of the present invention;
Figure 11 utilizes fragmentation product and joint component to make up the method flow diagram in order-checking library in the another embodiment of the present invention.
Embodiment
In order to make the object of the invention, technical scheme and advantage clearer,, the present invention is further elaborated below in conjunction with accompanying drawing and embodiment.
Target area of the present invention; Be the arbitrary sequence on any genome; Can select as required; Include but not limited to the regulation and control zone, outside of internal sequence, the gene of gene, the internal sequence of said gene includes but not limited to the intron zone, exon region of gene, contains the zone of intron and exon simultaneously.
Fig. 1 shows a kind of method flow that is checked order in the target area of the present invention, and this method may further comprise the steps:
S1. utilize Auele Specific Primer, increased in a plurality of target areas in the testing sample, and make up the order-checking library based on amplified production;
S2. the unit molecule amplification is carried out in the order-checking library, obtained a plurality of unit molecule amplified productions corresponding with said a plurality of target areas;
S3. simultaneously said a plurality of unit molecule amplified productions are carried out the high-throughput gene sequencing, obtain the sequence information of said a plurality of target areas.
Present method is carried out degree of depth order-checking through high throughput sequencing technologies to the target area of testing sample; This method can detect a plurality of target areas of testing sample simultaneously; Accurately obtain these regional sequence informations; The variation situation that comprises each mutational site of known mutations and unknown mutation, detection sensitivity is high, can accurately draw the frequency that morphs in each mutational site of each sample.In addition,, can remove the fragmentation step from, reduce experimental procedure, improve conventional efficient, reduce cost through controlling the size of each target area amplified production.
Through the sequence information of present method gained, can be used for various scientific researches, include but not limited to crowd's sequential analysis, gene functional research, protein function research.
Need to prove:
Testing sample described in the step S1 is the sample that can extract the arbitrary form of nucleic acid, includes but not limited to: whole blood, serum, blood plasma and tissue sample; Said tissue sample includes but not limited to: paraffin-embedded tissue, flesh tissue and frozen section.
In the step S1 gained order-checking library; There is multiple order-checking library molecule, the unit molecule amplification is carried out in the order-checking library, promptly be meant; With the multiple library molecule in the order-checking library; Form with denier (even unit molecule) is spatially isolated (but these library molecules still belong to same reaction system on the whole), and in space separately, realizes amplification, to promote the signal of various molecules in follow-up sequencing reaction.
In the prior art, the Sanger sequencing technologies can only check order to a certain section zone of a sample at every turn, realize the order-checking to a plurality of target areas, can only be to realize through repeatedly reacting.And in the present invention; After each molecule in the order-checking library increases through unit molecule; Each order-checking library molecule all forms unit molecule copy array, and each unit molecule copy array is in different positions when carrying out the high-throughput gene sequencing, make sequencing primer and unit molecule copy the hybridization between the array; And the extension under the enzyme effect can carry out simultaneously, do not disturb mutually each other.Therefore, can be simultaneously a large amount of (millions of up to ten million, even more) unit molecule copy array be carried out sequencing reaction simultaneously, then through gathering corresponding signal, and then obtain required sequence information, and the sensitivity of order-checking is higher than Sanger.
Wherein, the complementary fully or part complementation in described Auele Specific Primer of step S1 and target area.
Further, every pair is directed against in the primer of target area, and at least one primer and target area part are complementary, and 5 ' end of this primer has second sequence label.This second sequence label is used in amplification target area process, and the target area amplified production of different testing samples is carried out mark.
This second sequence label is preferably the nucleic acid molecule that has particular sequence, and its base number is not limit.The base number of this second sequence label is preferably 3～20, and more preferably 4～10.
In addition, said Auele Specific Primer also can have other affinity tag, includes but not limited to: biotin labeling, poly histidine mark, antigen, antibody, thus make that the purifying of target area amplified production is very convenient.
In addition, the amplification in the different target of same testing sample zone can be carried out simultaneously or independently carry out respectively or part is carried out simultaneously.In concrete experimentation, can select for use above-mentioned any scheme to carry out as required.
If increased respectively in each target area respectively; Can be consistent through the molecule number that the amount of measuring amplified production guarantees to be used among the step S1 target area amplified production in order-checking library, establishing target zone; Can not cause the different target zone copy number of same testing sample different because of amplification step, and then influence follow-up sequencing reaction result.
Certainly, big or small close when each target area is when GC content is also close; Through rational design primer; Utilize multiple PCR technique, step S1 can increase to a plurality of target areas simultaneously, and guarantees that the amplification efficiency between each target area keeps basically identical; So just can effectively improve conventional efficient, reduce the cost of reaction.
When testing sample has when a plurality of, the amplification of the target area of different samples must be carried out respectively.
In one embodiment, the concrete implementation procedure of step S1 is:
S11. utilize Auele Specific Primer, increased in a plurality of target areas in the testing sample, obtain and the corresponding amplified production in said a plurality of target areas;
S12. utilize joint component, connect, obtain the library of checking order with the corresponding amplified production in said a plurality of target areas; Said joint component adopts at least a in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure.
Need to prove:
Among the step S11,, can carry out simultaneously or independently carry out respectively or partly carry out simultaneously the amplification of a plurality of target areas in the same testing sample.Can be according to practical situation, as: the annealing temperature of specific amplification primer, the size of the target area of amplification, GC content, the quantity of the target area of amplification etc. are adjusted accordingly.The amplification of the target area of different testing samples must be carried out respectively.
Among the step S12, the mode of connection of said joint component and amplified production can adopt multiple mode to realize, comprises that joint component directly is connected with amplified production, or amplified production is connected after handling again.
Joint component among the step S12 is used for making up the order-checking library, can comprise one or more joints.
Wherein, at least one joint in the said joint component of step S12 includes first sequence label, and this first sequence label is used in the library construction process, and mark is carried out in the order-checking library of different testing samples.Like this, after obtaining order-checking library, target area respectively, the order-checking library, target area of different testing samples may be combined in the same reaction system, carries out the unit molecule amplified reaction, and then carries out high-flux sequence simultaneously.Improve the efficient of sequencing reaction, reduced the cost of sample detection.
This first sequence label is preferably the nucleic acid molecule that has specific base sequence, and its base number is not limit.Further, the base number of said first sequence label is 3～20, like this, and at every turn at least can be to 4
3Individual sample detects simultaneously.After taking all factors into consideration various situation, as: the specificity of label, the cost of joint, length of said joint etc., the base number of first sequence label is preferably 4～10.Through the combination of second label and first label, invention of the present invention can detect at least 4 at every turn
3* 4
3Individual sample, i.e. 4096 samples.
The modification mode of joint has multiple, includes but not limited to: by biotinylation or methylate, or simultaneously by biotinylation with methylate.In one embodiment, this joint is by biotinylation, and is connected the separation and purification that has the order-checking library that is beneficial to structure of vitamin H with not biotinylated fragmentation product.In another embodiment; This joint is methylated; And be connected with unmethylated fragmentation product, connect product with the digestion with restriction enzyme that only cuts methylate DNA then, because have only the connection product that successfully connects just can be cut; So have only successfully the connector that connects to be cut, thereby guarantee that enzyme cuts the unicity of product.
The structure formation of joint also has multiple, includes but not limited to: the joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure.Make up in the process of order-checking library and can use one or more joints.Wherein, the joint of protruding terminus joint, band loop-stem structure and y splice can prevent effectively that all a plurality of joints are from the generation that connects phenomenon in connection procedure.Above-mentioned joint form to joint below will provide a plurality of embodiment.
In first embodiment, joint component adopts flat end fitting, and this joint is double-stranded complementary nucleic acid molecule fully.
In a second embodiment, joint component adopts the protruding terminus joint, and this joint is a double chain acid molecule, and this double chain acid molecule comprises a protruding terminus at least.The base number of this protruding terminus does not have concrete restriction, is preferably 1～10 base.According to the structure of this double chain acid molecule, the protruding terminus joint can be divided into two types, is respectively single protruding terminus joint, two protruding terminus joint.
Single protruding terminus joint as shown in Figure 2, the one of which end is for flat terminal, and the other end is a protruding terminus.The single protruding terminus joint that wherein has y splice can prevent that joint is from connecting.In order to prevent that the end from connecting for flat terminal single protruding terminus joint certainly, can modify (including but not limited to use the amino-terminated hydroxyl) to 3 ' OH on the flat end, the 5 ' phosphate group that maybe will put down on the end is removed.
Two protruding terminus joints as shown in Figure 3, it contains two protruding terminuses, and these two protruding terminuses can be on a nucleotide chain, and (Fig. 3 is a) or on different nucleotide chains (Fig. 3 b).When these two protruding terminuses were on different nucleic acid chains, they were not complementary each other, in case joint when connecting, occurs from connecting.
In the 3rd embodiment, joint component adopts the joint of band loop-stem structure, and is as shown in Figure 4.This joint is a single stranded nucleic acid molecule; This single stranded nucleic acid molecule comprise the first complementary pairing district 1, stem ring district 2 and the second complementary pairing district 3 (Fig. 4 a), the first complementary pairing district 1 can with the second complementary pairing district, 3 complementary pairings, and the complementary pairing district that their form comprises at least one restriction enzyme enzyme recognition site; And cut recognition site through this enzyme; Specific endonuclease capable cuts stem ring district or excision, thereby single stranded nucleic acid molecule is become double chain acid molecule, so that follow-up operation.Shown in Fig. 4 b, the joint of band loop-stem structure also can have protruding terminus 4, and this protruding terminus can be positioned at the 5 ' end or the 3 ' end of single stranded nucleic acid molecule.The existence of protruding terminus 4 can prevent further that joint is from the generation that connects phenomenon.This protruding terminus is preferably T.
In the 4th embodiment, joint component adopts y splice, and as shown in Figure 5, this joint is a double chain acid molecule, comprises complementary district and crotch region, and two strands of said crotch region respectively comprise at least one amplimer binding site.Preferably, the complementation district of said y splice comprises at least one restriction enzyme enzyme recognition site, and this enzyme is cut recognition site can cut the formation end by enzyme in building the storehouse process, so that carry out follow-up operation.
The bifurcation design of this y splice can avoid a plurality of joints from connecting the appearance of phenomenon building the storehouse process; The amplimer binding site that comprises on the said crotch region can directly be used to combine amplimer, carries out amplified reaction
Wherein, every chain of the crotch region of said y splice contains N Nucleotide; Preferably, 9≤N≤30.Wherein, the Nucleotide logarithm of the collochore complementary pairing of said y splice is not limit; Preferably, the Nucleotide logarithm of complementary pairing is 7～15, and is preferred, and the Nucleotide logarithm of complementary pairing is 9～13.
Wherein, 3 ' of the collochore of said y splice end is a protruding terminus or flat terminal.Preferably, 3 ' end of the collochore of said y splice is a protruding terminus, this protruding terminus can with the sticky end complementary pairing of said fragmentation product, improved joint efficiency, be beneficial to make up order-checking library successful reaction and carry out.
Preferably, said y splice is the terminal y splice of T, and 3 ' end of the collochore of this joint is a protruding terminus, and last base of protruding terminus is T; The terminal y splice of T for example shown in Figure 6, N is any in A, T, C, the G base among the figure.
Preferably, 3 ' end of the collochore of said y splice is a protruding terminus, and the Nucleotide of protruding terminus comprises universal base.Wherein, the base number of protruding terminus does not have particular restriction, is preferably 1～4.Y splice for example shown in Figure 7, N is any in A, T, C, the G base among the figure, X is a universal base.
Preferably, said y splice is two deoxidation joints, and 3 ' end of the collochore of this joint is for flat terminal, and 3 ' terminal last Nucleotide is the Nucleotide that has pair deoxidation bases; Two deoxidation y splices for example shown in Figure 8, N is any in A, T, C, the G base among the figure, dd representes that this 3 ' terminal last Nucleotide is the cytidylic acid(CMP) that has two deoxidation bases.
Should be noted that above-mentioned joint component is part embodiment, not in order to restriction protection scope of the present invention.
Implementation about step S12:
In one embodiment, step S12 adopts joint component and the direct-connected mode of amplified production, constructs the order-checking library.
In another embodiment; When the target area amplified production is big or the order-checking library, target area that needs to make up hour; Then amplified production is carried out after fragmentation handles, the fragmentation product is connected with joint component again, makes up the order-checking library; As shown in Figure 9, step S12 may further comprise the steps:
S121. the amplified production corresponding with said a plurality of target areas carried out fragmentation, obtain the fragmentation product;
S122. utilize joint component, be connected, make up the order-checking library with the fragmentation product.
Through fragmentation step S121 the target area amplified production is become less fragmentation product, thereby help further degree of depth order-checking the target area.In addition, can also handle, different amplified productions is become the similar fragmentation product of length, can help follow-up unified order-checking through fragmentation.
Need to prove:
Among the step S121, the method for said fragmentation target area amplified production has multiple, includes but not limited to: ultrasonic method, spray method, chemical shearing method and enzyme cutting method.Can adopt the method that adapts to experimentize according to practical situation.
After handling, said fragmentation also can comprise the separation and purification of fragmentation product and end modified step.According to the fragment length needs of order-checking, the nucleic acid fragment for fragmentation obtains carries out the separation and purification of purpose nucleic acid fragment, and separation method can adopt domestic method, like gel electrophoresis, saccharose gradient or cesium chloride gradient sedimentation, column chromatography for separation etc.According to employed fragmentation method, further end modified to the purpose nucleic acid fragment of gained, include but not limited to: phosphorylation or dephosphorylation, end-filling and end add A, so that follow-up joint component connects.Above-mentioned purpose nucleic acid fragment length is not limit, and is preferably 25bp～500bp, more preferably 30bp～200bp, more preferably 40～100bp.
The length of the said fragmentation product of step S121 is not limit, and is preferably 25bp～500bp, more preferably 30bp～200bp, more preferably 40bp～100bp.Under the prerequisite of realization to the order-checking of target area, along with shortening of the target area fragment length that contains in the molecule of order-checking library, target area, the order-checking degree of depth to the target area of high throughput sequencing technologies is deepened; And the order-checking degree of depth is dark more, and promptly the order-checking number of times to each base position of target area is many more, and sequencing result is accurate more, and is just sensitiveer to the detection of a small amount of sudden change in the sample; So just can effectively prevent because have the ratio of target area of sudden change in the sample on the low sidely, and cause the absolute value of order-checking signal of this sudden change on the low side, the inaccurate phenomenon of sequencing result takes place.
In order to realize restriction, can after step S121 or S122, carry out separation and purification to fragmentation product or order-checking library, target area to order-checking library, target area size.The method of separation and purification has multiple, includes but not limited to: gel method, saccharose gradient or cesium chloride gradient sedimentation and column chromatography for separation.Can adopt the method that adapts to experimentize according to practical situation.
According to above-mentioned joint component,, will further explain this step through a plurality of embodiment and accompanying drawing below to step S122.
In one embodiment of the invention, directly connect joint and form the order-checking library at the two ends of fragmentation product.
Said joint can adopt at least a in joint and the y splice of above-mentioned flat end fitting, protruding terminus joint, band loop-stem structure.
In another embodiment of the present invention, shown in figure 10, step S122 specifically can be realized by following steps:
S1221. utilize first joint to be connected, the connection product of winning with the two ends of fragmentation product;
S1222. cyclisation first connects product, gets cyclisation product;
S1223.II s type digestion with restriction enzyme cyclisation product gets enzyme and cuts product;
S1224. cut the product two ends at enzyme and connect second joint and the 3rd joint, the library of must checking order.
In step S1221, said first joint can adopt a kind of in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure, and said first joint includes II s type digestion with restriction enzyme recognition site; Described II s type restriction enzyme is the restriction enzyme of cleavage site outside recognition sequence; Include but not limited to: Acu I, Alw I, Bbs I, BbV I, Bcc I, BceA I, BciV I, BfuA I, Bmr I, Bpm I, BpuE I, Bsa I, BseM II, BseR I, Bsg I, BsmA I, BsmB I, BsmF I, BspCN I, BspM I, BspQ I, BtgZ I, Ear I, Eci I, EcoP15 I, Fau I, Fok I, Hga I, Hph I, HpyAV, Mbo II, Mly I, Mme I, Mnl I, NmeAIII, Ple I, Sap I, SfaN I and TspDT I are preferably Acu I, Bsg I, EcoP15 I or Mme I.
When said first joint was y splice, this II s type digestion with restriction enzyme recognition site was positioned at complementary district; When said first joint is the joint of band loop-stem structure, the distance between restriction enzyme enzyme recognition site and the loop-stem structure, near than the distance between II s type digestion with restriction enzyme recognition site and the loop-stem structure.
If the fragmentation product is repaired through the terminal repair enzyme, and end adds the A reaction, and said first joint is preferably the terminal y splice of band T.If the fragmentation product is just repaired through the terminal repair enzyme, with the end-filling of fragmentation product, the preferred two deoxidation joints of then said first joint.
In step S1222, cyclisation first connects product has multiple implementation.
In one embodiment of this invention, step S1222 may further comprise the steps:
S12221. utilize enzyme to cut primer the first connection product is increased, get amplified production;
S12222. amplified production is carried out enzyme and cut, make amplified production form sticky end, and self loop changes into cyclisation product.
Said enzyme is cut 3 ' of primer and is held two terminal portions complementations that are connected product respectively with first, and 5 ' end all contains the restriction enzyme enzyme recognition site.The amplified production that the amplification of process step S12221 forms; Its two ends all contain the restriction enzyme enzyme recognition site, under the effect of corresponding enzyme, make the two ends of amplified production form sticky end then; And these two sticky end complementations can be carried out recirculation.
In another embodiment of the present invention; Said first joint includes 2 enzymes and cuts recognition site; One of them is the restriction enzyme enzyme recognition site, and the two ends that are used to make first of step S1222 formation connect product form sticky end under the effect of corresponding enzyme; And complementary between them, can carry out recirculation.Another is an II s type digestion with restriction enzyme recognition site, is used at step S1223, utilizes the enzyme identification cyclisation product of this restriction enzyme site of identification, carries out enzyme and cuts, and then obtain enzyme and cut product.
Should explain, more than two kinds of being merely among the present invention of two embodiment realize that cyclisation first connect the embodiments of products, do not do any concrete restriction for protection scope of the present invention.
In step S1223, the enzyme that utilization can be discerned on first joint is cut recognition site, and cutting cyclisation product (DNA) but the enzyme that do not cut first joint carries out enzyme cuts.Enzyme on said first joint is cut recognition site and included but not limited to: Mme I enzyme cuts that recognition site, Acu I enzyme are cut recognition site, Bsg I enzyme is cut recognition site.
Among the step S1224, said second joint can be a kind of in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure, can have biotin labeling.Said the 3rd joint can be a kind of in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure.Second joint and the 3rd joint can be identical or different.Preferably, said second joint is identical with the 3rd joint, is y splice.Preferred, said y splice is the terminal y splice of T or two deoxidation y splice.
What need special instruction is also can comprise step S1222A between step S1222 and the S1223: the rolling circle amplification cyclisation product gets the rolling circle amplification product.Through step S1222A, can guarantee that follow-up enzyme cuts step S1223 enough starting material are arranged.
Or, between step S1221 and S1222, also can comprise step S1221A: utilize amplimer to be connected product and increase first, amplified production.Said amplimer is connected the joint sequence complementation at product two ends respectively with first.Through step S1221A, can guarantee that follow-up cyclisation step has enough starting material.
This programme can avoid after step S1222, carrying out rolling circle amplification, replaces and carry out the common PCR amplification with the step S1221A before the step S1222, can effectively reduce follow-up enzyme to cut in the step consumption of II s type restriction enzyme.
Wherein, said first joint is preferably y splice.
Wherein, the complementation district of said y splice can comprise at least one enzyme and cuts recognition site.Said enzyme is cut recognition site and can be common restriction enzyme enzyme recognition site, also can be II s type digestion with restriction enzyme recognition site.
Wherein, the said amplimer of step S1221A is preferably the biotinylation primer, helps the recovery purifying of amplified production.
Wherein, the said amplimer of step S1221A has at least one specific enzymes and cuts recognition site.
If on the amplimer with specific enzymes to cut recognition site be the uridylic base, then utilize uridylic specificity excision reagent to carry out enzyme among the step S1222 and cut, and then connect cyclisation.
If it is the restriction enzyme enzyme recognition site that specific enzymes that amplimer is with is cut recognition site, then utilizes corresponding restriction enzyme to carry out enzyme among the step S1222 and cut, and then connect cyclisation.
In another embodiment of the present invention, shown in figure 11, step S122 specifically can be realized by following steps:
S1221 '. utilize the 4th joint to be connected, get second and connect product with the fragmentation product;
S1222 ' .II s type digestion with restriction enzyme second connects product, must have the endonuclease bamhi of the 4th joint;
S1223 '. the endonuclease bamhi that has the 4th joint is connected with the 5th joint, forms the order-checking library.
Need to prove:
In step S1221 ', said the 4th joint can adopt a kind of in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure, and said the 4th joint includes II s type digestion with restriction enzyme recognition site; When said the 4th joint was y splice, this II s type digestion with restriction enzyme recognition site was positioned at complementary district; When said the 4th joint is the joint of band loop-stem structure, the distance between restriction enzyme enzyme recognition site and the loop-stem structure, near than the distance between II s type digestion with restriction enzyme recognition site and the loop-stem structure.
In step S1222 ', the enzyme that utilization can be discerned on the 4th joint is cut recognition site, and cutting cyclisation product (DNA) but the enzyme that do not cut the 4th joint carries out enzyme cuts.Enzyme on said the 4th joint is cut recognition site and included but not limited to: Mme I enzyme cuts that recognition site, Acu I enzyme are cut recognition site, Bsg I enzyme is cut recognition site.If the fragmentation product is repaired through the terminal repair enzyme, and end adds the A reaction, and said the 4th joint is preferably the terminal y splice of band T.If the fragmentation product is just repaired through the terminal repair enzyme, the preferred two deoxidation joints of then said the 4th joint.
In step S1223 ', said the 5th joint can be a kind of in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure, can have biotin labeling.
In another embodiment of the present invention, step S122 specifically may further comprise the steps:
S1221 ". directly connect the joint of band loop-stem structure, form the fragmentation product of band loop-stem structure at the two ends of fragmentation product;
S1222 ". utilize restriction enzyme, the stem ring district of the fragmentation product of being with loop-stem structure is cut or excision, thereby form the order-checking library.
The joint of present technique scheme utilization band loop-stem structure has prevented that a plurality of joints are from the generation that connects phenomenon.
Very few when the quantity in the order-checking library that forms through above-mentioned several schemes, when being unfavorable for follow-up unit molecule amplification step, can also carry out following steps:
Utilizing the shank complementary primer with order-checking two ends, library, target area, is that masterplate increases with the order-checking library of gained, the order-checking library after must increasing.This step can satisfy the requirement of subsequent experimental to the amount in target order-checking library.
Wherein, The described unit molecule amplification of step S2 is meant the molecule in the order-checking library, target area; Form with denier (even unit molecule) is spatially isolated (but these library molecules still belong to same reaction system on the whole); And in space separately, realize amplification, to promote the signal of various molecules in follow-up sequencing reaction.The method of said unit molecule amplification includes but not limited to: and emulsion PCR (Emulsion PCR, EPCR), bridge-type PCR.
The maximum characteristics of said EPCR are can form the huge independent reaction space of number to carry out DNA cloning.Primary process is before PCR reaction, and the aqueous solution that will comprise all reacted constituents of PCR is injected into the MO surface of high speed rotating, and aqueous solution moment forms numerous by the little water droplet of MO parcel.These little water droplets have just constituted independently PCR reaction compartment.Under the perfect condition; Each little water droplet only contains a dna profiling (order-checking library, target area molecule) and a magnetic bead; Contain consensus sequence (introducing) complementary primer on the magnetic bead by joint component with order-checking library, target area molecule; After the PCR reaction, magnetic bead surfaces just is fixed with the dna profiling amplified production in the same source of copy huge amount.The concrete steps of EPCR can be with reference to PCR amplification from single DNA molecules on magnetic beads in emulsion:application for high-throughput screening of transcription factor targets; Takaaki Kojima, Yoshiaki Takei, Miharu Ohtsuka et al; Nucleic Acids Research; 2005, Vol.33, No.17; Dual primer emulsion PCR for nextgeneration DNA sequencing, Ming Yan Xu, Anthony D.Aragon, Monica R.Mascarenas et al, BioTechniques 48:409-412 (May 2010); BEAMing:single-molecule PCR on microparticles in water-in-oil emulsions, Frank Diehl, Meng Li, Yiping He, nature methods, Vol.3, No.7, July 2006 etc.
The ultimate principle of said bridge-type PCR is; The primer of bridge-type PCR is fixed on the solid phase carrier; Pcr amplification product can be fixed on the solid phase carrier in the PCR process; And pcr amplification product can with the primer complementary pairing on the solid phase carrier, Cheng Qiaozhuan, the primer of complementary pairing is that template increases with the amplified production with its Cheng Qiao then.Through the amount that the control original template adds, after bridge-type PCR reaction was accomplished, amplified production form with cluster bunch on solid phase carrier existed, and the amplified production of each bunch be with the dna profiling amplified production of originating.Principle that it is concrete and embodiment can be with reference to following document: CN20061009879.X, US6227604.
As previously mentioned, in the prior art, the Sanger sequencing technologies can only check order to a certain section zone of a sample owing to the technical limitation of self at every turn.For disposable realization to detecting a plurality of zone the time in the sample, the present invention takes the high-throughput gene order surveying method on sequence measurement.The relative Sanger PCR sequencing PCR of high-throughput gene sequencing detects the more convenient sensitivity of sequence information; After each molecule in the order-checking library increases through unit molecule; Each order-checking library molecule all forms unit molecule copy array, and each unit molecule copy array is in different positions when carrying out the high-throughput gene sequencing, make sequencing primer and unit molecule copy the hybridization between the array; And the extension under the enzyme effect can carry out simultaneously, do not disturb mutually each other.Therefore, can be simultaneously a large amount of (millions of up to ten million, even more) unit molecule copy array be carried out sequencing reaction simultaneously, then through gathering corresponding signal, and then obtain required sequence information accurately, and the sensitivity of order-checking is higher than Sanger.Especially the amplified production to a plurality of target areas has carried out the fragmentation processing, and being equivalent to has increased the order-checking number of times of each base of the target area molecule of identical sequence, can further improve the sensitivity of order-checking.
Wherein, the described high throughput sequencing technologies of step S3 includes but not limited to: based on the synthetic PCR sequencing PCR of polysaccharase, based on the connection PCR sequencing PCR of ligase enzyme.
Be based on band based on the synthetic PCR sequencing PCR of polysaccharase and can remove that the Nucleotide of mark carries out.In each building-up reactions, each template strand can only extend once at the most, and is following based on the roughly flow process of the synthetic PCR sequencing PCR of polysaccharase:
A. sequencing primer is combined on the total known array of unit molecule amplified production (this unit molecule amplified production is fixed on primer-solid phase carrier mixture) through complementary pairing; Under the effect of archaeal dna polymerase; The Nucleotide that can remove mark with band carries out the single-basic extension building-up reactions; Collect the marking signal that this time adds Nucleotide, can obtain base sequence information with the next bit of the unit molecule amplified production (being fixed on primer-solid phase carrier mixture) of sequencing primer 3 ' least significant end base complementrity.
B. excision can be removed mark; Then under the effect of archaeal dna polymerase; Can remove the Nucleotide of mark with band and proceed the single-basic extension building-up reactions; Collect the marking signal that adds Nucleotide, can obtain following two base sequence information with sequencing primer 3 ' terminal bases complementary unit molecule amplified production.
Repeat the b step, till can not proceeding building-up reactions, thus the full sequence information of acquisition unit molecule amplified production.
All be based on based on the connection PCR sequencing PCR of ligase enzyme and be with fluorescently-labeled oligonucleotide probe to carry out.Wherein a kind of connection PCR sequencing PCR of ligase enzyme is based on specific position and has that fluorescently-labeled oligonucleotide probe carries out; This oligonucleotide probe has n base, from a bit strip of its 5 ' terminal number fluorescent mark is arranged, and wherein different base pairs should specific fluorescent mark; Because 3 ' end of this oligonucleotide probe has carried out specific modification; Can not directly interconnect between the oligonucleotide probe, each ligation, each unit molecule amplified production can only connect an oligonucleotide probe.This roughly flow process that connects PCR sequencing PCR is following:
A. sequencing primer is combined on the total known array of unit molecule amplified production on (this unit molecule amplified production is fixed on primer-solid phase carrier mixture) through complementary pairing; Utilize above-mentioned oligonucleotide probe; Under the effect of ligase enzyme; Nucleic probe is connected with above-mentioned oligonucleotide chain, gathers fluorescent signal then, can obtain 3 ' terminal back a bit base sequence information with the total known array of unit molecule amplified production.
B. excise the fluorescent mark on the oligonucleotide; Under the effect of ligase enzyme, be raw material with above-mentioned oligonucleotide probe, proceed ligation; Gather fluorescent signal then, thereby obtain the base sequence information of the 2a position, 3 ' terminal back of the total known array of unit molecule amplified production.
Repeat the B step, till can not proceeding ligation, thus the base sequence information of 3 ' terminal back a of the known array that acquisition unit molecule amplified production has, 2a, 3a, 4a...... position.
Then the sex change from the unit molecule amplified production of sequencing primer and the oligonucleotide probe that connected thereof is eluted; Use the primer of comparing a 3 ' terminal few base with sequencing primer before instead and repeat above-mentioned reaction, thus the base sequence information of 3 ' terminal back a-1 of the known array that acquisition unit molecule amplified production has, 2a-1,3a-1,4a-1...... position.Repeat this step, obtain 3 ' terminal back a-(a-1), 2a-(a-1), 3a-(a-1), the 4a-(a-1) of the total known array of unit molecule amplified production at last ... the base sequence information of position, thereby obtain the full sequence information of single-stranded amplification product.
The connection PCR sequencing PCR of another kind of ligase enzyme equally also is based on and has that fluorescently-labeled oligonucleotide probe carries out; This oligonucleotide probe has n base; (the difference between on the same group is not: the specific position that different fluorescent marks are corresponding is different for the group of h≤n), the Different Alkali basic sequence of the corresponding same specific position of different fluorescent marks of same group of oligonucleotide probe to be divided into h; Because 3 ' end of this oligonucleotide probe has carried out specific modification; Can not directly interconnect between the oligonucleotide probe, each ligation, each unit molecule amplified production can only connect an oligonucleotide probe.This roughly flow process that connects PCR sequencing PCR is following:
A. sequencing primer is combined on the total known array of unit molecule amplified production on (this unit molecule amplified production is fixed on primer-solid phase carrier mixture) through complementary pairing; (the base position that fluorescent mark is corresponding is x to utilize in the above-mentioned oligonucleotide probe one group; X≤h); Under the effect of ligase enzyme, nucleic probe is connected with above-mentioned oligonucleotide chain, gather fluorescent signal then; Can obtain 3 ' terminal back x bit base sequence information with the total known array of single-stranded amplification product, the sex change from the unit molecule amplified production of sequencing primer and the oligonucleotide probe that connected thereof is eluted.
B. again sequencing primer is combined on the unit molecule amplified production then; (the base position that fluorescent mark is corresponding is y to use the oligonucleotide probe group different with a step instead; Y≤h); Under the effect of ligase enzyme, nucleic probe is connected with above-mentioned oligonucleotide chain, gather fluorescent signal then; Can obtain 3 ' terminal back y bit base sequence information with the total known array of single-stranded amplification product, the sex change from the unit molecule amplified production of sequencing primer and the oligonucleotide probe that connected thereof is eluted.
C. repeating step b carried out a ligation respectively until h group oligonucleotide probe, thereby obtained 3 ' terminal back the 1st, the 2...... of the total known array of unit molecule amplified production, the base sequence information of h position.
Use the primer of comparing 3 ' terminal many one or each universal base with sequencing primer before instead and react by above-mentioned principle, can prolong the total known array of the unit molecule amplified production of acquisition 3 ' terminal bases sequence read long.
This connection order-checking ratio juris and specific embodiments based on ligase enzyme can be with reference to CN200710170507.1.
Exons 19,21 to detect the EGFR gene is an example; The present invention proposes an embodiment, is designed for the Auele Specific Primer of amplification EGFR gene extron 19,21: 19F (SEQ ID NO:1), 19R (SEQID NO:2), 21F (SEQ ID NO:3), 21R (SEQ ID NO:4).
One, the extraction of testing sample DNA
Utilize nucleic acid extraction kit common on the market to extract the DNA of whole blood sample (1 to 10), serum sample (11 to 20), paraffin organization sample (21 to 30) respectively, and do corresponding mark respectively.
Two, the amplification of target area
The amplification of the EGFR gene extron 19,21 of same sample is carried out in same reaction system, and reaction system is following:
19F(10μM) 2μL；
19R(10μM) 2μL；
21F(10μM) 2μL；
21R(10μM) 2μL；
DNTP (each 2.5mM) 4 μ L;
Testing sample DNA 20ng;
Ex?Taq(5U/μL) 0.25μL；
10×Ex?Taq?Buffer 5μL；
ddH
2O up?to?50μL。
The PCR reaction conditions is following:
95℃3min；
94 ℃ of 30s, 58 ℃ of 30s, 72 ℃ of 30s; Repeat 25 circulations;
72℃7min。
Utilize PCR cleaning agents box, the amplified production to each sample cleans respectively, removes the primer and the dNTP of not amplification, reclaims amplified production.
Three, establishing target zone order-checking library
This step can have multiple embodiments, in one embodiment of the present of invention, comprises following two steps:
1. the fragmentation of amplified production
Utilizing ultrasonic method to carry out fragmentation handles.Concrete operations are: the amplified production (about 50 μ L) after the PCR cleaning recovery of each sample are added among the TE buffer of 400 μ L, and ultrasonic 4s under the 430W power condition, 20s 5 times repeatedly, gets the fragmentation product at interval.Utilize 1% sepharose that the fragmentation product of each sample is carried out separation and purification, cut glue and reclaim the fragmentation product of size between 40bp to 100bp.
2. make up the order-checking library
Before order-checking library, establishing target zone, need carry out end modified respectively to the fragmentation product of cutting the glue recovery, so that the connection of joint component.In the present embodiment, the end modified of fragmentation product that cuts the glue recovery comprised that phosphorylation, end-filling and end add A and react.
The concrete realization as follows:
1) phosphorylation and end-filling reaction
System is:
Cut the fragmentation product 20 μ L (about 2000ng) that glue reclaims;
10mM?dNTP 1.5μL；
T4DNA polysaccharase (5U/ μ L) 1 μ L;
Klenow archaeal dna polymerase 0.1 μ L;
T4 polynucleotide kinase (10U/ μ L) 0.5 μ L;
10m?MATP 1.5μL；
10 * T4 ligase enzyme damping fluid, 10 μ L;
Add ddH
2O to 100 μ L.
Reaction conditions is: hatch 20min for 20 ℃.Reaction finishes the back and utilizes the recovery test kit to carry out purifying and recovering.
2) end adds the A tail
Reaction system is:
Recovery product 60 μ L (about 1000ng) behind phosphorylation and the end-filling;
Klenow damping fluid (NEB Buffer2) 10 μ L;
10mM?dATP 2μL；
Klenow enzyme (3 ' to, 5 ' exo minus, 10U/ μ L) 1 μ L;
Add ddH
2O to 100 μ L.
Reaction conditions is: hatch 30min for 37 ℃.Reaction utilizes the purification kit purifying and recovering after finishing.
3) jointing 1
In the present embodiment; Adopt the terminal y splice of T as shown in Figure 6 as joint 1, the terminal y splice of the employed T of same sample is identical, and the terminal y splice of the T of different samples is different; Difference is that sequence label is different, and the sequence label that different samples are corresponding is as shown in the table.
Under the effect of T4 ligase enzyme, the terminal y splice of above-mentioned T respectively with add the A tail after the product of purifying and recovering be connected, form the fragment of belt lacing 1.Linked system is:
The product 50 μ L (about 500ng) that add purifying and recovering behind the A tail;
Joint 12 μ L (about 3000ng);
10mM?ATP 5μL；
T4DNA ligase enzyme (10U/ μ L) 1 μ L;
10 * T4 ligase enzyme damping fluid, 10 μ L;
Add ddH
2O to 100 μ L.
Reaction conditions is: hatch more than the 4h for 16 ℃.Reaction utilizes the purification kit purifying and recovering after finishing.
4) fragment of pcr amplification belt lacing 1
Amplification system is:
The about 300ng of the fragment of belt lacing 1;
10×Ex?Taq?Buffer 100μL；
Primer?F(100μM，SEQ?ID?NO：11) 10μL；
Primer?R(100μM，SEQ?ID?NO：12) 10μL；
Ex?Taq(5U/μL) 7.5μL；
ddH
2O?up?to?1000μL。
The PCR reaction conditions is following:
95℃3min；
94 ℃ of 30s, 58 ℃ of 30s, 72 ℃ of 30s; Repeat 25 circulations;
72℃7min。
Utilize PCR cleaning agents box, the amplified production to each sample cleans respectively, removes the primer and the dNTP of not amplification, reclaims the segmental amplified production of belt lacing 1.
5) II s type digestion with restriction enzyme
Utilize the segmental amplified production of the belt lacing 1 after the switchback of Acu I enzyme is received, reaction system is following:
The segmental amplified production 60 μ L (3～5 μ g) of the belt lacing 1 after the recovery;
10×NEB?Buffer?4 8μL；
Acu?I(NEB) 2μL(10U)；
SAM (3.2mM) 1 μ L (final concentration 50 μ M);
ddH
2O?up?to?80μL。
Reaction conditions: hatch 1h for 37 ℃.Reaction utilizes purification kit purifying and recovering enzyme to cut product after finishing.
6) jointing 2
Utilize protruding terminus y splice as shown in Figure 7 as joint 2, cut product with the enzyme that reclaims and be connected, the library of must checking order, linked system is following:
The enzyme that reclaims is cut product 2 μ g;
Joint 21 μ L (10pM);
10T4DNA ligase enzyme (3U/ μ L) 1 μ L;
10 * T4 ligase enzyme damping fluid, 2 μ L;
Add ddH
2O to 100 μ L.
Condition of contact is hatched 2h for 14 ℃.Reaction utilizes the purification kit purifying and recovering after finishing, and sex change forms strand, the library of must checking order then.
Four, the unit molecule amplification is carried out in order-checking library, target area
Mensuration (three) step obtains order-checking library, 30 target areas concentration separately, then by mixing with isoconcentration, carries out the unit molecule amplification then, gets the unit molecule amplified production, and the method for said unit molecule amplification can adopt EPCR or bridge-type PCR.
Be preferably the EPCR amplification, the unit molecule amplimer is preferably: SEQ ID NO:5 and SEQ ID NO:6.
Five, the unit molecule amplified production is carried out high-flux sequence
Said sequence measurement can adopt the synthetic PCR sequencing PCR based on synthetic enzyme, also can adopt the connection PCR sequencing PCR based on ligase enzyme.Sequencing result is carried out bioinformatic analysis, can obtain exons 19 and 21 the sequence information of the EGFR gene of above-mentioned 30 samples.Analytical sequence result can know, except that the exons 19 of the EGFR gene of sample 23 is undergone mutation (sequence information is seen SEQ ID NO:8, and mutation rate is 6.2%), each exon of other sample is wild-type.
Should be noted that present embodiment is a specific embodiment of the present invention, the present invention is not had any qualification effect, for example the Auele Specific Primer of EGFR gene can be replaced with other the primer of process appropriate design; In addition, a plurality of steps in the present embodiment all can be replaced with reference to aforesaid method, repeat no more at this.
To the sensitivity of the method that is checked order in the target area of the present invention, the present invention adopts following embodiment to verify.
Through conventional design, make up the plasmid that contains EGFR gene extron 19 wild-type sequences (SEQ IDNO:7) and mutant sequence (SEQ ID NO:8) respectively; The plasmid that contains EGFR gene extron 21 wild-type sequences (SEQ ID NO:9) and mutant sequence (SEQ ID NO:10).
Prepare mutation rate then and be respectively 20%, 10%, 5%, 3%, 1%, 0% plasmid mixed solution.Above-mentioned plasmid mixed solution to contain 1000 copy plasmids is a template, detects by the method with reference to the foregoing description then.Detected result is as shown in the table:
The result shows, the lowest detection of the method that is checked order in the target area of the present invention is limited to about 3%, 5% and more than detected result and practical situation basically identical.
A kind of test kit that is checked order in the target area comprises:
Auele Specific Primer is used for being increased in a plurality of target areas of testing sample;
Joint component is used for combining with amplified production making up the order-checking library.
This test kit is used for the target area order-checking; Can carry out degree of depth order-checking to a plurality of target areas of sample simultaneously, accurately draw the sequence information of these target areas, comprise the variation situation in each mutational site of known mutations and position sudden change; Accurately draw the frequency that morphs in each mutational site of each sample; Detection sensitivity is high, can be used for the large-scale crowd examination of target area, confirms the ratio of the range gene type of this target area.
Wherein, said joint component is used for order-checking library, establishing target zone, comprises at least a or multiple joint.
Wherein, said joint component can adopt various ways, as: at least a in the joint of flat end fitting, protruding terminus joint, band loop-stem structure, the y splice.
Wherein, said joint can be methylated or biotinylation, or simultaneously by biotinylation with methylate.
Wherein, at least one joint in the said joint component includes first sequence label, is used in the library construction process, and mark is carried out in the order-checking library of different testing samples.Said first sequence label is preferably the nucleic acid molecule that has specific base sequence, and its base number is not limit, and is preferably 3～20, and more preferably 4～20.
Wherein, the complementary or part complementation in described Auele Specific Primer and target area.
Further; In the Auele Specific Primer of each target area correspondence, at least one primer and this target area part are complementary, and 5 ' end of this primer includes second sequence label; Be used in amplification target area process, the target area amplified production of different testing samples is carried out mark.Said second sequence label is preferably the nucleic acid molecule that has specific base sequence, and its base length is not limit.
Further, the base number of said second sequence label is 3～20, more preferably 4～10.
Wherein, said test kit can also comprise pcr amplification reagent, and said pcr amplification reagent comprises PCR enzyme, dNTP, PCR damping fluid, Mg
2+Solution.
Wherein, said test kit can comprise that also the enzyme that is used to discern on the joint component cuts the enzyme of recognition site.
Should be noted that through method of the present invention or test kit and detect the gene order information that obtains, can be used for various scientific researches, include but not limited to crowd's sequential analysis, gene functional research, protein function research.For example; In conjunction with statistical study of follow-up further molecular biology test, clinical trial, clinical observation and integrated data etc.; Thereby realize multiple scientific research purpose, include but not limited to: the genotype distribution of some specific gene of certain specific crowd, the mutation type of each gene and relevant physiological active relation etc.
The above is merely preferred embodiment of the present invention, not in order to restriction the present invention, all any modifications of within spirit of the present invention and principle, being done, is equal to and replaces and improvement etc., all should be included within protection scope of the present invention.
Claims (11)
1. a method that is checked order in the target area is characterized in that, may further comprise the steps:
A. utilize Auele Specific Primer, increased in a plurality of target areas in the testing sample, and make up the order-checking library based on amplified production;
B. the unit molecule amplification is carried out in the order-checking library, obtained a plurality of unit molecule amplified productions corresponding with said a plurality of target areas;
C. simultaneously said a plurality of unit molecule amplified productions are carried out the high-throughput gene sequencing, obtain the sequence information of said a plurality of target areas.
2. the method that is checked order in the target area according to claim 1 is characterized in that, said steps A may further comprise the steps:
A1. utilize Auele Specific Primer, increased in a plurality of target areas in the testing sample, obtain and the corresponding amplified production in said a plurality of target areas;
A2. utilize joint component, connect, obtain the library of checking order with the corresponding amplified production in said a plurality of target areas; Said joint component adopts at least a in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure.
3. the method that is checked order in the target area according to claim 2 is characterized in that, said steps A 2 may further comprise the steps:
A21. the amplified production corresponding with said a plurality of target areas carried out fragmentation, obtain the fragmentation product;
A22. utilize joint component, be connected, make up the order-checking library with said fragmentation product.
4. the method that is checked order in the target area according to claim 3 is characterized in that, said steps A 22 may further comprise the steps:
A221. utilize first joint to be connected, the connection product of winning with the two ends of fragmentation product;
A222. cyclisation first connects product, gets cyclisation product;
A223.II s type digestion with restriction enzyme cyclisation product gets enzyme and cuts product;
A224. cut the product two ends at enzyme and connect second joint and the 3rd joint, the library of must checking order.
5. the method that is checked order in the target area according to claim 3 is characterized in that, said steps A 22 may further comprise the steps:
A221 '. utilize the 4th joint to be connected, get second and connect product with the fragmentation product;
A222 ' .II s type digestion with restriction enzyme second connects product, must have the endonuclease bamhi of the 4th joint;
A223 '. the endonuclease bamhi that has the 4th joint is connected with the 5th joint, forms the order-checking library.
6. according to each described method that is checked order in the target area of claim 2 to 5; It is characterized in that; At least one joint in the steps A 2 described joint components includes first sequence label, is used in the library construction process, and mark is carried out in the order-checking library of different testing samples.
7. according to each described method that is checked order in the target area of claim 1 to 5; It is characterized in that; In the Auele Specific Primer of each target area correspondence, have at least a primer and this target area part complementary, 5 ' end of this part complementary primer includes second sequence label; Be used in amplification target area process, the target area amplified production of different testing samples is carried out mark.
8. a test kit that is checked order in the target area is characterized in that, comprising:
Auele Specific Primer is used for being increased in a plurality of target areas of testing sample;
Joint component is used for combining with amplified production making up the order-checking library.
9. the test kit that is checked order in the target area according to claim 8 is characterized in that, said joint component adopts at least a in joint and the y splice of flat end fitting, protruding terminus joint, band loop-stem structure.
10. the test kit that is checked order in the target area according to claim 8; It is characterized in that; At least one joint in the said joint component includes first sequence label, is used in the library construction process, and mark is carried out in the order-checking library of different testing samples.
11. according to Claim 8 to 10 each described test kits that checked order in the target area; It is characterized in that; In the Auele Specific Primer of each target area correspondence, have at least a primer and this target area part complementary, 5 ' end of this part complementary primer includes second sequence label; Be used in amplification target area process, the target area amplified production of different testing samples is carried out mark.
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Effective date of registration: 20160927 Address after: 430040 No. 388, No. 21, No. three, biological medicine accelerator, two hi tech Road, East Lake New Technology Development Zone, Hubei, Wuhan Patentee after: Wuhan Kangxinrui Gene Health Technology Co., Ltd. Address before: 518057, Guangdong, Nanshan District hi tech Zone, two science and Technology Park, two software park, 11, 4, building 402, north room, Shenzhen Patentee before: Sheng Sichong |