CN108728522A - Drug Discovery detection method - Google Patents
Drug Discovery detection method Download PDFInfo
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- CN108728522A CN108728522A CN201810593680.0A CN201810593680A CN108728522A CN 108728522 A CN108728522 A CN 108728522A CN 201810593680 A CN201810593680 A CN 201810593680A CN 108728522 A CN108728522 A CN 108728522A
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- sample
- detection
- nucleic acid
- drug discovery
- extraction
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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
- C12Q1/6869—Methods for sequencing
Abstract
The present invention provides a kind of Drug Discovery detection method comprising following steps：S1, the object being applicable in based on drug determine the crowd of Drug Discovery detection；S2, based on determining crowd, extraction detection sample；Related gene group is nucleic acid-templated in S3, extraction detection sample, and to the nucleic acid-templated carry out Quality Control of extraction；S4, the nucleic acid-templated carry out high throughput detection by the sequencing library of structure to Quality Control qualification；S5, the high-flux sequence data obtained to detection are handled comprising：S51, high-flux sequence data are analyzed；S52, the data obtained after analysis are understood；S6, examining report is generated.The Drug Discovery detection method of the present invention is detected analysis by acquiring the biological sample of self-test patient, obtains the phenotype of the drug response of its sample, and then provide for the medication of detection patient and effectively instruct.
Description
Technical field
The present invention relates to technical field of gene detection more particularly to a kind of Drug Discovery detection methods.
Background technology
With the progress of two generation sequencing technologies, people deepen continuously to the understanding of autogene group, while with to facing
The continuous accumulation of bed data, the two have pushed the progress of Drug Discovery jointly.It is instructed currently with two generation sequencing results clinical
Medication is increasingly mature.Adverse drug reaction is mostly derived from pharmaceutically-active individual difference unpredictable at present, i.e., hereditary
Variation can cause different patients to make differential responses to same drug therapy.
With the development of genomics, the mechanism of drug effect individual difference is caused gradually to be set forth.Drug targets
Gene pleiomorphism, drug-metabolization enzymes and participate in the receptor gene polymorphism of drug-metabolization enzymes inducing action, transport protein and
The inherent causes such as protein-bonded gene pleiomorphism and the epigenetic of gene expression control the effect of determining drug and not
Good reaction.The control of gene pleiomorphism and expression is the basis of pharmaceutically-active individual difference.Pharmacogenomics are modern
One of core of medicine, and in the most swift and violent forward position of development.However, can not also be effectively combined Drug Discovery at present
Learn the clinical guidance realized to patient medication.Therefore, in view of the above-mentioned problems, it is necessary to propose further solution.
Invention content
The present invention is intended to provide a kind of Drug Discovery detection method, to overcome the deficiencies in the prior art.
In order to solve the above technical problems, the technical scheme is that：
A kind of Drug Discovery detection method comprising following steps：
S1, the object being applicable in based on drug determine the crowd of Drug Discovery detection；
S2, based on determining crowd, extraction detection sample；
Related gene group is nucleic acid-templated in S3, extraction detection sample, and to the nucleic acid-templated carry out Quality Control of extraction；
S4, the nucleic acid-templated carry out high throughput detection by the sequencing library of structure to Quality Control qualification；
S5, the high-flux sequence data obtained to detection are handled comprising：
S51, high-flux sequence data are analyzed；
S52, the data obtained after analysis are understood；
S6, examining report is generated.
As the present invention Drug Discovery detection method improvement, the detection sample by tissue samples, buccal swab,
Saliva sample and blood sample composition.
The improvement of Drug Discovery detection method as the present invention, the encoding list of the genome are：
The improvement of Drug Discovery detection method as the present invention, the step S3 include the following steps：
S31, the sample of number 1 is subjected to nucleic acid extraction and purifying, when the nucleic acid-templated concentration of extraction is more than 3ng/ μ l,
Start the structure of sequencing library, otherwise, executes step S32；
S32, when the template concentrations of the nucleic acid of extraction be less than 3ng/ μ l and more than 1ng/ μ l when, it is nucleic acid-templated wait for it is spare,
When the template concentrations of the nucleic acid of extraction are less than 1ng/ μ l, it is discarded and sample presentation again.
As the present invention Drug Discovery detection method improvement, the step S3 further include with the step S31 and
Following steps parallel step S32：
S33, the sample that will freeze the number under environment 2 carry out nucleic acid extraction and purifying, nucleic acid-templated dense when extraction
Degree is more than 3ng/ μ l, starts the structure of sequencing library, otherwise, executes step S34；
S34, when the template concentrations of the nucleic acid of extraction be less than 3ng/ μ l and more than 1ng/ μ l when, it is nucleic acid-templated wait for it is spare,
When the template concentrations of the nucleic acid of extraction are less than 1ng/ μ l, it is discarded and sample presentation again.
The improvement of Drug Discovery detection method as the present invention, the step S51 include the following steps：
S511, removal unrelated sequences；
S512, the result of sequencing is sheared；
S513, the sequence after shearing is matched；
S514, mutation inspection is carried out to the sequence after matching；
S515, the phenotype for determining sample；
The Quality Control of S516, data.
The improvement of Drug Discovery detection method as the present invention, the step S514 include the following steps：
S5141, the detection of single base mutation；
S5142, the detection of small fragment insertion and deletion；
S5143, structural variation detection.
The improvement of Drug Discovery detection method as the present invention, the step S515 include the following steps：
S5151, the phenotype for determining each sample according to the genotype of sample based on specific drug；
S5152, based on genomic drug database generate sample drug response phenotypic data.
The improvement of Drug Discovery detection method as the present invention, the step S516 include the following steps：
S5161, judge to be sequenced whether initial data average mass values are more than 30；
Whether S5162, the reads percentages compared to genome are more than 70%；
S5163, judge whether uniformity is more than 80%；
Whether S5164, check sample detection genotype and known type are consistent.
The improvement of Drug Discovery detection method as the present invention, the step S52 further include：Based on each sample
The Drug Discovery that gene phenotype data generate detection patient understands information.
Compared with prior art, the beneficial effects of the invention are as follows：The Drug Discovery detection method of the present invention passes through acquisition
The biological sample of self-test patient is detected analysis, obtains the phenotype of the drug response of its sample, and then is detection patient's
Medication offer is effectively instructed.
Description of the drawings
In order to more clearly explain the embodiment of the invention or the technical proposal in the existing technology, to embodiment or will show below
There is attached drawing needed in technology description to be briefly described, it should be apparent that, the accompanying drawings in the following description is only this
Some embodiments described in invention, for those of ordinary skill in the art, without creative efforts,
Other drawings may also be obtained based on these drawings.
Fig. 1 is the method flow schematic diagram of the Drug Discovery detection method of the present invention；
Fig. 2 be the present invention Drug Discovery detection method in step S3 method flow schematic diagram；
Fig. 3 be the present invention Drug Discovery detection method in step S5 and S6 method flow schematic diagram.
Specific implementation mode
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 describes, 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.
As shown in Figure 1, the present invention provides a kind of Drug Discovery detection method comprising following steps：
S1, the object being applicable in based on drug determine the crowd of Drug Discovery detection.
Wherein, selected genome includes 164 genes altogether, and the encoding list is：
S2, based on determining crowd, extraction detection sample.
Wherein, each information of the detection sample at least containing more than two patients, collected patient information are identified in
On this container.Name, date of birth can be as patient information remarks in every table of identifier.The detection sample by
Tissue samples, buccal swab, saliva sample and blood sample composition.Wherein, different samples use different collection method and matter
Control standard.
Related gene group is nucleic acid-templated in S3, extraction detection sample, and to the nucleic acid-templated carry out Quality Control of extraction.
As shown in Fig. 2, the step S3 specifically comprises the following steps：
S31, the sample of number 1 is subjected to nucleic acid extraction and purifying, when the nucleic acid-templated concentration of extraction is more than 3ng/ μ l,
Start the structure of sequencing library, otherwise, executes step S32；
S32, when the template concentrations of the nucleic acid of extraction be less than 3ng/ μ l and more than 1ng/ μ l when, it is nucleic acid-templated wait for it is spare,
When the template concentrations of the nucleic acid of extraction are less than 1ng/ μ l, it is discarded and sample presentation again.
Meanwhile the step S3 further includes the following steps parallel with the step S31 and step S32：
S33, the sample that will freeze the number under environment 2 carry out nucleic acid extraction and purifying, nucleic acid-templated dense when extraction
Degree is more than 3ng/ μ l, starts the structure of sequencing library, otherwise, executes step S34；
S34, when the template concentrations of the nucleic acid of extraction be less than 3ng/ μ l and more than 1ng/ μ l when, it is nucleic acid-templated wait for it is spare,
When the template concentrations of the nucleic acid of extraction are less than 1ng/ μ l, it is discarded and sample presentation again.
Then, by step S32 and step S34 obtain it is nucleic acid-templated mix, and be ready for the structure of sequencing library
It builds.Wherein, for the structure of sequencing library, the addition to the sequence measuring joints needed for detecting has been included, being different from different inspections
The addition of the Barcode of sample and for identify whether due to the factor that error is brought in system Index addition.
Meanwhile initial libraries are also needed to meet the distribution situation to different target fragments, realize being evenly distributed for each target fragment,
And require the minimum content of detection segment.
S4, the nucleic acid-templated carry out high throughput detection by the sequencing library of structure to Quality Control qualification.
Wherein, the method for the high-flux sequence according to the microarray dataset of Illumina companies Miseq sequencing handbook into
Row operation.
S5, the high-flux sequence data obtained to detection are handled comprising：
S51, high-flux sequence data are analyzed；
S52, the data obtained after analysis are understood.
As shown in figure 3, the step S51 includes the following steps：
S511, removal unrelated sequences.Specifically, the data that subsequent analysis may be influenced in sequencing result should be in data
The analysis first stage is removed, wherein the average mass values for removing whole sequence first are less than 20 sequence；Secondly will not have
Remove clean connector removal；Finally N bases are removed.
S512, the result of sequencing is sheared.Specifically, to the sequence in the artificial addition in sequencing result need into
Row shearing.
S513, the sequence after shearing is matched.Specifically, to the sequence and mankind's reference gene group hg19 after shearing
It is compared, is then considered passing through when matching, be extracted the object that mutation checks, the sequence of overlapping region is then needed to carry
Take out the object as subsequent data quality control.
S514, mutation inspection is carried out to the sequence after matching.The step S514 includes the following steps：
S5141, the detection of single base mutation.
The single base mutation detection is detected single base mutation, and the SNP of generation is also needed to by mutation
The sequencing depth in site, mass value are controlled, to determine whether SNP is credible.
S5142, the detection of small fragment insertion and deletion.
The small fragment insertion and deletion detection is the insertion of the small fragment sequence occurred on some position of genome
Or delete, length is usually in 50bp or less.Insertion and missing for small fragment can be detected using Samtool.
S5143, structural variation detection.
The structural variation detection is insertion or deletion, the chromosome of the long segment sequence to length in 50bp or more
Inversion, the sequence transposition inside chromosome or between chromosome, copy number variation and the increasingly complex variation of some forms into
Row detection.
S515, the phenotype for determining sample.Relative to genotype, Drug Discovery detection is more focused on the concern to phenotype,
Therefore the phenotype to detecting object is needed to judge testing result.The step S515 includes the following steps：
S5151, the phenotype for determining each sample according to the genotype of sample based on specific drug；
S5152, based on genomic drug database generate sample drug response phenotypic data.
The Quality Control of S516, data.The step S516 includes the following steps：
S5161, judge to be sequenced whether initial data average mass values are more than 30；
Whether S5162, the reads percentages compared to genome are more than 70%；
S5163, judge whether uniformity is more than 80%；
Whether S5164, check sample detection genotype and known type are consistent.
The step S52 includes the following steps：
The result understood according to the step S52 can effectively instruct the medication offer for detecting patient.The step S52
It specifically includes：
The Drug Discovery that gene phenotype data based on each sample generate detection patient understands information.Based on drug base
Because of a group database, according to the gene phenotype of detection object, the medication to detecting object is understood.The deciphering includes：Detection
Object with the relevant genotype of certain drug, the phenotype of the drug response, the direction of medication usage scheme of certain drug.
S6, examining report is generated.
In conclusion the Drug Discovery detection method of the present invention is examined by acquiring the biological sample of self-test patient
Analysis is surveyed, obtains the phenotype of the drug response of its sample, and then provide for the medication of detection patient and effectively instruct.
It is obvious to a person skilled in the art that invention is not limited to the details of the above exemplary embodiments, Er Qie
In the case of without departing substantially from spirit or essential attributes of the invention, the present invention can be realized in other specific forms.Therefore, no matter
From the point of view of which point, the present embodiments are to be considered as illustrative and not restrictive, and the scope of the present invention is by appended power
Profit requires rather than above description limits, it is intended that all by what is fallen within the meaning and scope of the equivalent requirements of the claims
Variation is included within the present invention.Any reference signs in the claims should not be construed as limiting the involved claims.
In addition, it should be understood that although this specification is described in terms of embodiments, but not each embodiment is only wrapped
Containing an independent technical solution, this description of the specification is merely for the sake of clarity, and those skilled in the art should
It considers the specification as a whole, the technical solutions in the various embodiments may also be suitably combined, forms those skilled in the art
The other embodiment being appreciated that.
Claims (10)
1. a kind of Drug Discovery detection method, which is characterized in that the Drug Discovery detection method includes the following steps：
S1, the object being applicable in based on drug determine the crowd of Drug Discovery detection；
S2, based on determining crowd, extraction detection sample；
Related gene group is nucleic acid-templated in S3, extraction detection sample, and to the nucleic acid-templated carry out Quality Control of extraction；
S4, the nucleic acid-templated carry out high throughput detection by the sequencing library of structure to Quality Control qualification；
S5, the high-flux sequence data obtained to detection are handled comprising：
S51, high-flux sequence data are analyzed；
S52, the data obtained after analysis are understood；
S6, examining report is generated.
2. Drug Discovery detection method according to claim 1, which is characterized in that the detection sample is by tissue sample
Sheet, buccal swab, saliva sample and blood sample composition.
3. Drug Discovery detection method according to claim 1, which is characterized in that the encoding list of the genome
For：
4. Drug Discovery detection method according to claim 1, which is characterized in that the step S3 includes following step
Suddenly：
S31, the sample of number 1 is subjected to nucleic acid extraction and purifying, when the nucleic acid-templated concentration of extraction is more than 3ng/ μ l, beginning
Otherwise the structure of sequencing library executes step S32；
S32, be less than 3ng/ μ l and when more than 1ng/ μ l when the template concentrations of the nucleic acid of extraction, it is nucleic acid-templated wait for it is spare, when carrying
When the template concentrations of the nucleic acid taken are less than 1ng/ μ l, it is discarded and sample presentation again.
5. Drug Discovery detection method according to claim 4, which is characterized in that the step S3 further include with it is described
Following steps parallel step S31 and step S32：
S33, the sample for freezing the number under environment 2 is subjected to nucleic acid extraction and purifying, when the nucleic acid-templated concentration of extraction is big
In 3ng/ μ l, start the structure of sequencing library, otherwise, executes step S34；
S34, be less than 3ng/ μ l and when more than 1ng/ μ l when the template concentrations of the nucleic acid of extraction, it is nucleic acid-templated wait for it is spare, when carrying
When the template concentrations of the nucleic acid taken are less than 1ng/ μ l, it is discarded and sample presentation again.
6. Drug Discovery detection method according to claim 1, which is characterized in that the step S51 includes following step
Suddenly：
S511, removal unrelated sequences；
S512, the result of sequencing is sheared；
S513, the sequence after shearing is matched；
S514, mutation inspection is carried out to the sequence after matching；
S515, the phenotype for determining sample；
The Quality Control of S516, data.
7. Drug Discovery detection method according to claim 6, which is characterized in that the step S514 includes following step
Suddenly：
S5141, the detection of single base mutation；
S5142, the detection of small fragment insertion and deletion；
S5143, structural variation detection.
8. Drug Discovery detection method according to claim 6, which is characterized in that the step S515 includes following step
Suddenly：
S5151, the phenotype for determining each sample according to the genotype of sample based on specific drug；
S5152, based on genomic drug database generate sample drug response phenotypic data.
9. Drug Discovery detection method according to claim 6, which is characterized in that the step S516 includes following step
Suddenly：
S5161, judge to be sequenced whether initial data average mass values are more than 30；
Whether S5162, the reads percentages compared to genome are more than 70%；
S5163, judge whether uniformity is more than 80%；
Whether S5164, check sample detection genotype and known type are consistent.
10. Drug Discovery detection method according to claim 1, which is characterized in that the step S52 further includes：Base
The Drug Discovery that detection patient is generated in the gene phenotype data of each sample understands information.
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| CN109920479A (en) * | 2019-03-13 | 2019-06-21 | 复旦大学附属妇产科医院 | A method of identifying embryo chromosome inversion carrier state |
| CN110033843A (en) * | 2019-04-16 | 2019-07-19 | 北京中佰耀因医药科技有限公司 | A kind of accurate medication intelligent reporting system of the information management module containing experimental file |
| CN110033840A (en) * | 2019-04-16 | 2019-07-19 | 北京中佰耀因医药科技有限公司 | A kind of accurate medication intelligent reporting system of the management module containing gene information |
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Application publication date: 20181102 |