WO2016082057A1 - 游离dna测序文库的构建方法 - Google Patents

游离dna测序文库的构建方法 Download PDF

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WO2016082057A1
WO2016082057A1 PCT/CN2014/001050 CN2014001050W WO2016082057A1 WO 2016082057 A1 WO2016082057 A1 WO 2016082057A1 CN 2014001050 W CN2014001050 W CN 2014001050W WO 2016082057 A1 WO2016082057 A1 WO 2016082057A1
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free dna
dna
library
concentration
linker
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PCT/CN2014/001050
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French (fr)
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赵鑫
崔路漫
刘耿
宋彬
侯勇
吴逵
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深圳华大基因研究院
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Priority to PCT/CN2014/001050 priority patent/WO2016082057A1/zh
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms

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  • the present invention relates to a method of constructing a free DNA sequencing library.
  • cfDNA tumor DNA
  • ctDNA tumor DNA
  • Plasma free DNA of cancer patients contains various tumor-associated mutant genes.
  • the ctDNA of cancer patients is mainly derived from the secretion, apoptosis or necrosis of tumor cells, and its concentration is up to 180 ng/mL, which is more than 20 times that of normal people. Studies have shown that the average length of ctDNA is 140-170 bp, and its gene mutation can directly reflect the gene mutation of tumor tissue [1,2].
  • the Nitzan Rosenfeld team used a new technology-target fragment deep sequencing method to verify that the technique can effectively monitor tumors by detecting ctDNA gene mutations in 62 plasma DNA samples from 37 ovarian cancer patients.
  • the results are highly consistent with the results of digital PCR assays.
  • the discovery of unknown mutations is even better than digital PCR, which is simpler to operate than digital PCR technology.
  • the Nitzan Rosenfeld team selected 30 patients with point mutations or genetic structural variations of PIK3CA or TP53 from 52 patients with metastatic breast cancer.
  • the mutations in 141 plasma DNA samples and the other two biomarkers, CA15- The level of 3 and the number of CTCs were compared.
  • EGFR mutation-positive tumors have better sensitivity to erlotinib or gefitinib and are less sensitive to other chemotherapeutic drugs, and EGFR mutations need to be performed before chemotherapy drugs such as Iressa and Tarceva. Detection.
  • tissue biopsy is often used to obtain tumor tissue and then perform genetic testing, which not only causes serious trauma to the patient, but also is cumbersome to operate, and can not achieve the purpose of real-time monitoring of drug sensitivity.
  • the conventional ILLUMINA Hiseq2000 library requires a large amount of gDNA (1-3 micrograms), not suitable for plasma micro Fragmentation of gDNA (about a few nanograms) to build a library.
  • the present invention provides a method of constructing a free DNA sequencing library.
  • the terminal repair is carried out in a terminal repair system containing DNA polymerase and nucleotide kinase in the end repair system
  • concentration may be 1.5U-3U / 50 ⁇ L, specifically 1.5U / 50 ⁇ L
  • concentration of the nucleotide kinase in the terminal repair system may be 5U-10U / 50 ⁇ L, specifically 5U / 50 ⁇ L;
  • the ligation library linker is carried out in a ligation system comprising a library linker and a DNA ligase, said library linker being
  • concentration in the adapter system is 20-40 pmol / 50 ⁇ L, specifically 20 pmol / 50 ⁇ L; the concentration of the DNA ligase in the addition of the linker system may be 1200U-2400U / 50 ⁇ L, specifically 1200U / 50 ⁇ L;
  • the number of cycles of the amplification may be 8-12, specifically 10.
  • the volume of the terminal repair system may be 20-100 ⁇ L, specifically 50 ⁇ L.
  • the DNA polymerase is T4 DNA polymerase
  • the nucleotide kinase is T4 polynucleotide kinase
  • the DNA ligase is T4 DNA ligase.
  • the terminal repair system contains a Klenow fragment (Klenow Fragment), and the concentration of the Klenow fragment in the terminal repair system may be 2.5-5 U/50 ⁇ L, specifically 2.5 U/ 50 ⁇ L.
  • the terminal repair can be carried out at 20 ° C for 30 min.
  • the end plus "A” can be carried out at 37 ° C for 30 min.
  • the ligation library linker can be carried out at 20 ° C for 15 min.
  • the amplification is carried out in an amplification system containing Platinum Pfx DNA polymerase (Platinum Pfx DNA polymerase) in the amplification system
  • Platinum Pfx DNA polymerase Platinum Pfx DNA polymerase
  • the concentration is 2U-4U/50 ⁇ L, specifically 2U/50 ⁇ L.
  • the cycle temperature of the amplification is 94 ° C for 20 s, then 62 ° C for 40 s, and finally 72 ° C for 50 s.
  • the constructing method may include the step of extracting the free DNA from a body fluid.
  • the free DNA may be free DNA in body fluid (ex vivo body fluid free DNA) such as blood free DNA (ex vivo blood free DNA), plasma free DNA (ex vivo plasma free DNA).
  • body fluid free DNA such as blood free DNA (ex vivo blood free DNA), plasma free DNA (ex vivo plasma free DNA).
  • the sequencing method of library construction using the construction method of the free DNA sequencing library of the present invention has an average coverage of 98.7% in the target region of plasma free DNA of peripheral blood, and the average capture efficiency of the target region reaches 61.2%. Compared with the average capture efficiency of about 10-15% in the same kind of research, the capture efficiency of the sequencing analysis method even reaches the capture efficiency of the target region of the cell line/tissue sample with complete genomic DNA and good quality samples.
  • the sequencing analysis method of the present invention can detect point mutations, short insertions/deletions of EGFR, copy number mutations of MET and EGFR in lung cancer patients.
  • the sequencing analysis method of the invention can detect the frequency ratio of the frequency of the extremely low frequency of the peripheral blood plasma of the lung cancer patient and the mutation frequency ratio of the drug resistance and the sensitivity degree.
  • Figure 1 is a 2100 detection peak map of peripheral blood plasma free DNA library of lung cancer patients.
  • Figure 2 is a distribution of capture coverage of plasma free DNA target regions in peripheral blood of patients with lung cancer.
  • Figure 3 shows the capture efficiency distribution of plasma free DNA target regions in peripheral blood of patients with lung cancer.
  • Figure 4 shows the change of MET gene copy number in the progression of different clinical stages of lung cancer patients with MET gene copy number: 1 represents disease progression phase I, 2 represents disease progression phase II, and 3 represents disease progression phase III.
  • the method for constructing the free DNA sequencing library provided below is a method suitable for constructing an free DNA sequencing library which is improved by the following steps in the construction method of the DNA sequencing library of ILLUMINA Hiseq2000:
  • the concentration of T4 DNA polymerase in the reaction system is 1.5U-3U/50 ⁇ L, specifically 1.5U/50 ⁇ L; T4 polynucleotide kinase is in the reaction system.
  • the concentration may be 5U-10U/50 ⁇ L, specifically 5U/50 ⁇ L;
  • the concentration of the Klenow fragment (3'-5'exo-) in the reaction system may be 2.5U-5U/50 ⁇ L, specifically 5U/50 ⁇ L;
  • the concentration of the library linker in the adaptor system is 20-40 pmol/50 ⁇ L, specifically 20 pmol/50 ⁇ L; the concentration of T4 DNA ligase in the adder system can be 1200 U- 2400U/50 ⁇ L, specifically 1200U/50 ⁇ L;
  • the number of cycles of amplification is increased to 8-12 cycles, specifically 10.
  • the method for constructing the free DNA sequencing library of the present application is exemplified below by taking a lung cancer patient as an example.
  • PNK 10 ⁇ Polynucleotide Kinase (PNK) Buffer, dNTP Solution Set, T4 DNA Polymerase, Klenow Fragment, T4Polynucleotide Kinase, Klenow (3'-5'exo-) kit, dATP, 2 ⁇ Rapid ligation buffer, T4 DNA Ligase (Rapid) ) are products of Enzymatics; PE Adapter oligo mix, Invitrogen Dynabeads M-280, Pfx DNA Polymerase Kit and Cot-1 DNA are products of Invitrogen; SnoMag TM Circulating DNA Kit is a product of SNOVA Biotechnologies; 2 ⁇ SC Hybridization Buffer and SC Hybridization Component A are products of Roche Nimblegen; SeqCap EZ Hybridization and Wash The kit is a product of ROCHE DIAGNOSTICS; AmpureXP beads are products of AGENCOURT; Flowcell primers F and Flowcell primers R are products of Illumina
  • Example 1 Construction method and application of plasma free DNA sequencing library of peripheral blood of lung cancer patients
  • This embodiment provides a sequencing analysis method for peripheral blood plasma free DNA, which comprises the steps of constructing a plasma free DNA sequencing library of a peripheral blood of a lung cancer patient and a sequencing and analysis of a plasma free DNA sequencing library of a peripheral blood of a lung cancer patient.
  • the library construction method is a construction method of a plasma free DNA sequencing library suitable for lung cancer patients which is improved based on the Hiseq library construction method.
  • Construction of a plasma free DNA sequencing library of peripheral blood of a lung cancer patient includes the following steps (1), (2), (3), (4), and (5).
  • the SnoMag TM Circulating DNA kit was used to extract plasma free DNA from peripheral blood of patients with lung cancer, as follows:
  • the EP tube was placed on a magnetic stand for 1 min, and the obtained supernatant was a plasma free DNA solution of peripheral blood of a lung cancer patient, and the supernatant was transferred to a new 1.5 mL EP tube.
  • the plasma free DNA concentration in peripheral blood of lung cancer patients in peripheral blood plasma of 16 patients with lung cancer was determined. The results are shown in Table 1:
  • End-repair method 50 ⁇ L end-repair system prepared according to Table 2, the concentration of T4 DNA polymerase was 1.5 U/50 ⁇ L in the 50 ⁇ L end-repair system, the concentration of T4 polynucleotide kinase was 5 U/50 ⁇ L, and the concentration of Klenow fragment was It is 2.5U/50 ⁇ L.
  • a 50 ⁇ L end-repair system was incubated in a Thermomixer constant temperature dry bath at 20 ° C for 30 min to obtain a terminally repaired free DNA solution.
  • the end-repaired free DNA obtained by purifying the magnetic beads with 90 ⁇ L of AmpureXP beads was purified, and the purified DNA at the end was purified by eluting the end-repaired free DNA from AmpureXP beads with 36 ⁇ L of Elution buffer (elution buffer) to obtain a purified end-repaired free DNA solution. .
  • the end of the "A” method was added to the 50 ⁇ L end of the "A” system prepared in accordance with Table 3, and the concentration of the Klenow fragment (3'-5'exo-) in the 50 ⁇ L end plus "A" system was 5 U / 50 ⁇ L.
  • the 50 ⁇ L end plus "A" system with the “A” method at the end was incubated in a Thermomixer constant temperature dry bath for 30 min at 37 ° C to obtain a free DNA solution with "A” added at the end.
  • the obtained free DNA of "A” was purified by using 90 ⁇ L of Ampure XP beads, and the free DNA of "A” was eluted from AmpureXP beads with 24 ⁇ L of Elution buffer to obtain a free DNA solution with "A” added at the end.
  • the concentration of the library adapter (PE Adapter oligo) was 20 pmol/50 ⁇ L, and the concentration of T4 DNA ligase was 1200 U/50 ⁇ L.
  • step (c) 22.5 ⁇ L 2 ⁇ Rapid ligation buffer (2 ⁇ Efficient ligation buffer) 25 ⁇ L PE Adapter oligo mix (double end joint mixture) (40 ⁇ M) 0.5 ⁇ L T4 DNA Ligase (Rapid) (T4 DNA ligase (high efficiency)) (600U/ ⁇ L) 2 ⁇ L total capacity 50 ⁇ L
  • the 50 ⁇ L plus linker system with the two ends connected to the library adaptor method in the Thermomixer constant temperature dry bath Incubate at 20 ° C for 15 min to obtain a free DNA solution with a linker.
  • the obtained free DNA with linker was purified using 75 ⁇ L of Ampure XP beads, and the free DNA with the linker was eluted from Ampure XP beads with 34 ⁇ L of Elution buffer to obtain a purified free DNA solution with a linker.
  • a 50 ⁇ L library PCR preamplification reaction system was prepared according to Table 5, and the concentration of Platinum Pfx DNA polymerase (Platinum Pfx DNA polymerase) in the 50 ⁇ L library PCR preamplification reaction system was 2 U/50 ⁇ L.
  • Platinum Pfx DNA polymerase Platinum Pfx DNA polymerase
  • step (iv) 32.2 ⁇ L 10 ⁇ PfxAmplification Buffer (10 ⁇ Pfx amplification buffer) 5 ⁇ L Public primer (10 ⁇ M) (common primer) 4 ⁇ L Indexprimer (10 ⁇ M) (label primer) 4 ⁇ L MgSO4 (concentration: 50 mM) (magnesium sulfate) 2 ⁇ L dNTP Solution Set (each dNTP concentration is 10 mM) (dNTP mixture) 2 ⁇ L Platinum Pfx DNA polymerase (2.5U/ ⁇ L) (Pfx DNA polymerase) 0.8 ⁇ L total capacity 50 ⁇ L
  • the 50 ⁇ L library PCR preamplification reaction system of the library PCR preamplification method was pre-heated on a PCR machine at 94 ° C for 2 min to fully denature the template DNA and then enter the amplification cycle; the amplification cycle temperature program was maintained at 94 ° C.
  • the template was denatured at 20 s, then kept at 62 ° C for 40 s to anneal the primer to the template, and finally held at 72 ° C for 50 s to allow the primer to extend on the template, synthesize DNA, complete a cycle, and perform 10 cycles in total to make the amplified DNA fragments large. Accumulation; then kept at 72 ° C for 10 min, to ensure that the product is extended and stored at 4 ° C.
  • Peripheral blood plasma free DNA library of lung cancer patients prepared by PCR pre-amplification was purified by 60 ⁇ L AmpureXP beads to obtain peripheral blood plasma free DNA library of lung cancer patients, and washed with AmpureXP beads (purified magnetic beads) with 22 ⁇ L of Elution buffer (elution buffer).
  • the peripheral blood plasma free DNA of detached lung cancer patients is obtained, and the peripheral blood plasma free DNA library (referred to as Pre-PCR library) of lung cancer patients is obtained.
  • Peripheral blood plasma free DNA library of lung cancer patients was quantified using the QubitdsDNA HS assay kit (Qubit Double-stranded DNA High Sensitivity Test Kit).
  • Sample name number Concentration (ng/ ⁇ L) Sample name number Concentration (ng/ ⁇ L) 1 6.86 9 15.5 2 13.35 10 19.96 3 16.16 11 17.87 4 17.7 12 24.51
  • the Pre-PCR l ibrary of step (5) was mixed according to the Pre-PCR library of 16 lung cancer patients to obtain a mixed pool for library hybridization, and finally one upper library was obtained.
  • the DNA content of a pool is 1000 ng
  • the Pre-PCR library content of each lung cancer patient is 62.5 ng.
  • a hybrid library system was prepared as shown in Table 7, and the hybrid library system was concentrated using a vacuum concentrator at 60 ° C for 15 min to obtain a dried hybrid library product.
  • Pre-PCR library A total of 1000ng Human Cot-1 DNA (1mg/mL) 5 ⁇ L P1 Common Block (200 ⁇ M) (Common Blocking Primer) 4 ⁇ L Indexblock (200 ⁇ M) (Label Closure Primer) 4 ⁇ L
  • step 4 Add 10.5 ⁇ L of the prepared hybridization buffer reaction system of step 3 to the dried hybrid library product of step 2, and treat at 95 ° C for 10 min to obtain a hybrid library system solution dissolved in the hybridization buffer reaction system.
  • Binding Buffer Binding buffer
  • step 1) Repeat step 1) once and wash a total of 2 times;
  • wash Buffer I washing buffer I
  • 47 ° C 100 ⁇ L to the magnetic bead pellet of step 4.
  • step 6 for 1 time, for a total of 2 times.
  • step 8 for 2 times for a total of 3 times.
  • the 100 ⁇ L bridge PCR amplification reaction system was pre-heated on a PCR machine at 94 ° C for 2 min to fully denature the template DNA and then enter the amplification cycle; the amplification cycle temperature program was 94 ° C for 15 s to denature the template, then 58 The temperature was kept at 30 ° for 30 s to anneal the primer to the template. Finally, the primer was extended at 30 ° C for 30 s to allow the primer to extend on the template, and the DNA was synthesized to complete a cycle. A total of 15 such cycles were performed to accumulate the amplified DNA fragments; then, the cells were kept at 72 ° C for 5 min. The product was extended and stored at 4 ° C to obtain a bridge PCR amplification product.
  • the QPCR results are greater than 5 nM, less than 500 nM, the mass concentration is greater than 0.5 ng/ ⁇ L, and the fragment range is 250-330 bp, which satisfies the requirements of the machine.
  • the data analysis of the machine data filtering, data comparison and mutation detection analysis of the sequencing data of the machine.
  • the target area capture coverage distribution of the sequencing analysis method is shown in Fig. 2. As can be seen from Fig. 2, the target area capture coverage averages 98.7%. It shows that the data obtained by this method covers almost all target areas and can fully meet the needs of subsequent mutation detection.
  • the target region capture efficiency distribution of the sequencing analysis method is shown in Figure 3. The average capture efficiency is 61.2%. Compared with the average capture efficiency of about 10-15% in the same study, the capture efficiency of the sequencing analysis method even reaches the cell line. /Collection of tissue and other target regions with complete genomic DNA and good quality samples capture the capture efficiency of the library.
  • EGFR G719X is a sensitive site for targeted drug use in patients, and the proportion of mutations in this patient population is around 3%.
  • the EGFR T790X mutation is a secondary mutation that may occur in patients undergoing targeted drug use and is one of the reasons for drug resistance in patients.
  • the mutation detection results obtained by the sequencing analysis showed that the mutation frequency of EGFR T790X was 1.5% in the population consisting of 223 peripheral blood plasma samples of lung cancer patients, and the mutation frequency of EGFR G719X was 0.5%. This sequencing analysis method can detect the frequency of mutation frequency of extremely low frequency and drug resistance and sensitivity in peripheral blood plasma.
  • the sequencing analysis method was used to detect the copy number of MET gene in peripheral blood plasma free DNA of a patient with lung cancer in different stage of clinical stage I, stage II and stage III of disease progression. The results showed that progression from disease progression I From the stage of disease progression to stage III, the copy number of MET gene in peripheral blood plasma free DNA of this patient with lung cancer is increasing (Fig. 4).
  • the clinical diagnosis results show that the lung cancer patient has developed resistance to targeted drugs from the first stage of the disease progression to the third stage of the disease progression, which can explain the plasma phase of the stage III disease of the lung cancer patient.
  • An abnormal increase in the copy number of MET for detecting cfDNA may be one of the genomic evidences for clinical signs of drug resistance in patients.
  • This sequencing analysis method can well track the progress of the patient's disease in real time for changes in copy number.
  • ALK gene breakpoint was 93.3% in a round of peripheral blood plasma samples of 15 lung cancer patients (the total number of samples detected was 15 and the ALK gene breakpoint was detected). The number of samples is 14).
  • the construction method of the free DNA sequencing library of the present invention can be used to construct the free DNA sequencing library, and the ctDNA mutation and content of the tumor patient can be obtained by sequencing analysis. Changes in the early diagnosis of tumors, genetic heterozygosity assessment, tumor dynamics monitoring, targeted therapy gene mutation analysis, early tumor treatment response evaluation, tumor micro-residue detection and real-time detection of tumor resistance.

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Abstract

本发明公开了一种游离DNA测序文库的构建方法。该方法包括：1)对游离DNA进行末端修复，得到末端被修复的游离DNA，该体系中T4 DNA聚合酶的浓度为1.5-3U/50μL，T4多聚核苷酸激酶的浓度为5-10U/50μL；2)给末端被修复的游离DNA进行末端加A，得到末端加A的游离DNA，该体系中Klenow片段(3'-5'exo-)的浓度为2.5-5U/50μL；3)给末端加A的游离DNA加接头得到带接头的游离DNA，该体系中文库接头的浓度为20-40pmol/50μL，T4 DNA连接酶的浓度为1200-2400U/50μL；4)扩增带接头的游离DNA，得到游离DNA文库。

Description

游离DNA测序文库的构建方法 技术领域
本发明涉及游离DNA测序文库的构建方法。
背景技术
人体血液中，含有组织细胞释放的游离DNA(cell-free DNA，cfDNA)，其中包含肿瘤组织释放的肿瘤DNA(circulating tumor DNA，ctDNA)，癌症患者血浆游离DNA含有与肿瘤相关的多种突变基因。临床上，癌症患者的ctDNA主要来源于肿瘤细胞分泌、凋亡或坏死，其浓度平均可达180ng/mL，是正常人的20倍以上。研究表明，ctDNA的平均长度为140-170bp，其基因突变情况能直接反映肿瘤组织的基因突变情况[1,2]。随着第二代测序技术的发展，基于基因组变异检测外周血样本的测序技术已经应用于产前诊断等临床层面；而在血液学恶性肿瘤中，高度复发的体细胞结构变异已被证实是有效的分子诊断标记物，包括BCR-ABL原癌基因、免疫球蛋白基因、T细胞受体基因、维甲酸受体α基因等，基于实时定量PCR的分析方法可以定量检测外周血中游离癌细胞的目标基因重排，这些分子诊断标记物可用于实时监控肿瘤发展情况，检测手术后肿瘤残余量，以及长期的临床管理等。Nitzan Rosenfeld团队利用新技术-目标片段深度测序法在37例卵巢癌患者的62份血浆DNA样本中验证了该技术可以有效通过检测ctDNA基因突变监控肿瘤，其结果与digital PCR检测结果高度相符，在发现未知突变方面甚至更优于digital PCR，而该技术较digital PCR技术操作简单。随后，Nitzan Rosenfeld团队从52例转移性乳腺癌患者中选取30例具有PIK3CA或TP53基因点突变或基因结构变异的患者，对141份血浆DNA样本基因突变情况与另外两个检测biomarker，即CA15-3水平和CTC数量进行了比较，检测血浆DNA突变的灵敏度及和病情进展情况的吻合度都较另外两个biomarker高[3,4]。2013年，Murtaza等人跟踪检测了2例乳腺癌、3例卵巢癌和1例肺癌在血浆中游离DNA的变异情况，并阐述了在EGFR、RB1以及MED1等基因在不同时期药物治疗后的突变情况的改变，提示治疗后监控癌症患者外周血血浆中的基因变异能够指导医生及时发现复发与转移的情况并及时调整治疗方案[5]。
近年来肿瘤发病率和死亡率一直呈上升趋势，肿瘤治疗是世界医学重大挑战。许多肿瘤常规化疗效果差，预后不良是困扰临床的重要难题，而肿瘤耐药性则是肿瘤化疗失败的关键因素，不仅产生严重毒副作用，延误治疗，而且给患者带来经济负担。如，EGFR突变阳性肿瘤对厄洛替尼或吉非替尼有较好敏感性而对其他化疗药物敏感性较差，易瑞沙和特罗凯等化疗药物用药前需要对患者EGFR突变情况进行检测。因此，对肿瘤患者进行药物敏感性相关基因检测，针对不同个体选择最优的化疗药物和治疗方案，对提高肿瘤治疗效果、实现个体化医疗有重要意义。而临床上常采用组织穿刺活检等方法获取患者肿瘤组织再进行基因检测，不仅对患者造成严重创伤，而且操作繁琐，也不能达到药物敏感性实时监测的目的。
常规的ILLUMINA Hiseq2000建库需要大量gDNA(1-3微克)，不适用于血浆微 量片段化gDNA(约几纳克)建库。
参考文献
1.Diehl,F.and M.Li,et al.(2005)."Detection and quantification of mutations in the plasma of patients with colorectal tumors."PNAS 102:16368-16373.
2.Diehl,F.and K.Schmidt,et al.(2008)."Circulating mutant DNA to assess tumor dynamics."Nat Med 14(9):985-90.
3.Forshew,T.and M.Murtaza,et al.(2012)."Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA."SciTransl Med 4(136):136ra68.
4.Dawson,S.J.and D.W.Tsui,et al.(2013)."Analysis of circulating tumor DNA to monitor metastatic breast cancer."N Engl J Med 368(13):1199-209.
5.Murtaza,M.and S.J.Dawson,et al.(2013)."Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA."Nature 497(7447):108-12.
发明公开
本发明提供了游离DNA测序文库的构建方法。
本发明所提供的游离DNA测序文库的构建方法，包括：
1)对游离DNA进行末端修复，得到末端被修复的游离DNA；所述末端修复在含有DNA聚合酶和核苷酸激酶的末端修复体系中进行，所述DNA聚合酶在所述末端修复体系中的浓度可为1.5U-3U/50μL，具体可为1.5U/50μL，所述核苷酸激酶在所述末端修复体系中的浓度可为5U-10U/50μL，具体可为5U/50μL；
2)给所述末端被修复的游离DNA进行末端加“A”，得到末端加“A”的游离DNA；所述末端加“A”在含有Klenow片段(3’-5’exo-)(Klenow(3’-5’exo-))的末端加“A”体系中进行，所述Klenow片段(3’-5’exo-)在所述末端加“A”体系中的浓度可为2.5U-5U/50μL，具体可为5U/50μL；
3)给所述末端加“A”的游离DNA连接文库接头得到带接头的游离DNA；所述连接文库接头在含有文库接头和DNA连接酶的加接头体系中进行，所述文库接头在所述加接头体系中的浓度为20-40pmol/50μL，具体可为20pmol/50μL；所述DNA连接酶在所述加接头体系中的浓度可为1200U-2400U/50μL，具体可为1200U/50μL；
4)扩增所述带接头的游离DNA，得到游离DNA文库；所述扩增的循环数可为8-12，具体可为10。
上述游离DNA测序文库的构建方法中，所述末端修复体系的体积可为20-100μL，具体可为50μL。
上述游离DNA测序文库的构建方法中，所述DNA聚合酶为T4 DNA聚合酶,所述核苷酸激酶为T4多聚核苷酸激酶，所述DNA连接酶为T4 DNA连接酶。
上述游离DNA测序文库的构建方法中，所述末端修复体系中含有Klenow片段(Klenow Fragment)，所述Klenow片段在所述末端修复体系的浓度可为2.5-5U/50μL，具体可为2.5U/50μL。
上述游离DNA测序文库的构建方法中，所述末端修复可在20℃进行30min。
上述游离DNA测序文库的构建方法中，所述末端加“A”可在37℃进行30min。
上述游离DNA测序文库的构建方法中，所述连接文库接头可在20℃进行15min。
上述游离DNA测序文库的构建方法中，4)所述扩增在含有Platinum Pfx DNA聚合酶(Platinum Pfx DNA polymerase)的扩增体系中进行，所述Platinum Pfx DNA聚合酶在所述扩增体系中的浓度为2U-4U/50μL，具体可为2U/50μL。
上述游离DNA测序文库的构建方法中，所述扩增的循环温度程序为先94℃20s，然后62℃40s，最后72℃50s。
上述游离DNA测序文库的构建方法中，所述构建方法可包括从体液中提取所述游离DNA的步骤。
上述游离DNA测序文库的构建方法在游离DNA的序列测定中的应用也属于本发明的保护范围。
上述游离DNA测序文库的构建方法在检测游离DNA变异情况中的应用也属于本发明的保护范围。
上文中，所述游离DNA可为体液中的游离DNA(离体的体液游离DNA)，如血液游离DNA(离体的血液游离DNA)、血浆游离DNA(离体的血浆游离DNA)。
实验证明，采用本发明的游离DNA测序文库的构建方法进行文库构建的测序分析方法，对外周血血浆游离DNA的目标区域捕获覆盖度平均达到98.7％，目标区域平均捕获效率达到了61.2％，与同类研究平均10-15％左右的捕获效率相比，该测序分析方法的捕获效率甚至达到细胞系/组织样本等有完整基因组DNA且质量较好样本的目标区域捕获建库的捕获效率。本发明的测序分析方法可以检出肺癌患者EGFR的点突变、短插入/缺失，MET和EGFR的拷贝数突变。本发明的测序分析方法可以检出肺癌患者外周血血浆中频率极低的突变的频率比例和药物耐药及敏感程度的突变频率比例。
附图说明
图1为肺癌患者外周血血浆游离DNA文库2100检测峰图。
图2为肺癌患者外周血血浆游离DNA目标区域捕获覆盖度分布。
图3为肺癌患者外周血血浆游离DNA目标区域捕获效率分布。
图4为临床用药MET基因拷贝数在同一肺癌患者不同病程进展中MET基因拷贝数的改变情况：1代表病程进展Ⅰ期，2代表病程进展Ⅱ期，3代表病程进展Ⅲ期。
实施发明的最佳方式
以下的实施例便于更好地理解本发明，但并不限定本发明。下述实施例中的实验方法，如无特殊说明，均为常规方法。下述实施例中所用的试验材料， 如无特殊说明，均为自常规生化试剂商店购买得到的。以下实施例中的定量试验，均设置三次重复实验，结果取平均值。
下面提供的游离DNA测序文库的构建方法是对ILLUMINA Hiseq2000的DNA测序文库的构建方法中的如下步骤进行改进得到的适合构建游离DNA测序文库的方法：
1)对DNA进行末端修复的操作中，T4 DNA聚合酶在反应体系中的浓度分别为1.5U-3U/50μL，具体可为1.5U/50μL；T4多聚核苷酸激酶在反应体系中的浓度可为5U-10U/50μL，具体可为5U/50μL；
2)DNA进行末端加“A”的操作中，Klenow片段(3’-5’exo-)在反应体系中的浓度可为2.5U-5U/50μL，具体可为5U/50μL；
3)对DNA进行连接文库接头的操作中，文库接头在加接头体系中的浓度为20-40pmol/50μL，具体可为20pmol/50μL；T4 DNA连接酶在加接头体系中的浓度可为1200U-2400U/50μL，具体可为1200U/50μL；
4)扩增带接头DNA的操作中，扩增的循环数增至8-12个循环，具体可为10。
下面以肺癌患者为例阐明本申请的游离DNA测序文库的构建方法。
10×Polynucleotide Kinase(PNK)Buffer、dNTP Solution Set、T4 DNA Polymerase、Klenow Fragment、T4Polynucleotide Kinase、Klenow(3’-5’exo-)试剂盒、dATP、2×Rapid l igation buffer、T4 DNA Ligase(Rapid)均为Enzymatics公司的产品；PE Adapter oligo mix、Invitrogen Dynabeads M-280、
Figure PCTCN2014001050-appb-000001
Pfx DNA Polymerase试剂盒和Cot-1DNA为Invitrogen公司的产品；SnoMagTM Circulating DNA试剂盒为SNOVA Biotechnologies公司的产品；2×SC Hybridization Buffer和SC Hybridization Component A为Roche Nimblegen公司的产品；SeqCap EZ Hybridization and Wash试剂盒为ROCHE DIAGNOSTICS公司的产品；AmpureXP beads为AGENCOURT公司的产品；Flowcell primers F和Flowcell primers R为Illumina公司产品。
实施例1、肺癌患者外周血血浆游离DNA测序文库的构建方法及其应用
本实施例提供了外周血血浆游离DNA的测序分析方法，包括构建肺癌患者外周血血浆游离DNA测序文库和肺癌患者外周血血浆游离DNA测序文库的测序及分析这两个步骤。
文库构建方法为在Hiseq文库构建方法基础上改进得到的适合肺癌患者外周血血浆游离DNA测序文库的构建方法。
一、构建肺癌患者外周血血浆游离DNA测序文库
构建肺癌患者外周血血浆游离DNA测序文库包括下述步骤(一)、(二)、(三)、(四)和(五)。
(一)肺癌患者外周血血浆游离DNA的提取
采用SnoMagTM Circulating DNA试剂盒进行肺癌患者外周血血浆游离DNA的提取，具体如下:
1、取200μL肺癌患者外周血血浆于1.5mLEP管，加入600μL buffer LSB (LSB缓冲液)。
2、加入20μLNanoMag Circulating Beads混匀，室温放置10min，每2-3min混匀一次。
3、将EP管置于磁力架上吸附1min，弃上清。
4、取下EP管加入150μL Buffer WA(WA缓冲液)，混匀。
5、将EP管置于磁力架上吸附1min，弃上清。
6、取下EP管加入150μL 75％乙醇，混匀。
7、将EP管置于磁力架上吸附1min，弃上清。
8、重复步骤6-7一次。
9、室温干燥EP管中的磁珠5min。
10、加入32μL elution buffer(洗脱液)混匀磁珠，室温静置5min。
11、将EP管置于磁力架上吸附1min，得到的上清液即为肺癌患者外周血血浆游离DNA溶液，转移该上清液至新的1.5mL EP管。测定16例肺癌患者外周血血浆游离DNA溶液中肺癌患者外周血血浆游离DNA的浓度。结果如表1所示：
表1、肺癌患者外周血血浆游离DNA的浓度
Figure PCTCN2014001050-appb-000002
(二)对肺癌患者外周血血浆游离DNA进行末端修复，得到末端被修复的游离DNA
末端修复方法按照表2配制的50μL末端修复体系，该50μL末端修复体系中，T4 DNA聚合酶的浓度为1.5U/50μL，T4多聚核苷酸激酶的浓度为5U/50μL，Klenow片段的浓度为2.5U/50μL。
表2、末端修复方法的50μL末端修复体系
Figure PCTCN2014001050-appb-000003
Figure PCTCN2014001050-appb-000004
将50μL末端修复体系在Thermomixer恒温干浴器中20℃温育30min，得到末端被修复的游离DNA溶液。采用90μL AmpureXP beads纯化磁珠纯化获得的末端被修复的游离DNA，并用36μL Elution buffer(洗脱缓冲液)从AmpureXP beads洗脱该末端被修复的游离DNA得到纯化后的末端被修复的游离DNA溶液。
(三)对末端被修复的游离DNA进行末端加“A”，得到末端加A的游离DNA
末端加“A”方法按照表3配制的50μL末端加“A”体系，该50μL末端加“A”体系中，Klenow片段(3’-5’exo-)的浓度为5U/50μL。
表3、末端加“A”方法的50μL末端加“A”体系
步骤(二)的末端被修复的游离DNA溶液 34μL
10×blue buffer(10×blue缓冲液) 5μL
dATP(1mM) 10μL
Klenow(3’-5’exo-)(5U/μL) 1μL
总体积 50μL
将末端加“A”方法的50μL末端加“A”体系在Thermomixer恒温干浴器中37℃温育30min，得到末端加“A”的游离DNA溶液。采用90μL AmpureXP beads纯化获得的末端加“A”的游离DNA，并用24μL Elution buffer从AmpureXP beads洗脱该末端加“A”的游离DNA得到末端加“A”的游离DNA溶液。
(四)对末端加“A”的游离DNA的两端连接Illumina Hiseq2000文库接头，得到带接头的游离DNA
在反应体系中，文库接头(PE Adapter oligo)的浓度为20pmol/50μL，T4 DNA连接酶的浓度为1200U/50μL。
表4、两端连接文库接头方法的50μL加接头体系
步骤(三)的纯化的末端加“A”的游离DNA溶液 22.5μL
2×Rapid ligation buffer(2×高效连接缓冲液) 25μL
PE Adapter oligo mix(双末端接头混合液)(40μM) 0.5μL
T4 DNA Ligase(Rapid)(T4 DNA连接酶(高效))(600U/μL) 2μL
总体积 50μL
将两端连接文库接头方法的50μL加接头体系在Thermomixer恒温干浴器中 20℃温育15min，得到带接头的游离DNA溶液。采用75μL AmpureXP beads纯化获得的带接头的游离DNA，并用34μL Elution buffer从AmpureXP beads洗脱该带接头的游离DNA得到纯化后的带接头的游离DNA溶液。
(五)对带接头的游离DNA进行文库PCR预扩增反应，构建肺癌患者外周血血浆游离DNA文库
文库PCR预扩增方法按照表5配制50μL文库PCR预扩增反应体系，该50μL文库PCR预扩增反应体系中Platinum Pfx DNA聚合酶(Platinum Pfx DNA polymerase)的浓度为2U/50μL。
表5、文库PCR预扩增方法的50μL文库PCR预扩增反应体系
步骤(四)的纯化的带接头的游离DNA溶液 32.2μL
10×PfxAmplification Buffer(10×Pfx扩增缓冲液) 5μL
公共primer(10μM)(公共引物) 4μL
Indexprimer(10μM)(标签引物) 4μL
MgSO4(浓度为50mM)(硫酸镁) 2μL
dNTP Solution Set(每种dNTP浓度均为10mM)(dNTP混合液) 2μL
Platinum Pfx DNA polymerase(2.5U/μL)(Pfx DNA聚合酶) 0.8μL
总体积 50μL
将文库PCR预扩增方法的50μL文库PCR预扩增反应体系预先在PCR仪上于94℃预加热2min，使模板DNA充分变性然后进入扩增循环阶段；扩增的循环温度程序为94℃保持20s使模板变性，然后62℃保持40s使得引物与模板退火，最后72℃保持50s使引物在模板上延伸，合成DNA，完成一个循环，共进行10次这样的循环，使扩增的DNA片段大量积累；随后72℃保持10min，保证产物延伸完整，4℃保存。将经过PCR预扩增制备的肺癌患者外周血血浆游离DNA文库采用60μL AmpureXP beads纯化获得肺癌患者外周血血浆游离DNA文库，并用22μL Elution buffer(洗脱缓冲液)从AmpureXP beads(纯化磁珠)洗脱扩增的肺癌患者外周血血浆游离DNA，获得肺癌患者外周血血浆游离DNA文库(简称Pre-PCR library)。对肺癌患者外周血血浆游离DNA文库使用QubitdsDNA HS assay kit(Qubit双链DNA高敏检测试剂盒)定量确定该文库中DNA的浓度。
结果表明，肺癌患者外周血血浆游离DNA的Pre-PCR 16个文库的浓度如表6所示：
表6：血浆游离DNA的Pre-PCR文库浓度
样品名称编号 浓度(ng/μL) 样品名称编号 浓度(ng/μL)
1 6.86 9 15.5
2 13.35 10 19.96
3 16.16 11 17.87
4 17.7 12 24.51
5 8.47 13 13.73
6 8.65 14 6.8
7 22.09 15 17.36
8 18.55 16 20.27
二、肺癌患者外周血血浆游离DNA测序文库的测序及分析
(一)肺癌患者外周血血浆游离DNA文库与Nimblegen芯片杂交，进行目标区域DNA的捕获
1、将步骤一中(五)的Pre-PCR l ibrary，按照16例肺癌患者的Pre-PCR library混合在一起的方式进行混合得到一个混合池进行文库杂交，最终得到1个上机文库。一个混合池中DNA的含量是1000ng，每例肺癌患者的Pre-PCR library含量是62.5ng。
2、按照表7所示制备杂交文库体系，将该杂交文库体系使用真空浓缩仪于60℃浓缩15min，获得干燥的杂交文库产物。
表7、肺癌患者外周血血浆游离DNA与Nimblegen芯片杂交文库体系
Pre-PCR library 共1000ng
人Cot-1 DNA(1mg/mL) 5μL
P1公用Block(200μM)(公用封闭引物) 4μL
Indexblock(200μM)(标签封闭引物) 4μL
3、按照表8配置杂交缓冲液反应体系。
表8、杂交缓冲液反应体系
2×SC Hybridization Buffer(2×SC杂交缓冲液) 7.5μL
SC Hybridization Component A(SC杂交组件A) 3μL
总体积 10.5μL
4、向步骤2获得干燥的杂交文库产物中加入10.5μL配制好的步骤3的杂交缓冲液反应体系，于95℃处理10min，获得溶解于杂交缓冲液反应体系中的杂交文库体系溶液。
5、文库与探针杂交反应：取4.5μL Nimblegen芯片加入步骤4杂交文库体系溶液，于47℃杂交72h，获得杂交产物溶液。
(二)杂交后进行肺癌患者外周血血浆游离DNA目标区域DNA洗脱
1、将Invitrogen Dynabeads M-280磁珠剧烈震荡混匀重悬，备用。
2、添加100μL Invitrogen Dynabeads M-280磁珠至1.5mL EP管中，洗涤磁珠，步骤如下：
1)加入200μL Binding Buffer(Binding缓冲液)，剧烈震荡5s使得Invitrogen Dynabeads M-280重悬，置于磁力架上静置2min，待液体完全澄清后小心吸弃上清，获得Invitrogen Dynabeads M-280沉淀；
2)重复步骤1)1次，共洗涤2次；
3)向装有Invitrogen Dynabeads M-280沉淀的1.5mL的EP管中加入100μL Beads Wash Buffer(磁珠洗涤缓冲液)重悬该磁珠。
3、把重悬后的磁珠转到含有步骤(一)的杂交产物溶液的样本管中，置于PCR仪中47℃孵育45min，每隔15min混匀一次，共三次。
4、将孵育结束后的磁珠悬浊液转移到新的1.5mLEP管中，置于磁力架上静置后弃上清。
5、向步骤4的磁珠沉淀中加入Wash Buffer I(洗涤缓冲液I)(47℃)100μL，混匀样本，置于磁力架上静置3-5min，待液体完全澄清，小心吸弃上清。
6、向步骤5的磁珠沉淀中加入Stringent buffer(Stringent缓冲液)(47℃)200μL，混匀，置于Thermomixer中47℃孵育5min，瞬时离心，置于磁力架上置于3-5min，待液体完全澄清，小心吸弃上清。
7、重复步骤6操作1次，共2次。
8、向步骤7的磁珠沉淀中加入Wash Buffer I(RT)200μL，置于Thermomixer中于20℃1400rpm离心2min，之后置于磁力架上静置3-5min，待液体完全澄清，小心吸弃上清。
9、重复步骤8操作2次，共3次。
10、向步骤9的磁珠沉淀中加入140μL Nuclease Free-water(无核酸水)重悬磁珠，得到含有捕获目标区域DNA的磁珠悬浊液。
(三)对捕获的目标区域DNA进行桥式PCR扩增
1、按照表9在1.5mL EP管中配置100μL桥式PCR扩增反应体系。
表9、桥式PCR扩增反应体系
步骤(二)的含有捕获目标区域DNA的磁珠悬浊液 70μL
10×PfxAmplification Buffer(10×Pfx扩增缓冲液) 10μL
Flowcellprimers F(10μM)(Flowcell引物正向) 5μL
Flowcellprimers R(10μM)(Flowcell引物反向) 5μL
MgSO4(50mM)(硫酸镁) 4μL
dNTP Solution Set(10mM)(dNTP混合液) 4μL
Platinum Pfx DNA polymerase(2.5U)(Pfx DNA聚合酶) 2μL
总体积 100μL
将100μL桥式PCR扩增反应体系预先在PCR仪上于94℃预加热2min，使模板DNA充分变性然后进入扩增循环阶段；扩增的循环温度程序为94℃保持15s使模板变性，然后58℃保持30s使得引物与模板退火，最后72℃保持30s使引物在模板上延伸，合成DNA，完成一个循环，共进行15次这样的循环，使扩增的DNA片段大量积累；随后72℃保持5min，保证产物延伸完整，4℃保存，得到桥式PCR扩增产物。
2、桥式PCR扩增产物纯化：将装有步骤1的桥式PCR扩增产物的PCR管置于磁力架上，静置3-5min至澄清，小心吸取上清转入新的1.5mLEP管中，加入120μL AmpureXP beads纯化上清液，最后用31μL Elution buffer(洗脱液)洗脱产物，得到最终上机文库。
3、上机文库质检：应用Agilent 2100Bioanalyzer和荧光定量PCR(QPCR)进行文库质量检测，2100检测峰图如图1所示，检测结果如表10所示：
表10：文库2100和QPCR检测结果
Figure PCTCN2014001050-appb-000005
QPCR结果大于5nM,小于500nM，质量浓度大于0.5ng/μL,片段范围250-330bp即满足上机要求。该结果表明，文库的大部分片段集中在280-300bp，且浓度均符合上机测序要求。
(四)对捕获的目标区域DNA进行上机测序及数据分析
1、Illumina Hiseq2000上机测序：以QPCR检测浓度为准，按照Illumina Hiseq2000上机测序程序对步骤(三)中的纯化的桥式PCR产物进行上机测序。
2、下机数据分析：对上机测序数据进行数据过滤、数据比对以及变异检测分析。
2.1目标区域捕获覆盖度及捕获效率
测序分析方法的目标区域捕获覆盖度分布如图2所示，从图2中可以看出，目标区域捕获覆盖度平均达到98.7％。说明该方法得到的数据几乎覆盖到了所有目标区域，能够完全满足后续突变检测的需要。该测序分析方法的目标区域捕获效率分布如图3所示，平均捕获效率达到了61.2％，与同类研究平均10-15％左右的捕获效率相比，该测序分析方法的捕获效率甚至达到细胞系/组织样本等有完整基因组DNA且质量较好样本的目标区域捕获建库的捕获效率。
2.2突变检测结果
临床上，肺癌患者EGFR的点突变、短插入/缺失，MET和EGFR的拷贝数检测已经成为使用靶向药物易瑞沙和特罗凯治疗前必须进行的检查。采用该测序分析方法进行测序分析的肺癌患者外周血血浆中也检测到了这些基因的上述突变情况，同时将该结果与患者临床信息进行的比较，结果发现该测序分析方法的突变检测结果与临床结果一致。
临床上EGFR G719X是患者使用靶向药物敏感位点，该位点在患者群中发生突变的比例在3％左右。EGFR T790X突变是患者在使用靶向药物过程中可能产生的耐药继发突变，是患者产生抗药性的原因之一。该测序分析方法得到的突变检测结果表明，在由223例肺癌患者外周血血浆样本组成的群体中，EGFR T790X的突变频率是1.5％，EGFR G719X的突变频率是0.5％。说明该测序分析方法可以检出外周血血浆中频率极低的和药物耐药及敏感程度的突变频率比例。
临床上随着靶向药物治疗的进行，MET等基因拷贝数的增加会引起患者对靶向药物的耐药，进而出现病程进展。采用该测序分析方法检测了一例肺癌患者在不同临床分期病程进展I期、病程进展II期和病程进展III期的外周血血浆游离DNA中的MET基因的拷贝数变化情况，结果表明从病程进展I期至病程进展III期，该例肺癌患者的外周血血浆游离DNA中的MET基因的拷贝数不断增加(图4)。临床诊断结果表明，该例肺癌患者从病程进展I期至病程进展III期出现了对靶向药物耐药的情况，可以从另一方面解释了该例肺癌患者的病程进展III期的血浆样本中检测cfDNA的MET的拷贝数异常增加可能是患者出现临床耐药症状的基因组证据之一。说明该测序分析方法可以很好地针对拷贝数的变化实时跟踪患者的病程进展情况。
肺癌患者ALK基因与其他基因的发生融合，也是肺癌患者的一种显著分子诊断标记物。采用该测序分析方法在一轮15个肺癌患者外周血血浆样本的测试中发现，ALK基因断裂点(breakpoint)的检出频率为93.3％(检测总样本数为15个，检出ALK基因断裂点样本数为14个)。
工业应用
鉴于ctDNA的基因突变情况能直接反映肿瘤组织的基因突变情况，可以采用本发明的游离DNA测序文库的构建方法进行游离DNA测序文库的构建，进而通过测序分析获得肿瘤患者的ctDNA突变情况及其含量的变化，以进行肿瘤的早期诊断检测、遗传杂合性评估、肿瘤动态变化监测、靶向治疗基因突变分析、肿瘤早期治疗反应评价、肿瘤微量残留检测和肿瘤耐药性实时检测等。

Claims (14)

  1. 游离DNA测序文库的构建方法，包括：
    1)对游离DNA进行末端修复，得到末端被修复的游离DNA；所述末端修复在含有DNA聚合酶和核苷酸激酶的末端修复体系中进行，所述DNA聚合酶在所述末端修复体系中的浓度为1.5U-3U/50μL，所述核苷酸激酶在所述末端修复体系中的浓度为5U-10U/50μL；
    2)给所述末端被修复的游离DNA进行末端加“A”，得到末端加“A”的游离DNA；所述末端加“A”在含有Klenow片段(3’-5’exo-)的末端加A体系中进行，所述Klenow片段(3’-5’exo-)在所述末端加“A”体系中的浓度为2.5U-5U/50μL；
    3)给所述末端加“A”的游离DNA连接文库接头得到带接头的游离DNA；所述连接文库接头在含有文库接头和DNA连接酶的加接头体系中进行，所述文库接头在所述加接头体系中的浓度为20-40pmol/50μL，所述DNA连接酶在所述加接头体系中的浓度为1200U-2400U/50μL；
    4)扩增所述带接头的游离DNA，得到游离DNA文库。
  2. 根据权利要求1所述的构建方法，其特征在于：所述末端修复体系的体积为20-100μL。
  3. 根据权利要求1所述的构建方法，其特征在于：所述DNA聚合酶为T4DNA聚合酶,所述核苷酸激酶为T4多聚核苷酸激酶，所述DNA连接酶为T4DNA连接酶。
  4. 根据权利要求1所述的构建方法，其特征在于：4)所述扩增在含有Platinum Pfx DNA聚合酶的扩增体系中进行，所述Platinum Pfx DNA聚合酶在所述扩增体系中的浓度为2U-4U/50μL。
  5. 根据权利要求4所述的构建方法，其特征在于：所述扩增的循环温度程序为先94℃20s，然后62℃40s，最后72℃50s。
  6. 根据权利要求1所述的构建方法，其特征在于：所述构建方法包括从体液中提取所述游离DNA的步骤。
  7. 根据权利要求1所述的构建方法，其特征在于：所述游离DNA为体液中的游离DNA。
  8. 根据权利要求7所述的构建方法，其特征在于：所述体液为血液。
  9. 权利要求1所述的构建方法在游离DNA的序列测定中的应用。
  10. 根据权利要求9所述的应用，其特征在于：所述游离DNA为体液中的游离DNA。
  11. 根据权利要求10所述的应用，其特征在于：所述体液为血液。
  12. 权利要求1所述的构建方法在检测游离DNA变异情况中的应用。
  13. 根据权利要求12所述的应用，其特征在于：所述游离DNA为体液中的游离DNA。
  14. 根据权利要求13所述的应用，其特征在于：所述体液为血液。
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