CN109295230A - A method of the polygene combined abrupt climatic change based on ctDNA assesses tumour dynamic change - Google Patents
A method of the polygene combined abrupt climatic change based on ctDNA assesses tumour dynamic change Download PDFInfo
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Abstract
The present invention relates to field of medical technology, the method for in particular a kind of polygene combined abrupt climatic change assessment tumour dynamic change based on ctDNA.In the present invention, the tissue samples before treating, the changing rule of the peripheral blood sample screening-gene mutation after peripheral blood sample before treatment, and treatment, the genetic mutation with clinical value is found out, and then realizes the guidance to clinical lung cancer therapy curative effect evaluation and drug resistance recurrence monitoring index.
Description
Technical field
The present invention relates to field of medical technology, specially a kind of polygene combined abrupt climatic change assessment based on ctDNA is swollen
The method of tumor dynamic change.
Background technique
Although lung cancer diagnosis and treatment have made some progress in over the past several decades, current lung cancer is still disease incidence and death
The highest malignant tumour of rate accounts for the 22.7% of China's whole mortality of malignant tumors, and overall survival only has 16% or so within 5 years.
It is expected that lung cancer annual neopathy people in the year two thousand twenty China is up to 1,000,000, smoking, industrial pollution (such as haze) is that China's lung cancer occurs
Principal element.Its grade malignancy is high, progression of the disease is rapid, and Postoperative recurrent rate is high, and therapeutic effect is undesirable.
The lung cancer of clinical diagnosis at present has 3/4 patient to lose operative chance or shifted, for this kind of patient
Current main therapeutic modality be chemotherapy or targeted drug treatment etc., however the basic reason why tumour is difficult to cure exists
In its heterogeneity, i.e., the tumour cell of human body is not duplicate, and otherwise a drug gets off and all knocks out certainly, they are very
" microassociation " of a variety of cancer cell population compositions, is impossible to kill all cancer cells with any one drug.It uses each time
Chemotherapeutics can only kill a certain proportion of cancer cell.Targeted drug is also in this way, and can drug resistance.Main cause is tumour tool
There is heterogeneity, and generate many gene mutations when tumour cell division, to increase this heterogeneity, cancer cell is holding and increases
Add the heterogeneous magic weapon that survival advantage is obtained as it.And this mode for obtaining survival advantage is the evolution of cancer cell
Therefore mode combines high throughput sequencing technologies in the prior art (Next Generation regarding to the issue above
Sequencing, NGS), bioinformatics method and high-flux sequence patent build library RingCapTM ring and be situated between link amplification technique
(domestic patent of invention number 2015104960495, international patent of invention PCT PCT/CN2015/095393), proposes that one kind is based on
The method of the polygene combined abrupt climatic change assessment tumour dynamic change of ctDNA.
Summary of the invention
The purpose of the present invention is to provide a kind of, and the polygene combined abrupt climatic change based on ctDNA assesses tumour dynamic change
Method, the tissue samples before treating, the peripheral blood sample screening-gene mutation after peripheral blood sample before treatment, and treatment
Changing rule, find out the genetic mutation with clinical value, and then realize multiple to clinical lung cancer therapy curative effect evaluation and drug resistance
The guidance of monitoring index is sent out, to solve the problems mentioned in the above background technology.
To achieve the above object, the invention provides the following technical scheme:
A method of the polygene combined abrupt climatic change based on ctDNA assesses tumour dynamic change, before treatment
Follow-up period after data acquisition and treatment, the data acquisition before the treatment include tissue samples acquisition and treatment before treating
Preceding peripheral blood sample acquisition, the follow-up period after the treatment include according to the peripheral blood sample screening-gene mutation after treatment
The obtained clinical lung cancer therapy curative effect evaluation of changing rule and drug resistance recurrence monitoring index, the specific operation method is as follows:
1, (primary to the tumor tissues before patient's treatment by utilizing high throughput sequencing technologies and bioinformatics method
Stove or transfer stove) carry out body cell full sequencing of extron group, obtain tumor tissues sample in mutated gene information;
2, the peripheral blood with the full exon region panel of 17 lung cancer genes identical when survey tissue specimen to patient is selected
Plasma free Tumour DNA (ctDNA) sequencing is carried out, obtains the information of mutated gene in plasma specimen, and then examine two kinds of samples
The consistency of gained testing result;
3, by extracting DNA from tumour paraffin-embedded tissue, accurate PCR is carried out to target sequence using special Mdification primer
Amplification carries out end modified, connection specificity using RingCapTM ring Jie link amplification technique at the same time to amplified production
End sequence, it is flat in regular-PCR in conjunction with the use of special PCR response procedures, T4 ligase and high special RingCap-Taq enzyme
It is realized on platform and the library construction used for high-flux sequence, concrete operations is carried out to target sequence in sample DNA/RNA are as follows:
(1), target sequence is expanded using the Spacegen-Taq enzyme of the specific primer of modified and high specific
Increase capture, and product is made to form cohesive end;
(2), asymmetric linking probe and cohesive end are attached using DNA ligase, form annular product, avoids
It is combined with each other between product;
(3), specific amplification amplification is carried out to annular product using specific primer, to obtain target sequence and simultaneously
In conjunction with the special labeling sequence of upper needs.
4, the periphery blood specimen of follow-up period after the treatment, interim acquisition patient selects as before 147
A 17 gene panel of lung cancer carries out ctDNA sequencing to patient, about 3~5 times, up to progression of disease, observes in sequencing result and dashes forward
Become the dynamic change of gene to disclose drug resistance mode and biological behaviour of the tumour cell after treating;
5, it is analyzed after summarizing the abrupt climatic change result information for respectively taking peripheral blood sample, and several genes of acquisition is dashed forward
Be deteriorated different carry out statistic of classification, rear to realize that the assessment of clinical lung cancer therapy curative effect and drug resistance are multiple by analyzing and comparing each group of data
Send out the index of monitoring.
Preferably, clinical sample selected by the follow-up period after the data before the treatment are acquired and treated are as follows: logical
It crosses into group the surgical tissue sample of 10 patients with lung cancer with clinical typicalness and peripheral blood sample and 10 patients' warps
Each observation course for the treatment of (it is expected that every patient observes 4 courses for the treatment of, until progression of disease) respectively takes peripheral blood sample after treatment.
Preferably, the high throughput sequencing technologies include Ion torrent platform and Illumina platform, wherein Ion
Torrent platform is by the fixed dna chain in the micropore of semiconductor chip, and archaeal dna polymerase is using single stranded DNA as template, by base
Complementarity principle, synthesizes complementary DNA chain, when DNA chain one base of every extensions, will discharge a proton, lead to local PH change
Change, sensing layer detects pH variation, and chemical signal is converted into digital signal, reaches real-time interpretation base, Illumina platform
On the basis of the sequencing approaches such as Sanger, with four kinds of different dNTP of fluorescent marker of different colours, when archaeal dna polymerase synthesizes
It is every to add a kind of dNTP and release different fluorescence when complementary strand, according to the fluorescence signal of capture and by specific meter
Calculation machine software processing, to obtain the sequence information of DNA to be measured.
Preferably, in the follow-up period after the treatment, using bioinformatic analysis method, to belonging to tumor patient
DNA fragmentation is compared with normal sample gene order, and combine the database tumors correlation variation database such as COSMIC into
Row compares, and can find specific gene variation relevant to targeted drug whether is carried in tumor patient DNA sequence dna.
Compared with prior art, the beneficial effects of the present invention are: before treating tissue samples, peripheral blood sample before treatment
This, and the changing rule of the peripheral blood sample screening-gene mutation after treatment, the genetic mutation with clinical value is found out, into
And realize the guidance to clinical lung cancer therapy curative effect evaluation and drug resistance recurrence monitoring index.
Detailed description of the invention
Fig. 1 is the technical route figure that high-flux sequence patent builds library RingCapTM ring Jie's link amplification technique in the present invention;
Fig. 2 is that a kind of polygene combined abrupt climatic change based on ctDNA of the present invention is assessed in the method for tumour dynamic change
17 gene tablet menus of lung cancer correlation in experiment sample;
Fig. 3 is the method skill that a kind of polygene combined abrupt climatic change based on ctDNA of the present invention assesses tumour dynamic change
Art route map;
Specific embodiment
Following will be combined with the drawings in the embodiments of the present invention, and technical solution in the embodiment of the present invention carries out clear, complete
Site preparation description, it is clear that described embodiments are only a part of the embodiments of the present invention, instead of all the embodiments.It is based on
Embodiment in the present invention, it is obtained by those of ordinary skill in the art without making creative efforts every other
Embodiment shall fall within the protection scope of the present invention.
Fig. 1-3 is please referred to, the present invention provides a kind of technical solution:
A method of the polygene combined abrupt climatic change based on ctDNA assesses tumour dynamic change, before treatment
Follow-up period after data acquisition and treatment, before the data before treatment are acquired including tissue samples acquisition before treating and treating
Peripheral blood sample acquisition, the follow-up period after treatment include the variation rule according to the peripheral blood sample screening-gene mutation after treatment
Obtained clinical lung cancer therapy curative effect evaluation and drug resistance recurrence monitoring index are restrained, the specific operation method is as follows:
1, (primary to the tumor tissues before patient's treatment by utilizing high throughput sequencing technologies and bioinformatics method
Stove or transfer stove) carry out body cell full sequencing of extron group, obtain tumor tissues sample in mutated gene information;
2, the peripheral blood with the full exon region panel of 17 lung cancer genes identical when survey tissue specimen to patient is selected
Plasma free Tumour DNA (ctDNA) sequencing is carried out, obtains the information of mutated gene in plasma specimen, and then examine two kinds of samples
The consistency of gained testing result;
3, by extracting DNA from tumour paraffin-embedded tissue, accurate PCR is carried out to target sequence using special Mdification primer
Amplification carries out end modified, connection specificity using RingCapTM ring Jie link amplification technique at the same time to amplified production
End sequence, it is flat in regular-PCR in conjunction with the use of special PCR response procedures, T4 ligase and high special RingCap-Taq enzyme
It is realized on platform and the library construction used for high-flux sequence, concrete operations is carried out to target sequence in sample DNA/RNA are as follows:
(1), target sequence is expanded using the Spacegen-Taq enzyme of the specific primer of modified and high specific
Increase capture, and product is made to form cohesive end;
(2), asymmetric linking probe and cohesive end are attached using DNA ligase, form annular product, avoids
It is combined with each other between product;
(3), specific amplification amplification is carried out to annular product using specific primer, to obtain target sequence and simultaneously
In conjunction with the special labeling sequence of upper needs.
4, the periphery blood specimen of follow-up period after the treatment, interim acquisition patient selects as before 147
A 17 gene panel of lung cancer carries out ctDNA sequencing to patient, about 3~5 times, up to progression of disease, observes in sequencing result and dashes forward
Become the dynamic change of gene to disclose drug resistance mode and biological behaviour of the tumour cell after treating;
5, it is analyzed after summarizing the abrupt climatic change result information for respectively taking peripheral blood sample, and several genes of acquisition is dashed forward
Be deteriorated different carry out statistic of classification, rear to realize that the assessment of clinical lung cancer therapy curative effect and drug resistance are multiple by analyzing and comparing each group of data
Send out the index of monitoring.
Further, clinical sample selected by the follow-up period after the data before treatment are acquired and treated are as follows: by entering
The surgical tissue sample and peripheral blood sample of 10 patients with lung cancer of the group with clinical typicalness and 10 patients are through treating
Each observation course for the treatment of (it is expected that every patient observes 4 courses for the treatment of, until progression of disease) respectively takes peripheral blood sample, the high throughput afterwards
Sequencing technologies include Ion torrent platform and Illumina platform, wherein Ion torrent platform passes through in semiconductor core
Fixed dna chain in the micropore of piece, archaeal dna polymerase, by base complementrity principle, synthesize complementary DNA chain using single stranded DNA as template,
When DNA chain one base of every extension, a proton will be discharged, local PH is caused to change, sensing layer detects pH variation, and will change
Learn signal be converted into digital signal, reach real-time interpretation base, Illumina platform on the basis of the sequencing approaches such as Sanger,
With four kinds of different dNTP of fluorescent marker of different colours, when archaeal dna polymerase synthesizes complementary strand, it is every add a kind of dNTP will
Different fluorescence is released, according to the fluorescence signal of capture and passes through specific software processing, to obtain DNA to be measured
Sequence information, in the follow-up period after the treatment, using bioinformatic analysis method, to DNA belonging to tumor patient
Segment is compared with normal sample gene order, and the database tumors correlation variation databases such as COSMIC is combined to be compared
It is right, it can find specific gene variation relevant to targeted drug whether is carried in tumor patient DNA sequence dna.
Further, in drug therapy premutation gene appearance, first by the surgical tissue before extraction patient medication
Genomic DNA carry out full sequencing of extron group, the individual of full sequencing of extron group can be found a large amount of by sequence alignment
Single nucleotide polymorphism (SNP), insertion and deletion (InDel, Insertion/Deletion) and structure variation (SV,
Structure Variation) site analyzes the architectural difference between Different Individual genome by biological information means, in conjunction with
Bioinformatics and the software for handling NGS data carry out the calculating analysis of subsequent result, complete SNP and genome structure note
It releases, the peripheral blood sample before treatment is sequenced using 17 gene Panel of lung cancer correlation afterwards, whether has verified that related mutation
In peripheral blood and mutation rate situation, as the observation base after treatment.
Further, it is mutated in gene appearance after drug therapy, the therapeutic scheme course for the treatment of for patient in group is node, often
A course for the treatment of node extracts peripheral blood in patients and extracts DNA, carries out 17 detection in Gene Mutation of lung cancer, obtains mutation status and mutation
Rate.Each patient extracts 3~5 course for the treatment of nodes, until progression of disease.
This method, the surgical tissue sample and peripheral blood sample that there are 10 patients with lung cancer of clinical typicalness by entering group
This and 10 patients each observation course for the treatment of (it is expected that every patient observes 4 courses for the treatment of, until progression of disease) after treating are each
Take the abrupt climatic change result information of peripheral blood sample to be analyzed: by above-mentioned three kinds of samples obtain several gene mutation differences into
Row statistic of classification, to realize the guidance to clinical lung cancer therapy curative effect evaluation and drug resistance recurrence monitoring index, suitable popularization makes
With.
It although an embodiment of the present invention has been shown and described, for the ordinary skill in the art, can be with
A variety of variations, modification, replacement can be carried out to these embodiments without departing from the principles and spirit of the present invention by understanding
And modification, the scope of the present invention is defined by the appended.
Claims (4)
1. a kind of method of the polygene combined abrupt climatic change assessment tumour dynamic change based on ctDNA, including the number before treatment
According to the follow-up period after acquisition and treatment, it is characterised in that: the data acquisition before the treatment includes tissue samples before treating
Peripheral blood sample acquisition before acquisition and treatment, the follow-up period after the treatment include according to the peripheral blood sample sieve after treatment
Select the clinical lung cancer therapy curative effect evaluation and drug resistance recurrence monitoring index that the changing rule of gene mutation obtains, concrete operation method
It is as follows:
(1), by utilizing high throughput sequencing technologies and bioinformatics method, to the tumor tissues (primary tumor before patient's treatment
Or transfer stove) carry out body cell full sequencing of extron group, obtain tumor tissues sample in mutated gene information;
(2), select with identical 17 lung cancer genes full exon region panel when survey tissue specimen to the peripheral blood of patient into
Row plasma free Tumour DNA (ctDNA) sequencing obtains the information of mutated gene in plasma specimen, and then examines two kinds of sample institutes
Obtain the consistency of testing result;
(3), by extracting DNA from tumour paraffin-embedded tissue, accurate PCR expansion is carried out to target sequence using special Mdification primer
Increase, at the same time, carries out end modified, the specific sequence of connection to amplified production using RingCapTM ring Jie link amplification technique
End is arranged, in conjunction with the use of special PCR response procedures, T4 ligase and high special RingCap-Taq enzyme, in regular-PCR platform
Upper realization carries out the library construction used for high-flux sequence, concrete operations to target sequence in sample DNA/RNA are as follows:
A, amplification capture is carried out to target sequence using the Spacegen-Taq enzyme of the specific primer of modified and high specific,
And product is made to form cohesive end;
B, asymmetric linking probe is attached using DNA ligase with cohesive end, forms annular product, avoided between product
It is combined with each other;
C, specific amplification amplification is carried out to annular product using specific primer, to obtain target sequence and in combination with upper
The special labeling sequence needed.
(4), the periphery blood specimen of follow-up period after the treatment, interim acquisition patient selects as before 147
17 gene panel of lung cancer carries out ctDNA sequencing to patient, about 3~5 times, up to progression of disease, observes and is mutated in sequencing result
The dynamic change of gene is to disclose drug resistance mode and biological behaviour of the tumour cell after treating;
(5), it is analyzed after summarizing the abrupt climatic change result information for respectively taking peripheral blood sample, and by several gene mutations of acquisition
Difference carries out statistic of classification, the rear assessment and drug resistance recurrence that clinical lung cancer therapy curative effect is realized by analyzing and comparing each group of data
The index of monitoring.
2. a kind of polygene combined abrupt climatic change assessment tumour dynamic change based on ctDNA according to claim 1
Method, it is characterised in that: clinical sample selected by the data acquisition before the treatment and the follow-up period after treatment are as follows: logical
It crosses into group the surgical tissue sample of 10 patients with lung cancer with clinical typicalness and peripheral blood sample and 10 patients' warps
Each observation course for the treatment of (it is expected that every patient observes 4 courses for the treatment of, until progression of disease) respectively takes peripheral blood sample after treatment.
3. a kind of polygene combined abrupt climatic change assessment tumour dynamic change based on ctDNA according to claim 1
Method, it is characterised in that: the high throughput sequencing technologies include Ion torrent platform and Illumina platform, wherein Ion
Torrent platform is by the fixed dna chain in the micropore of semiconductor chip, and archaeal dna polymerase is using single stranded DNA as template, by base
Complementarity principle, synthesizes complementary DNA chain, when DNA chain one base of every extensions, will discharge a proton, lead to local PH change
Change, sensing layer detects pH variation, and chemical signal is converted into digital signal, reaches real-time interpretation base, Illumina platform
On the basis of the sequencing approaches such as Sanger, with four kinds of different dNTP of fluorescent marker of different colours, when archaeal dna polymerase synthesizes
It is every to add a kind of dNTP and release different fluorescence when complementary strand, according to the fluorescence signal of capture and by specific meter
Calculation machine software processing, to obtain the sequence information of DNA to be measured.
4. a kind of polygene combined abrupt climatic change assessment tumour dynamic change based on ctDNA according to claim 1
Method, it is characterised in that: in the follow-up period after the treatment, using bioinformatic analysis method, to belonging to tumor patient
DNA fragmentation be compared with normal sample gene order, and combine the database tumors correlation variation database such as COSMIC
It is compared, can find whether carry specific gene variation relevant to targeted drug in tumor patient DNA sequence dna.
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CN112575069A (en) * | 2020-11-17 | 2021-03-30 | 哈尔滨医科大学 | Tumor evolution regulation and control model based on subclone level sensitive drug screening and establishment method thereof |
CN113096728A (en) * | 2021-06-10 | 2021-07-09 | 臻和(北京)生物科技有限公司 | Method, device, storage medium and equipment for detecting tiny residual focus |
CN113284554A (en) * | 2021-04-28 | 2021-08-20 | 中山大学肿瘤防治中心(中山大学附属肿瘤医院、中山大学肿瘤研究所) | Circulating tumor DNA detection system for screening micro residual focus after colorectal cancer operation and predicting recurrence risk and application |
CN114622015A (en) * | 2021-05-13 | 2022-06-14 | 四川大学华西医院 | NGS panel for predicting postoperative recurrence of non-small cell lung cancer based on circulating tumor DNA and application thereof |
CN114672562A (en) * | 2022-03-01 | 2022-06-28 | 武汉凯德维斯医学检验实验室有限公司 | Method, device, equipment and medium for monitoring drug resistance of PARP inhibitor |
CN116884598A (en) * | 2023-06-28 | 2023-10-13 | 曜立科技(北京)有限公司 | Cardiovascular and cerebrovascular disease screening auxiliary system based on metadata |
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CN113284554A (en) * | 2021-04-28 | 2021-08-20 | 中山大学肿瘤防治中心(中山大学附属肿瘤医院、中山大学肿瘤研究所) | Circulating tumor DNA detection system for screening micro residual focus after colorectal cancer operation and predicting recurrence risk and application |
CN114622015A (en) * | 2021-05-13 | 2022-06-14 | 四川大学华西医院 | NGS panel for predicting postoperative recurrence of non-small cell lung cancer based on circulating tumor DNA and application thereof |
CN114622015B (en) * | 2021-05-13 | 2023-05-05 | 四川大学华西医院 | NGS panel for predicting postoperative recurrence of non-small cell lung cancer based on circulating tumor DNA and application thereof |
CN113096728A (en) * | 2021-06-10 | 2021-07-09 | 臻和(北京)生物科技有限公司 | Method, device, storage medium and equipment for detecting tiny residual focus |
CN114672562A (en) * | 2022-03-01 | 2022-06-28 | 武汉凯德维斯医学检验实验室有限公司 | Method, device, equipment and medium for monitoring drug resistance of PARP inhibitor |
CN116884598A (en) * | 2023-06-28 | 2023-10-13 | 曜立科技(北京)有限公司 | Cardiovascular and cerebrovascular disease screening auxiliary system based on metadata |
CN116884598B (en) * | 2023-06-28 | 2024-05-28 | 曜立科技(北京)有限公司 | Cardiovascular and cerebrovascular disease screening auxiliary system based on metadata |
CN116913380A (en) * | 2023-09-12 | 2023-10-20 | 臻和(北京)生物科技有限公司 | Method and device for judging dynamic change of ctDNA of advanced tumor |
CN116913380B (en) * | 2023-09-12 | 2023-12-05 | 臻和(北京)生物科技有限公司 | Method and device for judging dynamic change of ctDNA of advanced tumor |
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