CN102978206A - High-throughput sequencing joint applied to hybrid library building and library building method thereof - Google Patents

High-throughput sequencing joint applied to hybrid library building and library building method thereof Download PDF

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Publication number
CN102978206A
CN102978206A CN2012104876576A CN201210487657A CN102978206A CN 102978206 A CN102978206 A CN 102978206A CN 2012104876576 A CN2012104876576 A CN 2012104876576A CN 201210487657 A CN201210487657 A CN 201210487657A CN 102978206 A CN102978206 A CN 102978206A
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joint
product
library
sequence
library building
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蒋智
刘少卿
吴静
彭献军
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Nuo Hezhi Source Beijing Bioinformation Science And Technology Ltd
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Nuo Hezhi Source Beijing Bioinformation Science And Technology Ltd
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Abstract

The invention provides a joint containing a new Index sequence on the basis of the Illumina Hiseq sequencing platform principle. A hybrid library building method which can be used for building multiple libraries is successfully built by combining a Truseq reagent library building method and an NEB reagent library building method, so that the library building cost and time are saved and the library building efficiency is improved.

Description

A kind ofly be applied to mix high-flux sequence joint and the banking process thereof of building the storehouse
Technical field
The present invention relates to the high-flux sequence field, specifically, relate to a kind ofly save time, the improvement of cost and the library constructing method of raising the efficiency.
Background technology
Usually it is simple to build the required flow process in storehouse with Truseq reagent, builds Kucheng's power height, but somewhat expensive, and the time is long, will consume plenty of time and expense when many building the storehouse number.Although and that NEB reagent is built the storehouse expense is relatively low, flow process is relatively loaded down with trivial details.
Mix that to build the storehouse be improvement on Truseq reagent and NEB reagent banking process.Then different libraries are mixed the Index that can identify different libraries by before the Piece Selection step, adding.The glue of cutting that the method and traditional method are follow-up than making carries out saving a large amount of reagent costs, human cost and time on Piece Selection and the PCR step.The method is specially adapted to the little biological genome of genome resurvey order and the order-checking degree of depth low gene order-checking.
Summary of the invention
An object of the present invention is the double-stranded joint of synthetic Illumina company, and substitute I ndex, Index quantity increased.
Double-stranded linker DNA sequence molecule A provided by the invention comprises forward and reverse two chains.Forward chain 5 ' is terminal different except 6 bases of Index part to 3 ' terminal Hiseq2000 order-checking platform sequencing sequence P7 from Illumina company, and all the other are all identical, and carry out phosphorylation modification at 5 ' end; Reverse strand is identical with the Hiseq2000 order-checking platform sequencing sequence P5 of Illumina company.The structure of joint A as shown in Figure 1.
The aforesaid oligonucleotide fragment identical with the Hiseq2000 order-checking platform sequencing sequence p7 of illumina company is 1-33 position and the 40-63 position of sequence in the sequence table 1.
The Index part of aforesaid replacement is the 34-39 position in the sequence 1,2,3.
Aforesaidly carry out phosphorylation modification at forward chain 5 ' end, the phosphorylation modification that carries out for sequence in the sequence table 1,2,3 the 1st deoxyribonucleotide.
Aforesaid reverse strand is sequence 4 in the sequence table.
Second purpose of the present invention is to use above-mentioned joint A, mixes making up different samples library; In conjunction with Truseq reagent and NEB reagent banking process, mix the structure library and comprise the steps, as shown in Figure 2:
1) genomic dna being smashed size concentrates on about 300 bp;
2) after product purification reclaims to smashing of obtaining of step 1), carry out end-filling.The product of end-filling is carried out 3 ' add dATP, the product that will add dATP connects joint A;
3) to step 2) after the connection product that obtains mixes, run the agarose gel electrophoresis analysis, as shown in Figure 3; Select fragment according to required library size, as shown in Figure 4;
4) with fragment purification and quantitative laggard performing PCR amplification, and with the amplified production purifying, then check order at the Hiseq2000 of Illumina company order-checking platform;
5) carry out analysis of biological information.
The above-mentioned joint A of aforesaid utilization mixes the method that makes up different samples library, and wherein in the step 1), the described condition of smashing is for using covaris to smash instrument and adjust corresponding parameter.
The above-mentioned joint A of aforesaid utilization mixes the method that makes up different samples library, wherein step 2) in, the method that product is smashed in described recovery reclaims for adopting the PCR product to reclaim test kit; Described end-filling system is carried out for the Quick Blunting kit that uses NEB company; The system of the described dATP of adding comprises: dATP, and 10 * NEB Buffer 2, Klenow exo-polysaccharase, the concentration of described dATP is 100 mM, the concentration of described polysaccharase in described reaction system is 25 U/ul; The linked system of described joint A comprises: joint A, and 2XQuick Ligation Buffer, Quick T4 DNA Ligase, the concentration of described joint A is 8 uM.
The above-mentioned joint A of aforesaid utilization mixes the method that makes up different samples library, and wherein in the step 4), described purifying adopts the glue of Qiagen company to reclaim test kit and reclaims; The PCR system comprises: primer, polysaccharase mixture, and the connection product that obtains in the step 3).
Further, described PCR system comprises: primer, polysaccharase mixture, and the connection product that obtains in the step 3) comprises: the concentration of primer is 0.2 uM, described polysaccharase mixture volume of shared 50% in described PCR system.
Of the present invention experimental results show that, linkers A provided by the invention, can be connected to the two ends of dna fragmentation, use banking process of the present invention, successful structure the DNA library, and successful application checks order at the order-checking platform of the Hiseq2000 of illumina company, and the new Index that introduces can well separate the library; The storehouse is built in the mixing that simultaneously, can realize a plurality of samples.It is a kind of convenient to the invention provides, efficient, makes up fast the method in library, has saved in a large number reagent cost, human cost and time.
Description of drawings
Fig. 1 is the structural representation of joint A;
Fig. 2 is for building the storehouse schematic flow sheet;
Fig. 3 is for having connected the agarose gel electrophoresis figure of joint A;
Fig. 4 cuts the agarose gel electrophoresis figure that glue has been selected clip size for having connected joint A;
Fig. 5 is 2100 detected results;
Fig. 6 builds storehouse sequencing quality control result for mixing.
Embodiment
Describe below with reference to the accompanying drawings and in conjunction with the embodiments the present invention in detail.
Method is ordinary method if no special instructions described in the following embodiment, and used nucleotide sequence is synthetic by Shanghai Invitrogen biotech firm.Agents useful for same is the product of NEB company if no special instructions, and institute's water is ultrapure water.
One, quality examination.
1. sample concentration is measured: use Qubit (U.S.) to the sample DNA concentration determination, carry out precisely quantitatively, and use 0.8% sepharose, and 120v voltage, electrophoresis 1 hour, the test sample quality guarantees that genome DNA sample is complete without degraded.
Two, genomic fragment is broken.
2. genomic dna is used the covaris(U.S.) be crushed to about 300 bp, to use Qiagen PCR test kit to reclaim and smash product, concrete steps are carried out according to Qiagen test kit process specifications.
3. above-mentioned recovery product is carried out end-filling; Reaction system and reaction conditions are as follows: smash product D NA 30 μ l, and 10 * Blunting Buffer, 5 μ l, 1 mM dNTP, 10 μ l, Quick Blunting kit Enzyme Mix, 1 μ l adds H 2O 9 μ l, total system 50 μ l; Reaction conditions: hatch 30 min for 30 ℃.Ampure XP beads with 1.6 times of volumes carries out purifying to filling product.
Three, smash the fragment end and repair, add dATP.
4. the purified product in the step 3 is added dATP; Reaction system and condition are as follows: fill product, 20 μ l, 100 mM dATP1 μ l, 10 * NEB Buffer, 23 μ l, Klenow exo in the step 3 -(NEB) (50,000 units/ml) 0.5 μ l, H 2O 5.5 μ l, cumulative volume 30 μ l; Reaction conditions: abundant mixing, hatch 30 min for 37 ℃, 75 ℃ of 20 min heat inactivation.
Four, add the dATP product and add joint A.
5. to adding the dATP product, add joint A, joint A structure as shown in Figure 1; Reaction system is connected with condition: connect product 24 μ l, and 2XQuick Ligation Buffer 30 μ l, Quick T4 DNA Ligase 1.2 μ l, 8 uM joint A, 5 μ l, cumulative volume 60 μ l connect 30 min under the room temperature.Ampure XP beads with 1.6 times of volumes carries out purifying to connecting product, and purge process is carried out in strict accordance with working instructions.
6. it is quantitative the connection product in the step 5 to be carried out Qubit, according to the sequencing data amount connection product of different samples is carried out balanced mix.
7. prepare 2% agarose gel electrophoresis, as shown in Figure 3; The connection product that mixes is cut glue select clip size, as shown in Figure 4; Adopt the glue recovery test kit of Qiagen company to reclaim; To carry out Qubit quantitative to reclaiming product, is used for next step pcr amplification.
Five, pcr amplification.
8. with the product that reclaims in 7, precisely quantitatively 10ng is used for the PCR reaction, and the PCR product that obtains is constructed library.Reaction system and condition are as follows: DNA sample 3 μ l, PCR Primer 11 μ l, PCR Primer 21 μ l, 2 * Phusion PCR Master Mix, 25 μ l, H 2O 20 μ l, 50 μ l altogether, the condition of answering is: first 98 ℃ of denaturation 1min; Then 98 ℃ of 10 s, 60 ℃ of 30 s, 72 ℃ of 30 s, totally 10 circulations; Last 72 ℃ are extended 5 min.The sequence of Primer 1 is 5 '-AATGATACGGCGACCACCGA-3 '; The sequence of Primer 2 is 5 '-CAAGCAGAAGACGGCATACGA-3 '.
9. with twice of the PCR product equal-volume AMP μ re XP Beads purifying in the step 8; Purge process is carried out in strict accordance with working instructions; Take out 1ul and carry out 2100 detections, the result shows that obtaining the library size is 351 bp:, as shown in Figure 5.
10. it is precisely quantitative the purified product in the step 9 to be carried out Q μ bit.
Six, the inspection of storehouse, library and upper machine.
11. the purified product of gained in the step 9 is diluted to 1ng/ul, takes out 1ul and be used for Agilent2100(U.S. Agilent company) detect, get again in addition 1ul and be used for qPCR(Biorad company) detect, according to detected result, machine concentration in the decision.
12. according to the concentration of step 1 gained, the library is diluted to upper confidential asking after, check order at the Hiseq2000 of Illumina company order-checking platform.
Seven, as a result Quality Control of upper machine.
Utilize aforesaid method that 3 honeybees order sample of resurveying is mixed and builds the storehouse.
In conjunction with shown in Figure 6, interpretation of result is as follows:
Q20, Q30: the Q20 of PoolBee as we know from the figure, Q30 reaches more than 98%, and for the order project of resurveying: require Q20 to be not less than 90%; Q30 is not less than 85%, requires to be not less than 95% even if De novo project is Q20 only; Q30 is not less than 90%, so this time sequencing quality is good.
The Adapter pollution rate: this time mix the adapter rate that builds the storehouse and be respectively 0.02%, 0.03%, 0.02%, Adapter rate is thinking normal below 5%, so it is normal this time to build storehouse Adapter rate.
Duplication: this time mix the Duplication1.85%, 2.26%, 2.53 that builds the storehouse, it is generally higher that storehouse Duplication is built in mixing, and this builds storehouse Duplication in allowed band.
Data volume: this target data 25M that checks order, about real data 20M, lacked the 5M data.And the data that Poolbee-1, Poolbee-2, Poolbee-3 obtain are difference to some extent, when this may be with biased sample in gimmick and the library actual effective concentration relevant.
It is qualified this time to build in sum the storehouse, and sequencing quality is good.
The above is the preferred embodiments of the present invention only, is not limited to the present invention, and for a person skilled in the art, the present invention can have various modifications and variations.Within the spirit and principles in the present invention all, any modification of doing, be equal to replacement, improvement etc., all should be included within protection scope of the present invention.
Sequence table 1
<110〉promise standing grain in Beijing causes source bioinformation Science and Technology Ltd.
<120〉a kind ofly be applied to mix high-flux sequence joint and the banking process thereof of building the storehouse
<160> 2
<210> 1
<211> 63
<212> DNA
<213〉artificial sequence
<220>
<223〉carry out phosphorylation modification at the 1st bit base
<400> 1
gatcggaaga gcacacgtct gaactccagt cactgcagta tctcgtatgc cgtcttctgc 60
ttg 63
Sequence table 2
<110〉promise standing grain in Beijing causes source bioinformation Science and Technology Ltd.
<120〉a kind ofly be applied to mix high-flux sequence joint and the banking process thereof of building the storehouse
<160> 2
<210> 1
<211> 63
<212> DNA
<213〉artificial sequence
<220>
<223〉carry out phosphorylation modification at the 1st bit base
<400> 1
gatcggaaga gcacacgtct gaactccagt cac tagatca tctcgtatgc cgtcttctgc 60
ttg 63
Sequence table 3
<110〉promise standing grain in Beijing causes source bioinformation Science and Technology Ltd.
<120〉a kind ofly be applied to mix high-flux sequence joint and the banking process thereof of building the storehouse
<160> 2
<210> 1
<211> 63
<212> DNA
<213〉artificial sequence
<220>
<223〉carry out phosphorylation modification at the 1st bit base
<400> 1
gatcggaaga gcacacgtct gaactccagt caccacgga tctcgtatgc cgtcttctgc 60
ttg 63
Sequence table 4
<110〉promise standing grain in Beijing causes source bioinformation Science and Technology Ltd.
<120〉a kind ofly be applied to mix high-flux sequence joint and the banking process thereof of building the storehouse
<160> 2
<210> 2
<211> 58
<212> DNA
<213〉artificial sequence
<220>
<400> 2
aatgatacgg cgaccaccga gatctacact ctttccctac acgacgctct tccgatct 58

Claims (6)

1. joint sequence A is characterized in that:
The joint that is formed by the nucleotide sequence shown in sequence in the sequence table 1 or 2 or 3 and 4.
2. one kind is used joint A as claimed in claim 1, mixes the method that makes up different samples library, it is characterized in that, comprises the steps:
1) genomic dna is smashed, size concentrates on about 300 bp;
2) after product purification reclaims to smashing of obtaining of step 1), carry out end-filling; The product of end-filling is carried out 3 ' add dATP; The product that will add dATP connects joint A;
3) to step 2) after the connection product that obtains mixes, run the agarose gel electrophoresis analysis; Select fragment according to required library size;
4) with fragment purification and quantitative laggard performing PCR amplification, and with the amplified production purifying, then check order at the Hiseq2000 of Illumina company order-checking platform;
5) carry out analysis of biological information.
3. method according to claim 2 is characterized in that:
In conjunction with Truseq reagent and NEB reagent banking process, and a plurality of DNA library made up simultaneously.
4. method according to claim 2, it is characterized in that: method according to claim 2 is characterized in that:
By connecting different Index joint A, constructed dna library.
5. method according to claim 2 is characterized in that:
Its described material DNA source is plant, animal or microorganism.
6. method according to claim 2 is characterized in that:
The order-checking platform is illumina Hiseq2000 order-checking platform.
CN2012104876576A 2012-11-27 2012-11-27 High-throughput sequencing joint applied to hybrid library building and library building method thereof Pending CN102978206A (en)

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Cited By (12)

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CN103667273A (en) * 2013-12-05 2014-03-26 北京诺禾致源生物信息科技有限公司 Double chain adaptor, application thereof and method for constructing end-pairing DNA library
CN104232627A (en) * 2013-06-13 2014-12-24 深圳华大基因科技有限公司 2b-RAD pooling technology
WO2015100736A1 (en) * 2014-01-03 2015-07-09 深圳华大基因研究院 Minimally-invasive method for postoperative monitoring of cancer patients
CN104789552A (en) * 2015-03-11 2015-07-22 南方科技大学 Method for rapid preparation of high-throughput sequencing library and application
CN104894651A (en) * 2015-06-29 2015-09-09 天津诺禾医学检验所有限公司 Building method of high-throughput sequencing library of trace starter DNA (deoxyribonucleic acid) and high-throughput sequencing library built by building method
CN105200530A (en) * 2015-10-13 2015-12-30 北京百迈客生物科技有限公司 Method for establishing multi-sample hybrid library suitable for high-flux whole-genome sequencing
CN105671644A (en) * 2016-02-26 2016-06-15 武汉冰港生物科技有限公司 Preparation method of genome mixing sequencing library
CN106676095A (en) * 2015-11-09 2017-05-17 中国科学院植物研究所 Complete set reagent for developing genetic markers and method for developing genetic markers through high-throughput sequencing
CN106795650A (en) * 2014-09-26 2017-05-31 深圳华大基因股份有限公司 The quick banking process of PF and its application
CN107475403A (en) * 2017-09-14 2017-12-15 深圳因合生物科技有限公司 The analysis method of the method for detection Circulating tumor DNA, kit and its sequencing result from peripheral blood dissociative DNA
CN107849546A (en) * 2015-05-15 2018-03-27 先锋国际良种公司 To the quick sign of CAS endonuclease systems, PAM sequences and guide RNA element
WO2020043174A1 (en) * 2018-08-31 2020-03-05 成都先导药物开发股份有限公司 High-throughput next-generation sequencing method for double-stranded nucleotide sequencing

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Publication number Priority date Publication date Assignee Title
CN104232627A (en) * 2013-06-13 2014-12-24 深圳华大基因科技有限公司 2b-RAD pooling technology
CN104232627B (en) * 2013-06-13 2017-05-10 深圳华大基因科技有限公司 2b-RAD pooling technology
CN103667273A (en) * 2013-12-05 2014-03-26 北京诺禾致源生物信息科技有限公司 Double chain adaptor, application thereof and method for constructing end-pairing DNA library
CN103667273B (en) * 2013-12-05 2016-01-20 北京诺禾致源生物信息科技有限公司 Double-stranded adapters, its application and build end pairing DNA library method
WO2015100736A1 (en) * 2014-01-03 2015-07-09 深圳华大基因研究院 Minimally-invasive method for postoperative monitoring of cancer patients
CN105849282A (en) * 2014-01-03 2016-08-10 深圳华大基因研究院 Minimally-invasive method for postoperative monitoring of cancer patients
CN106795650A (en) * 2014-09-26 2017-05-31 深圳华大基因股份有限公司 The quick banking process of PF and its application
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CN104789552A (en) * 2015-03-11 2015-07-22 南方科技大学 Method for rapid preparation of high-throughput sequencing library and application
CN107849546A (en) * 2015-05-15 2018-03-27 先锋国际良种公司 To the quick sign of CAS endonuclease systems, PAM sequences and guide RNA element
CN104894651A (en) * 2015-06-29 2015-09-09 天津诺禾医学检验所有限公司 Building method of high-throughput sequencing library of trace starter DNA (deoxyribonucleic acid) and high-throughput sequencing library built by building method
CN105200530A (en) * 2015-10-13 2015-12-30 北京百迈客生物科技有限公司 Method for establishing multi-sample hybrid library suitable for high-flux whole-genome sequencing
CN106676095A (en) * 2015-11-09 2017-05-17 中国科学院植物研究所 Complete set reagent for developing genetic markers and method for developing genetic markers through high-throughput sequencing
CN105671644A (en) * 2016-02-26 2016-06-15 武汉冰港生物科技有限公司 Preparation method of genome mixing sequencing library
CN107475403A (en) * 2017-09-14 2017-12-15 深圳因合生物科技有限公司 The analysis method of the method for detection Circulating tumor DNA, kit and its sequencing result from peripheral blood dissociative DNA
WO2020043174A1 (en) * 2018-08-31 2020-03-05 成都先导药物开发股份有限公司 High-throughput next-generation sequencing method for double-stranded nucleotide sequencing

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Application publication date: 20130320