CN105512508A - Gene detection report automatic generation method and device - Google Patents
Gene detection report automatic generation method and device Download PDFInfo
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Abstract
The invention discloses a gene detection report automatic generation method and device; the method comprises the following steps: obtaining heredity information and sample information of a detected object; querying a gene database by using heredity information, and obtaining representation information corresponding to the heredity information; calling a gene detection report standardization template, and introducing the sample information and the representation information corresponding to the heredity information into the standardization template, thus automatically generating the gene detection report. The novel method and device can save mass time, can ensure accuracy, thus timely updating the gene detection report.
Description
Technical field
The present invention relates to a kind of method and device of automatic generation genetic test report.
Background technology
Genetic test is from chromosome structure, DNA sequence dna, DNA variant sites or degree of gene expression, is supplied to the foundation of some disease, physique or the idiosyncrasys relevant with gene genetic of person under inspection and medical research human assessment.
Genetic test report is with can for person under inspection and the readable mode of clinical research personnel to represent genetic test result, and it not only comprises the direct result of genetic test, further comprises the deciphering to result.Wherein, can provide the deciphering of result and the prediction and prevention of risk is advised, can person under inspection and reference for clinicians be supplied, there is very important practical value.At present, the genetic test report that many genetic test mechanisms provide is nearly all the mode relying on manual typing.
But manual extracts needs the time of at substantial, and accuracy can not be guaranteed.In addition, if there is new research to find, can not updating record in time.
Summary of the invention
The technical matters that the present invention mainly solves is to provide a kind of method and device of automatic generation genetic test report, can save the plenty of time, ensure accuracy, make genetic test report be upgraded in time.
For solving the problems of the technologies described above, the technical scheme that the present invention adopts is: a kind of method providing automatic generation genetic test report, comprising: the hereditary information and the sample information that obtain detected object; By described hereditary information query gene database, obtain the characterization information corresponding with described hereditary information, in described gene database, preserve the corresponding relation between described hereditary information and characterization information; Call the normalized template of genetic test report, and described sample information and the characterization information corresponding with described hereditary information are imported in described normalized template, automatically generate genetic test report.
Wherein, the described normalized template calling genetic test report, and described sample information and the characterization information corresponding with described hereditary information are imported in described normalized template, before the step of automatic generation genetic test report, comprising: the form determining the normalized template that described genetic test is reported; La Taihe LaTeX source code is adopted to write the normalized template of described genetic test report.
Wherein, described hereditary information is genotypic results, and described characterization information is disease information, and described gene database is disease gene database.
Wherein, the described normalized template calling genetic test report, and described sample information and the characterization information corresponding with described hereditary information are imported in described normalized template, automatically generate the step of genetic test report, comprising: the normalized template calling described genetic test report; Described sample information and the disease information corresponding with described genotypic results are imported in described normalized template; Screening conditions with disease association are set; According to the described screening conditions with disease association, run the text-only file of described generation genetic test report, obtain the text-only file of genetic test report; The text-only file described genetic test reported generates the genetic test report of Portable document form PDF.
Wherein, described by described hereditary information query gene database, before obtaining the step of the characterization information corresponding with described hereditary information, comprising: the data message relevant to described hereditary information needed for extracting from documents and materials or database; Determine the data layout of described data message; Described gene database is set up according to described data message and described data layout.
For solving the problems of the technologies described above, another technical solution used in the present invention is: the device providing a kind of automatic generation genetic test report, and described device comprises: the first acquisition module, for obtaining hereditary information and the sample information of detected object; Second acquisition module, for by described hereditary information query gene database, obtains the characterization information corresponding with described hereditary information, preserves the corresponding relation between described hereditary information and characterization information in described gene database; Report generation module, for calling the normalized template of genetic test report, and imports in described normalized template by described sample information and the characterization information corresponding with described hereditary information, automatically generates genetic test report.
Wherein, described device also comprises: the first determination module, for determining the form of the normalized template that described genetic test is reported; Write module, for the normalized template adopting La Taihe LaTeX source code to write described genetic test report.
Wherein, described hereditary information is genotypic results, and described characterization information is disease information, and described gene database is disease gene database.
Wherein, described report generation module comprises: call unit, for calling the normalized template of described genetic test report; Import unit, for importing in described normalized template by described sample information and the disease information corresponding with described genotypic results; Setting unit, for arranging the screening conditions with disease association; Running unit, for according to the described screening conditions with disease association, runs the text-only file of described generation genetic test report, obtains the text-only file of genetic test report; Generation unit, the text-only file for described genetic test being reported generates the genetic test report of Portable document form PDF.
Wherein, described device also comprises: extraction module, for the data message relevant to described hereditary information from documents and materials or database needed for extraction; Second determination module, for determining the data layout of described data message; Set up module, for setting up described gene database according to described data message and described data layout.
The invention has the beneficial effects as follows: the situation being different from prior art, the present invention obtains hereditary information and the sample information of detected object; By hereditary information query gene database, obtain the characterization information corresponding with hereditary information; Call the normalized template of genetic test report, and sample information and the characterization information corresponding with hereditary information are imported in normalized template, automatically generate genetic test report.After getting characterization information by hereditary information, call standard form, after sample information and characterization information are imported standard form, automatically can generate genetic test report, thus not typing by hand, can save the plenty of time, avoid personal error, can ensure accuracy, and gene database can find to upgrade in time corresponding information according to new research, thus genetic test report can be made in time to be upgraded.
Accompanying drawing explanation
Fig. 1 is the process flow diagram that the present invention generates method one embodiment of genetic test report automatically;
Fig. 2 is the process flow diagram that the present invention generates another embodiment of method of genetic test report automatically;
Fig. 3 is the process flow diagram that the present invention generates the another embodiment of method of genetic test report automatically;
Fig. 4 is the process flow diagram that the present invention generates the another embodiment of method of genetic test report automatically;
Fig. 5 is the structural representation that the present invention generates device one embodiment of genetic test report automatically;
Fig. 6 is the structural representation that the present invention generates another embodiment of device of genetic test report automatically;
Fig. 7 is the structural representation that the present invention generates the another embodiment of device of genetic test report automatically;
Fig. 8 is the structural representation that the present invention generates the another embodiment of device of genetic test report automatically.
Embodiment
Consult Fig. 1, Fig. 1 is the process flow diagram that the present invention generates method one embodiment of genetic test report automatically, comprising:
Step S101: the hereditary information and the sample information that obtain detected object.
Hereditary information refers to biological for copying the thing identical with oneself, the information being passed to cell when filial generation or each cell divide at every turn by cell is passed to, i.e. the putting in order of base-pair (or referring to the putting in order of deoxynucleotide of DNA molecular) by parental generation.Hereditary information herein can be represent the hereditary information of individual difference, the hereditary information of DNA mutation or with hereditary information of gene genetic disease association etc.The basic condition information of sample information mainly detected object, as name, sex, age, sample type, detection date, detects unit etc.
Step S102: by hereditary information query gene database, obtains the characterization information corresponding with hereditary information, preserves the corresponding relation between hereditary information and characterization information in gene database.
The trait expression of individual difference that characterization information refers to can be characterized in organism surface according to hereditary information, can observe, includes but not limited to appearance, height, body weight, the colour of skin, personality etc.
Owing to preserving the corresponding relation between hereditary information and characterization information in gene database, therefore, by hereditary information query gene database, the characterization information corresponding with hereditary information can be obtained.
Step S103: the normalized template calling genetic test report, and sample information and the characterization information corresponding with hereditary information are imported in normalized template, automatically generate genetic test report.
The normalized template of genetic test report creates complete according to preset requirement, after acquisition sample information and characterization information, calls normalized template, automatically can generate genetic test report.
Embodiment of the present invention obtains hereditary information and the sample information of detected object; By hereditary information query gene database, obtain the characterization information corresponding with hereditary information; Call the normalized template of genetic test report, and sample information and the characterization information corresponding with hereditary information are imported in normalized template, automatically generate genetic test report.After getting characterization information by hereditary information, call standard form, after sample information and characterization information are imported standard form, automatically can generate genetic test report, thus not typing by hand, can save the plenty of time, avoid personal error, can ensure accuracy, and gene database can find to upgrade in time corresponding information according to new research, thus genetic test report can be made in time to be upgraded.
Consult Fig. 2, if the normalized template of genetic test report does not create in advance, so before step S103, also comprise following content:
Step S201: the form determining the normalized template that genetic test is reported.
Step S202: adopt La Taihe LaTeX source code to write the normalized template of genetic test report.
LaTeX (transliteration " La Taihe ") is a kind of composing system based on Τ Ε Χ, developed in phase early 1980s by american computer scholar Lesley Lambert (LeslieLamport), utilize this form, even if user does not have the knowledge of typesetting and program design can give full play to the power provided by TeX yet, the printed matter much with books quality can be generated in several days, even several hours.For generation complicate list form and mathematical formulae, this point shows particularly outstanding.Therefore it is highly suitable for the science and technology and the Mathematics document that generate high printing quality, and this system is equally applicable to the document of the every other kind generated from simple mail to completed books.
Present embodiment carrys out standard of compiling template by using LaTeX source code, can carry out batch processing, realizes robotization and generates genetic test report.
In actual applications, except using LaTeX source code to come except standard of compiling template, the source code of other plain texts also can be adopted to carry out standard of compiling template, such as: Markdown, troff, TeX etc.
Consult Fig. 3, when hereditary information is genotypic results, characterization information is disease information, and when gene database is disease gene database, step S103 specifically can comprise following content:
Step S301: the normalized template calling genetic test report.
Step S302: sample information and the disease information corresponding with genotypic results are imported in normalized template.
Genotyping (Genotyping) is the technology utilizing biological detection method to measure idiotype (Genotype).Some conventional genotyping technique have: restriction fragment length polymorphism (RestrictionFragmentLengthPolymorphism, RFLP), terminal restriction length polymorphism (TerminalRestrictionFragmentLengthPolymorphism, t-RFLP), AFLP (Amplifiedfragmentlengthpolymorphisms, AFLP), multiple linking probe amplification (multiplexligation-dependentprobeamplification, MLPA), single nucleotide polymorphism (SingleNucleotidePolymorphisms, SNP) etc.Genotypic analyses can diagnose the illness the hereditary variation caused, as microsatellite sequence instability (MicrosatelliteInstability, MSI), Trisomy (Trisomy), aneuploid (Aneuploidy), loss of heterozygosity (lossofheterozygosity, LOH) etc.; Microsatellite sequence is unstable relevant with the tumor cell gene type of colon cancer, breast cancer, cervix cancer with loss of heterozygosity; No. 21 chromosomal Trisomy is kind of a common aneuploid, and clinical manifestation is mongolism (DownSyndrome).
Step S303: the screening conditions with disease association are set.
With the threshold limit value that the screening conditions of disease association can be some parameters, such as: the minimum value minRisk of integrated risk coefficient, after arranging the minimum value of integrated risk coefficient, when being greater than this value and value is larger, risk is larger.
Step S304: according to the screening conditions with disease association, runs the text-only file generating genetic test report, obtains the text-only file of genetic test report.
Step S305: text-only file genetic test reported generates the genetic test report of Portable document form PDF.
Genetic test report can comprise the disease information corresponding with genotypic results, and excessive risk, risk, low-risk disease statistics.
By present embodiment, the genetic test report of the PDF of detailed disease information and relevant statistic document can be obtained.
Consult Fig. 4, when gene database is not also set up time, before step S102, also comprise:
Step S401: the data message relevant to hereditary information needed for extracting from documents and materials or database.
Step S402: the data layout determining data message.
Step S403: set up gene database according to data message and data layout.
By present embodiment, gene database can be built.
Illustrate that the present invention generates the method for genetic test report automatically, specifically for the SNP in genotyping technique with a concrete application example below.
(1) gene database builds.Choose the SNP site that 103 kinds of common human diseasess are corresponding, then compared with snp database (dbSNP), hg19 database and HapMap database by SNP site, obtain corresponding genotype, other SNP information and relevant disease information can also be supplemented, form the gene database of form.Disease information comprises disease Chinese and English title, good age of onset, crowd's incidence of disease, sex risk factor, hereditary form, health check-up suggestion, disease brief introduction, sums up and advise.SNP information comprises positive SNP coding, Disease-causing gene, normal alkali fundamental mode, crowd SNP positive rate, positive risk factor, pathogenesis, genome etc.
(2) normalized template builds.Determine the template that genetic test is reported, write template with the form of LaTeX source code.
(3) input file is prepared, as the information (patientInfo.txt) of sample, lower machine data numbering (ncId2SampleID.txt) and genotypic results (report.xls).Sample information comprises sample ID, sample number into spectrum, sex, age, sample type, date received, censorship unit.Genotypic results comprises GC_Score etc., and obtains the information of positive genotype in conjunction with gene database.
(4) Run Script, the disease information in query gene database and SNP information, and calculate the positive incidence of disease (computing formula is as follows) of the positive incidence of disease, integrated risk coefficient and weighting, then call LaTeX template file.
2) calculating of the positive incidence of disease:
The incidence of disease is relevant to sex:
The male sex: the positive incidence of disease={ (positive risk factor-1) × sex risk factor+1} × crowd's incidence of disease
The incidence of disease and sex have nothing to do: the positive incidence of disease=positive risk factor × crowd's incidence of disease
3) if disease has multi-mutant site:
(5) filtercondition is set, the minimum value minRisk comprising integrated risk coefficient (is defaulted as 1, if desired arrange and can not be less than 1), the minimum value minGCScore of GCScore (is defaulted as 0, if desired arrange and can not be less than 0), the maximal value maxMutRate (be defaulted as 1, if desired arrange and can not be greater than 1) of crowd SNP positive rate, the maximal value maxFreq (be defaulted as 1, if desired arrange and can not be greater than 1) of SNP frequency detected.
(6) working procedure, exports RST000000000.report.tex document and some statistics files, comprises the statistical information to disease and SNP, and excessive risk, risk, low-risk disease statistics.
(7) utilize LaTeX compilation run RST000000000.report.tex document, generate PDF genetic test report RST000000000.report.pdf.
Consult Fig. 5, Fig. 5 is the structural representation that the present invention generates device one embodiment of genetic test report automatically, and this device comprises: the first acquisition module 101, second acquisition module 102 and report generation module 103.
First acquisition module 101 is for obtaining hereditary information and the sample information of detected object.
Hereditary information refers to biological for copying the thing identical with oneself, is passed to the information being passed to cell when filial generation or each cell divide at every turn by cell by parental generation, i.e. the putting in order of base-pair.Hereditary information herein can be represent the hereditary information of individual difference, the hereditary information of DNA mutation or with hereditary information of gene genetic disease association etc.The basic condition information of sample information mainly detected object, as name, sex, age, sample type, detection date, detects unit etc.
Second acquisition module 102, for by hereditary information query gene database, obtains the characterization information corresponding with hereditary information, preserves the corresponding relation between hereditary information and characterization information in gene database.
The trait expression of individual difference that characterization information refers to can be characterized in organism surface according to hereditary information, can observe, includes but not limited to appearance, height, body weight, the colour of skin, personality etc.
Owing to preserving the corresponding relation between hereditary information and characterization information in gene database, therefore, by hereditary information query gene database, the characterization information corresponding with hereditary information can be obtained.
Sample information and the characterization information corresponding with hereditary information for calling the normalized template of genetic test report, and import in normalized template by report generation module 103, automatically generate genetic test report.
The normalized template of genetic test report creates complete according to preset requirement, after acquisition sample information and characterization information, calls normalized template, automatically can generate genetic test report.
Embodiment of the present invention obtains hereditary information and the sample information of detected object; By hereditary information query gene database, obtain the characterization information corresponding with hereditary information; Call the normalized template of genetic test report, and sample information and the characterization information corresponding with hereditary information are imported in normalized template, automatically generate genetic test report.After getting characterization information by hereditary information, call standard form, after sample information and characterization information are imported standard form, automatically can generate genetic test report, thus not typing by hand, can save the plenty of time, avoid personal error, can ensure accuracy, and gene database can find to upgrade in time corresponding information according to new research, thus genetic test report can be made in time to be upgraded.
Consult Fig. 6, if the normalized template of genetic test report does not create in advance, this device also comprises: the first determination module 201 and write module 202.
First determination module 201 is for determining the form of the normalized template that genetic test is reported.
Write the normalized template of module 202 for adopting La Taihe LaTeX source code to write genetic test report.
LaTeX (transliteration " La Taihe ") is a kind of composing system based on Τ Ε Χ, utilize this form, even if user does not have the knowledge of typesetting and program design can give full play to the power provided by TeX yet, the printed matter much with books quality can be generated in several days, even several hours.Therefore it is highly suitable for the science and technology and the Mathematics document that generate high printing quality, and this system is equally applicable to the document of the every other kind generated from simple mail to completed books.
Present embodiment carrys out standard of compiling template by using LaTeX source code, can carry out batch processing, realizes robotization and generates genetic test report.
In actual applications, except using LaTeX source code to come except standard of compiling template, the source code of other plain texts also can be adopted to carry out standard of compiling template.
Consult Fig. 7, when hereditary information is genotypic results, characterization information is disease information, and when gene database is disease gene database, report generation module 103 comprises: call unit 1031, importing unit 1032, setting unit 1033, running unit 1034 and generation unit 1035.
Call unit 1031 is for calling the normalized template of genetic test report.
Import unit 1032 for sample information and the disease information corresponding with genotypic results being imported in normalized template.
Genotyping utilizes biological detection method to measure Id technology.Some conventional genotyping technique have: the amplification of restriction fragment length polymorphism (RFLP), terminal restriction length polymorphism (t-RFLP), AFLP (AFLP), multiple linking probe (MLPA), single nucleotide polymorphism (SNP) etc.Genotypic analyses can diagnose the illness the hereditary variation caused, as microsatellite sequence instability (MSI), Trisomy (Trisomy), aneuploid (Aneuploidy), loss of heterozygosity (LOH) etc.; Microsatellite sequence is unstable relevant with the tumor cell gene type of colon cancer, breast cancer, cervix cancer with loss of heterozygosity; No. 21 chromosomal Trisomy is kind of a common aneuploid, and clinical manifestation is mongolism (DownSyndrome).
Setting unit 1033 is for arranging the screening conditions with disease association.
Running unit 1034, for according to the screening conditions with disease association, runs the text-only file generating genetic test report, obtains the text-only file of genetic test report.
Generation unit 1035 generates the genetic test report of Portable document form PDF for text-only file genetic test reported.
Genetic test report can comprise the disease information corresponding with genotypic results, and excessive risk, risk, low-risk disease statistics.
By present embodiment, the genetic test report of the PDF of detailed disease information and relevant statistic document can be obtained.
Consult Fig. 8, when gene database is not also set up time, device also comprises: extraction module 301, second determination module 302 and set up module 303.
Extraction module 301 is for the data message relevant to hereditary information from documents and materials or database needed for extraction.
Second determination module 302 is for determining the data layout of data message;
Set up module 303 for setting up gene database according to data message and data layout.
By present embodiment, gene database can be built.
The foregoing is only embodiments of the present invention; not thereby the scope of the claims of the present invention is limited; every utilize instructions of the present invention and accompanying drawing content to do equivalent structure or equivalent flow process conversion; or be directly or indirectly used in other relevant technical fields, be all in like manner included in scope of patent protection of the present invention.
Claims (10)
1. automatically generate a method for genetic test report, it is characterized in that, described method comprises:
Obtain hereditary information and the sample information of detected object;
By described hereditary information query gene database, obtain the characterization information corresponding with described hereditary information, in described gene database, preserve the corresponding relation between described hereditary information and characterization information;
Call the normalized template of genetic test report, and described sample information and the characterization information corresponding with described hereditary information are imported in described normalized template, automatically generate genetic test report.
2. method according to claim 1, it is characterized in that, described in call the normalized template of genetic test report, and described sample information and the characterization information corresponding with described hereditary information are imported in described normalized template, before the step of automatic generation genetic test report, comprising:
Determine the form of the normalized template that described genetic test is reported;
La Taihe LaTeX source code is adopted to write the normalized template of described genetic test report.
3. method according to claim 2, is characterized in that, described hereditary information is genotypic results, and described characterization information is disease information, and described gene database is disease gene database.
4. method according to claim 3, it is characterized in that, described in call the normalized template of genetic test report, and described sample information and the characterization information corresponding with described hereditary information are imported in described normalized template, the step of automatic generation genetic test report, comprising:
Call the normalized template of described genetic test report;
Described sample information and the disease information corresponding with described genotypic results are imported in described normalized template;
Screening conditions with disease association are set;
According to the described screening conditions with disease association, run the text-only file of described generation genetic test report, obtain the text-only file of genetic test report;
The text-only file described genetic test reported generates the genetic test report of Portable document form PDF.
5. the method according to any one of Claims 1-4, is characterized in that, described by described hereditary information query gene database, before obtaining the step of the characterization information corresponding with described hereditary information, comprising:
The data message relevant to described hereditary information needed for extracting from documents and materials or database;
Determine the data layout of described data message;
Described gene database is set up according to described data message and described data layout.
6. automatically generate a device for genetic test report, it is characterized in that, described device comprises:
First acquisition module, for obtaining hereditary information and the sample information of detected object;
Second acquisition module, for by described hereditary information query gene database, obtains the characterization information corresponding with described hereditary information, preserves the corresponding relation between described hereditary information and characterization information in described gene database;
Report generation module, for calling the normalized template of genetic test report, and imports in described normalized template by described sample information and the characterization information corresponding with described hereditary information, automatically generates genetic test report.
7. device according to claim 6, is characterized in that, described device also comprises:
First determination module, for determining the form of the normalized template that described genetic test is reported;
Write module, for the normalized template adopting La Taihe LaTeX source code to write described genetic test report.
8. the device of generation genetic test report according to claim 7, it is characterized in that, described hereditary information is genotypic results, and described characterization information is disease information, and described gene database is disease gene database.
9. device according to claim 8, is characterized in that, described report generation module comprises:
Call unit, for calling the normalized template of described genetic test report;
Import unit, for importing in described normalized template by described sample information and the disease information corresponding with described genotypic results;
Setting unit, for arranging the screening conditions with disease association;
Running unit, for according to the described screening conditions with disease association, runs the text-only file of described generation genetic test report, obtains the text-only file of genetic test report;
Generation unit, the text-only file for described genetic test being reported generates the genetic test report of Portable document form PDF.
10. the device according to any one of claim 6 to 9, is characterized in that, described device also comprises:
Extraction module, for the data message relevant to described hereditary information from documents and materials or database needed for extraction;
Second determination module, for determining the data layout of described data message;
Set up module, for setting up described gene database according to described data message and described data layout.
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