CN105512508B - Automatically generate the method and device of genetic test report - Google Patents

Abstract

The invention discloses a kind of method and device for automatically generating genetic test report, this method includes：Obtain the hereditary information and sample information of detected object；By hereditary information query gene database, characterization information corresponding with hereditary information is obtained；The normalized template of genetic test report is called, and sample information and characterization information corresponding with hereditary information are imported in normalized template, automatically generates genetic test report.By the above-mentioned means, the present invention can save the plenty of time, ensure accuracy, in time report genetic test and updated.

Description

Method and device for automatically generating gene detection report

technical field

The invention relates to a method and device for automatically generating a gene detection report.

Background technique

Genetic testing is based on chromosome structure, DNA sequence, DNA variation site or gene expression level, which provides the basis for the subjects and medical researchers to evaluate some diseases, physical constitution or personal characteristics related to genetic inheritance.

The genetic test report presents the genetic test results in a way that can be understood by the subjects and clinical researchers. It includes not only the direct results of the genetic test, but also the interpretation of the results. Among them, the interpretation of the results can provide the prediction of disease risk and preventive suggestions, which can be used as a reference for examinees and clinicians, and has very important practical value. At present, the genetic test reports issued by many genetic testing institutions are almost all manually entered.

However, manual excerpts are time-consuming and accuracy cannot be guaranteed. In addition, if there are new research findings, the report cannot be updated in a timely manner.

Contents of the invention

The technical problem mainly solved by the present invention is to provide a method and device for automatically generating a gene detection report, which can save a lot of time, ensure accuracy, and update the gene detection report in time.

In order to solve the above technical problems, a technical solution adopted by the present invention is to provide a method for automatically generating a gene detection report, including: obtaining the genetic information and sample information of the subject to be tested; querying the genetic database through the genetic information, obtaining and The characterization information corresponding to the genetic information, the gene database stores the correspondence between the genetic information and the characterization information; calls the standardized template of the genetic detection report, and matches the sample information with the genetic information Import the characterization information into the standardized template to automatically generate a gene detection report.

Wherein, calling the standardized template of the gene detection report, and importing the sample information and the characterization information corresponding to the genetic information into the standardized template, before the step of automatically generating the gene detection report, includes: determining the gene The format of the standardized template of the test report; the standardized template of the genetic test report is written using LaTeX source code.

Wherein, the genetic information is a genotyping result, the characterization information is disease information, and the gene database is a disease gene database.

Wherein, the step of calling the standardized template of the gene detection report, importing the sample information and the characterization information corresponding to the genetic information into the standardized template, and automatically generating the gene detection report includes: calling the gene detection report A standardized template for reporting; importing the sample information and disease information corresponding to the genotyping result into the standardized template; setting disease-related screening conditions; according to the disease-related screening conditions, running the Generating a plain text file of the genetic testing report to obtain the plain text file of the genetic testing report; generating a genetic testing report in a portable file format PDF from the plain text file of the genetic testing report.

Wherein, before the step of querying the gene database through the genetic information and obtaining the characterization information corresponding to the genetic information, it includes: extracting the required data information related to the genetic information from literature or databases; determining The data format of the data information; the gene database is established according to the data information and the data format.

In order to solve the above-mentioned technical problems, another technical solution adopted by the present invention is to provide a device for automatically generating a genetic test report, the device comprising: a first acquisition module, used to acquire the genetic information and sample information of the subject; The second acquisition module is used to query the gene database through the genetic information to obtain the characterization information corresponding to the genetic information, and the genetic database stores the correspondence between the genetic information and the characterization information; a report generation module , for invoking a standardized template of a gene detection report, and importing the sample information and characterization information corresponding to the genetic information into the standardized template to automatically generate a gene detection report.

Wherein, the device further includes: a first determining module, used to determine the format of the standardized template of the genetic testing report; a writing module, used to write the standardized template of the genetic testing report using LaTeX source code.

Wherein, the genetic information is a genotyping result, the characterization information is disease information, and the gene database is a disease gene database.

Wherein, the report generation module includes: a calling unit, used to call the standardized template of the gene detection report; an import unit, used to import the sample information and the disease information corresponding to the genotyping result into the standardized In the template; the setting unit is used to set the screening conditions related to the disease; the operation unit is used to run the plain text file of the gene detection report generated according to the disease-related screening conditions to obtain the plain text of the genetic detection report A file; a generating unit, configured to generate a genetic detection report in a portable file format PDF from the plain text file of the genetic detection report.

Wherein, the device also includes: an extraction module, used to extract the required data information related to the genetic information from literature or databases; a second determination module, used to determine the data format of the data information; A module for establishing the gene database according to the data information and the data format.

The beneficial effects of the present invention are: different from the situation of the prior art, the present invention obtains the genetic information and sample information of the subject to be tested; queries the genetic database through the genetic information to obtain the characterization information corresponding to the genetic information; calls the standardization of the genetic detection report template, and import sample information and characterization information corresponding to genetic information into the standardized template to automatically generate a genetic test report. After the characterization information is obtained through the genetic information, the standard template is called, and after the sample information and characterization information are imported into the standard template, the genetic test report can be automatically generated, so there is no need for manual entry, which can save a lot of time, avoid human errors, and ensure accuracy. Moreover, the gene database can update the corresponding information in time according to new research findings, so that the gene test report can be updated in time.

Description of drawings

Fig. 1 is a flowchart of an embodiment of the method for automatically generating a gene detection report in the present invention;

Fig. 2 is a flowchart of another embodiment of the method for automatically generating a gene detection report of the present invention;

Fig. 3 is a flowchart of another embodiment of the method for automatically generating a gene detection report in the present invention;

Fig. 4 is a flowchart of another embodiment of the method for automatically generating a gene detection report in the present invention;

Fig. 5 is a structural schematic diagram of an embodiment of the device for automatically generating a gene detection report according to the present invention;

Fig. 6 is a structural schematic diagram of another embodiment of the device for automatically generating a gene detection report according to the present invention;

Fig. 7 is a structural schematic diagram of another embodiment of the device for automatically generating a gene detection report according to the present invention;

Fig. 8 is a structural schematic diagram of another embodiment of the device for automatically generating a gene detection report according to the present invention.

Detailed ways

Referring to Fig. 1, Fig. 1 is a flowchart of an embodiment of the method for automatically generating a gene detection report of the present invention, including:

Step S101: Obtain the genetic information and sample information of the subject.

Genetic information refers to the information that organisms pass from parent to offspring, or from cell to cell each time each cell divides, in order to copy the same thing as itself, that is, the sequence of base pairs (or the deoxygenated nucleus of the DNA molecule sequence of nucleotides). The genetic information here may be genetic information representing individual differences, genetic information of DNA mutations, or genetic information related to genetic diseases, etc. The sample information is mainly the basic situation information of the tested object, such as name, gender, age, sample type, testing date, testing unit, and so on.

Step S102: Query the gene database through the genetic information to obtain the representation information corresponding to the genetic information, and the gene database stores the correspondence between the genetic information and the representation information.

Representation information refers to the performance of individual differences that can be represented on the surface of organisms and can be observed based on genetic information, including but not limited to appearance, height, weight, skin color, personality, etc.

Since the gene database stores the correspondence between the genetic information and the characterization information, the characterization information corresponding to the genetic information can be obtained by querying the gene database through the genetic information.

Step S103: call the standardized template of the genetic testing report, import the sample information and the characterization information corresponding to the genetic information into the standardized template, and automatically generate the genetic testing report.

The standardized template of the genetic testing report is created according to the preset requirements. After obtaining the sample information and characterization information, the standardized template can be called to automatically generate the genetic testing report.

The embodiment of the present invention obtains the genetic information and sample information of the subject to be tested; queries the gene database through the genetic information to obtain the characterization information corresponding to the genetic information; calls the standardized template of the gene detection report, and compares the sample information and the characterization information corresponding to the genetic information The information is imported into the standardized template, and the genetic testing report is automatically generated. After the characterization information is obtained through the genetic information, the standard template is called, and after the sample information and characterization information are imported into the standard template, the genetic test report can be automatically generated, so there is no need for manual entry, which can save a lot of time, avoid human errors, and ensure accuracy. Moreover, the gene database can update the corresponding information in time according to new research findings, so that the gene test report can be updated in time.

Referring to Figure 2, if the standardized template of the genetic testing report has not been created in advance, then before step S103, the following content is also included:

Step S201: Determine the format of the standardized template of the genetic testing report.

Step S202: Using the LaTeX source code of LaTeX to write the standardized template of the gene detection report.

LaTeX (transliteration "La Taihe") is a TEX-based typesetting system developed by American computer scientist Leslie Lamport in the early 1980s. Using this format, even users No knowledge of typesetting and programming can give full play to the powerful functions provided by TeX, and can generate many book-quality prints in a few days, or even a few hours. This is especially true for generating complex tables and mathematical formulas. It is therefore well suited for producing high print quality technical and mathematical documents, and the system is equally suitable for producing all other kinds of documents, from simple letters to complete books.

In this embodiment, by using LaTeX source code to write standardized templates, batch processing can be performed to realize automatic generation of genetic testing reports.

In practical applications, in addition to using LaTeX source code to write standardized templates, other plain text source codes can also be used to write standardized templates, such as: Markdown, troff, TeX, etc.

Referring to Figure 3, when the genetic information is the genotyping result, the characterization information is disease information, and the gene database is a disease gene database, step S103 may specifically include the following:

Step S301: Invoking the standardized template of the gene detection report.

Step S302: Import sample information and disease information corresponding to genotyping results into a standardized template.

Genotyping (Genotyping) is the use of biological detection methods to determine the individual genotype (Genotype) technology. Some commonly used genotyping techniques are: restriction fragment length polymorphism (Restriction Fragment Length Polymorphism, RFLP), terminal restriction length polymorphism (Terminal Restriction Fragment Length Polymorphism, t-RFLP), amplified fragment length polymorphism ( Amplified fragment length polymorphisms (AFLP), multiplex ligation-dependent probe amplification (multiplex ligation-dependent probe amplification, MLPA), single nucleotide polymorphisms (Single Nucleotide Polymorphisms, SNP), etc. Genotyping analysis can diagnose genetic variation caused by diseases, such as microsatellite instability (Microsatellite Instability, MSI), trisomy (Trisomy), aneuploidy (Aneuploidy), loss of heterozygosity (loss of heterozygosity, LOH), etc; Microsatellite instability and loss of heterozygosity are related to the tumor cell genotypes of colon cancer, breast cancer, and cervical cancer; trisomy of chromosome 21 is a common aneuploidy, and the clinical manifestation is congenital stupidity ( Down Syndrome).

Step S303: Set the filtering conditions related to the disease.

Disease-related screening conditions can be critical thresholds of some parameters, for example: the minimum value of the comprehensive risk coefficient minRisk, after setting the minimum value of the comprehensive risk coefficient, when it is greater than this value and the value is larger, the risk is greater.

Step S304: According to the screening conditions related to the disease, run and generate the plain text file of the gene detection report to obtain the plain text file of the gene detection report.

Step S305: Generating the genetic testing report in the portable file format PDF from the plain text file of the genetic testing report.

The genetic testing report may include disease information corresponding to genotyping results, as well as statistics of high-risk, medium-risk, and low-risk diseases.

Through this embodiment, a gene detection report in PDF format with detailed disease information and related statistical documents can be obtained.

Referring to Figure 4, when the gene database has not been established, before step S102, it also includes:

Step S401: Extracting required data information related to genetic information from literature or databases.

Step S402: Determine the data format of the data information.

Step S403: Establish a gene database according to the data information and data format.

According to this embodiment, a gene database can be constructed.

A specific application example is used below to illustrate the method of the present invention for automatically generating a gene detection report, specifically taking SNP in genotyping technology as an example.

(1) Gene database construction. Select the SNP loci corresponding to 103 common human diseases, and then compare the SNP loci with the SNP database (dbSNP), hg19 database and HapMap database to obtain the corresponding genotype, and can also supplement other SNP information and related diseases Information, forming a gene database in tabular form. Disease information includes disease name in Chinese and English, best age of onset, population incidence rate, gender risk coefficient, genetic type, medical examination suggestion, disease profile, summary and suggestion, etc. SNP information includes positive SNP codes, pathogenic genes, normal base types, population SNP positive rates, positive risk coefficients, pathogenic mechanisms, gene maps, etc.

(2) Standardized template construction. Determine the template of the genetic testing report, and write the template in the form of LaTeX source code.

(3) Prepare input files, such as sample information (patientInfo.txt), off-machine data number (ncId2SampleID.txt) and genotyping results (report.xls). Sample information includes sample name, sample number, gender, age, sample type, date of sample receipt, and inspection unit. Genotyping results include GC_Score, etc., combined with the gene database to obtain positive genotype information.

(4) Run the script to query the disease information and SNP information in the gene database, and calculate the positive incidence rate, comprehensive risk coefficient and weighted positive incidence rate (the calculation formula is as follows), and then call the LaTeX template file.

2) Calculation of positive incidence rate:

Incidence is sex-related:

Male: positive incidence rate = {(positive risk coefficient - 1) × sex risk coefficient + 1} × population incidence rate

The incidence rate has nothing to do with gender: positive incidence rate = positive risk coefficient × population incidence rate

3) If the disease has multiple mutation sites:

(5) Set filter conditions, including the minimum value of the comprehensive risk coefficient minRisk (the default is 1, if necessary, the setting cannot be less than 1), the minimum value of GCScore minGCScore (the default is 0, if necessary, the setting cannot be less than 0), the population SNP positive rate The maximum value of maxMutRate (the default is 1, if you need to set it cannot be greater than 1), the maximum value of the detected SNP frequency maxFreq (the default is 1, if you need to set it cannot be greater than 1).

(6) Run the program to output the RST000000000.report.tex file and some statistical files, including statistical information on diseases and SNPs, and statistics on high-risk, medium-risk, and low-risk diseases.

(7) Use LaTeX to compile and run the RST000000000.report.tex document to generate a PDF gene detection report RST000000000.report.pdf.

Referring to FIG. 5 , FIG. 5 is a structural diagram of an embodiment of the device for automatically generating a genetic test report according to the present invention. The device includes: a first acquisition module 101 , a second acquisition module 102 and a report generation module 103 .

The first acquisition module 101 is used to acquire the genetic information and sample information of the subject.

Genetic information refers to the information that organisms pass from parent to offspring, or from cell to cell each time each cell divides, in order to copy the same thing as itself, that is, the sequence of base pairs. The genetic information here may be genetic information representing individual differences, genetic information of DNA mutations, or genetic information related to genetic diseases, etc. The sample information is mainly the basic situation information of the tested object, such as name, gender, age, sample type, testing date, testing unit, and so on.

The second acquiring module 102 is used to query the gene database through the genetic information, and acquire the characteristic information corresponding to the genetic information, and the gene database stores the correspondence between the genetic information and the characteristic information.

Representation information refers to the performance of individual differences that can be represented on the surface of organisms and can be observed based on genetic information, including but not limited to appearance, height, weight, skin color, personality, etc.

Since the gene database stores the correspondence between the genetic information and the characterization information, the characterization information corresponding to the genetic information can be obtained by querying the gene database through the genetic information.

The report generation module 103 is used to call the standardized template of the gene detection report, import the sample information and the characterization information corresponding to the genetic information into the standardized template, and automatically generate the gene detection report.

The standardized template of the genetic testing report is created according to the preset requirements. After obtaining the sample information and characterization information, the standardized template can be called to automatically generate the genetic testing report.

The embodiment of the present invention obtains the genetic information and sample information of the subject to be tested; queries the gene database through the genetic information to obtain the characterization information corresponding to the genetic information; calls the standardized template of the gene detection report, and compares the sample information and the characterization information corresponding to the genetic information The information is imported into the standardized template, and the genetic testing report is automatically generated. After the characterization information is obtained through the genetic information, the standard template is called, and after the sample information and characterization information are imported into the standard template, the genetic test report can be automatically generated, so there is no need for manual entry, which can save a lot of time, avoid human errors, and ensure accuracy. Moreover, the gene database can update the corresponding information in time according to new research findings, so that the gene test report can be updated in time.

Referring to FIG. 6 , if the standardized template of the gene detection report has not been created in advance, the device further includes: a first determination module 201 and a writing module 202 .

The first determination module 201 is used to determine the format of the standardized template of the gene detection report.

The writing module 202 is used to write the standardized template of the gene detection report by using LaTeX source code.

LaTeX (transliteration "La Taihe") is a typesetting system based on TEX. Using this format, users can give full play to the powerful functions provided by TeX even if they have no knowledge of typesetting and programming. Even produce many book-quality prints in a few hours. It is therefore well suited for producing high print quality technical and mathematical documents, and the system is equally suitable for producing all other kinds of documents, from simple letters to complete books.

In this embodiment, by using LaTeX source code to write standardized templates, batch processing can be performed to realize automatic generation of genetic testing reports.

In practical applications, in addition to using LaTeX source code to write standardized templates, other plain text source codes can also be used to write standardized templates.

Referring to Fig. 7, when the genetic information is the genotyping result, the characterization information is the disease information, and the gene database is the disease gene database, the report generation module 103 includes: a call unit 1031, an import unit 1032, a setting unit 1033, an operation unit 1034 and a generation Unit 1035.

The calling unit 1031 is used to call the standardized template of the gene detection report.

The import unit 1032 is used for importing the sample information and the disease information corresponding to the genotyping result into the standardized template.

Genotyping is the technique of determining an individual's genotype using biological assays. Some of the commonly used genotyping techniques are: restriction fragment length polymorphism (RFLP), terminal restriction length polymorphism (t-RFLP), amplified fragment length polymorphism (AFLP), multiplex ligation probe amplification (MLPA), single nucleotide polymorphism (SNP), etc. Genotyping analysis can diagnose genetic variation caused by diseases, such as microsatellite sequence instability (MSI), trisomy (Trisomy), aneuploidy (Aneuploidy), loss of heterozygosity (LOH), etc.; microsatellite sequence instability And loss of heterozygosity is related to the tumor cell genotype of colon cancer, breast cancer, and cervical cancer; the trisomy of chromosome 21 is a common aneuploidy, and the clinical manifestation is Down Syndrome.

The setting unit 1033 is used to set the screening conditions related to the disease.

The running unit 1034 is used to run and generate the plain text file of the gene detection report according to the screening conditions related to the disease, and obtain the plain text file of the gene detection report.

The generation unit 1035 is used to generate a genetic detection report in a portable file format PDF from the plain text file of the genetic detection report.

The genetic testing report may include disease information corresponding to genotyping results, as well as statistics of high-risk, medium-risk, and low-risk diseases.

Through this embodiment, a gene detection report in PDF format with detailed disease information and related statistical documents can be obtained.

Referring to FIG. 8 , when the gene database has not been established, the device further includes: an extraction module 301 , a second determination module 302 and an establishment module 303 .

The extraction module 301 is used to extract the required data information related to the genetic information from literature or databases.

The second determination module 302 is used to determine the data format of the data information;

The establishment module 303 is used to establish the gene database according to the data information and data format.

According to this embodiment, a gene database can be constructed.

The above is only the embodiment of the present invention, and does not limit the patent scope of the present invention. Any equivalent structure or equivalent process conversion made by using the description of the present invention and the contents of the accompanying drawings, or directly or indirectly used in other related technologies fields, all of which are equally included in the scope of patent protection of the present invention.

Claims (8)

1. A method for automatically generating a gene detection report, characterized in that the method comprises: Obtain the genetic information and sample information of the subject; Querying a gene database through the genetic information to obtain characterization information corresponding to the genetic information, and the genetic database stores the correspondence between the genetic information and the characterization information; Invoking a standardized template for a genetic testing report, and importing the sample information and characterization information corresponding to the genetic information into the standardized template to automatically generate a genetic testing report; The genetic information is the sequence of base pairs; the sample information is the basic information of the subject; the characterization information is the performance of individual differences that can be represented on the surface of organisms and can be observed according to the genetic information ; The step of calling the standardized template of the gene detection report, and importing the sample information and the characterization information corresponding to the genetic information into the standardized template, before the step of automatically generating the gene detection report, includes: Determine the format of the standardized template of the genetic testing report; The standardized template of the genetic testing report was written using LaTeX source code. 2. The method according to claim 1, wherein the genetic information is a genotyping result, the characterization information is disease information, and the gene database is a disease gene database. 3. The method according to claim 2, wherein the standardized template of the genetic testing report is called, and the sample information and the characterization information corresponding to the genetic information are imported into the standardized template to automatically generate The steps of genetic testing report include: calling the standardized template of the genetic testing report; importing the sample information and the disease information corresponding to the genotyping result into the standardized template; Set disease-related screening conditions; According to the screening conditions related to the disease, run the plain text file for generating the gene detection report to obtain the plain text file of the gene detection report; The plain text file of the genetic detection report is generated into a genetic detection report in a portable file format PDF. 4. The method according to any one of claims 1 to 3, characterized in that, before the step of querying the gene database through the genetic information and obtaining the characterization information corresponding to the genetic information, the method includes: Extracting the required data information related to the genetic information from the literature or database; Determine the data format of the data information; The gene database is established according to the data information and the data format. 5. A device for automatically generating a gene detection report, characterized in that the device comprises: The first obtaining module is used to obtain the genetic information and sample information of the subject; The second acquisition module is used to query a gene database through the genetic information, and obtain the representation information corresponding to the genetic information, and the genetic database stores the correspondence between the genetic information and the representation information; The report generation module is used to call the standardized template of the genetic detection report, and import the sample information and the characterization information corresponding to the genetic information into the standardized template to automatically generate the genetic detection report; The genetic information is the sequence of base pairs; the sample information is the basic information of the subject; the characterization information is the performance of individual differences that can be represented on the surface of organisms and can be observed according to the genetic information ; The device also includes: The first determination module is used to determine the format of the standardized template of the genetic detection report; The writing module is used to write the standardized template of the gene detection report by adopting the LaTeX source code of LaTeX. 6. The device for generating a gene detection report according to claim 5, wherein the genetic information is a genotyping result, the characterization information is disease information, and the gene database is a disease gene database. 7. The device according to claim 6, wherein the report generating module comprises: A calling unit, used to call the standardized template of the gene detection report; an import unit, configured to import the sample information and disease information corresponding to the genotyping result into the standardized template; A setting unit, used to set the screening conditions related to the disease; An operating unit, configured to run the plain text file for generating the gene detection report according to the disease-related screening conditions to obtain the plain text file of the gene detection report; The generation unit is used to generate the genetic detection report in the portable file format PDF from the plain text file of the genetic detection report. 8. The device according to any one of claims 5 to 7, characterized in that the device further comprises: An extraction module, used to extract the required data information related to the genetic information from literature or databases; A second determining module, configured to determine the data format of the data information; The establishment module is used to establish the gene database according to the data information and the data format.