CN109754856A - Automatically generate method and device, the electronic equipment of genetic test report - Google Patents
Automatically generate method and device, the electronic equipment of genetic test report Download PDFInfo
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Abstract
The invention discloses a kind of method and devices for automatically generating genetic test report, electronic equipment, comprising: obtains the hereditary information and sample information of subject, the sample information includes variation comment file, and the variation comment file includes gene annotation information；Choose genetic test report template；Screening and filtering condition is set；According to the screening and filtering condition, Service functions are inquired, obtain annotation query result, inquiry variation comment file obtains variation annotation result；According to annotation query result and variation annotation as a result, automatically generating genetic test report according to selected genetic test report template.The present invention can automatically generate cancer gene examining report, and science is accurate.
Description
Technical field
The present invention relates to technical field of biological information, particularly relate to a kind of method and dress for automatically generating genetic test report
It sets, electronic equipment.
Background technique
In recent years, the disease incidence of China's malignancy disease constantly rises, and medical research shows that the morbidity of malignant tumour is former
It is related with many factors such as heredity, external environment, mental element, immune function because of complexity, the treatment method of malignant tumour with control
Therapeutic effect also varies with each individual.With deepening continuously for gene molecule level research, more and more tumour cell signal path quilts
It was found that a large amount of clinical researches show that amplification/mutation/expression status of the specific gene in access and targeting, chemotherapeutics have
Effect property is closely related, therefore, is detected by cancer gene, can provide early screening and prevention for people at highest risk, for patient
More efficiently therapeutic scheme is formulated for doctor.
Genetic test report is the gene showed in a manner of being easy to understand for subject and clinical research personnel
Testing result not only includes the direct result of genetic test, further includes interpretation, disease risks prompt and prevention to testing result
It is recommended that etc., for subject and reference for clinicians, there is important practical value.
Summary of the invention
In view of this, it is an object of the invention to propose it is a kind of automatically generate genetic test report method and device, electricity
Sub- equipment, can automatically generate cancer gene examining report, and science is accurate.
Based on above-mentioned purpose, the present invention provides a kind of methods for automatically generating genetic test report, comprising:
The hereditary information and sample information of subject are obtained, the sample information includes variation comment file, the variation
Comment file includes gene annotation information；
Choose genetic test report template；
Screening and filtering condition is set；
According to the screening and filtering condition, Service functions are inquired to obtain annotation query result and inquire the change
Different comment file obtains variation annotation result；
According to the annotation query result and variation annotation as a result, being given birth to automatically according to the genetic test report template
It is reported at genetic test.
Optionally, the screening and filtering condition include: phenotype, hereditary pattern, the pathogenic, Service functions of variation,
The assortment of genes, variation type, gene.
Optionally, the Service functions include dbSNP database, ClinVar database, public crowd's frequency number
According to library, HPO database；
The HPO database is used to filter out corresponding pathogenic base from the variation comment file according to the phenotype
Cause；
According to the screening and filtering condition, the HPO database, dbSNP database, ClinVar database, public is inquired
Crowd's frequency database therefrom obtains the genetic mutation-clinical related information for meeting the screening and filtering condition；
According to the Disease-causing gene and genetic mutation-clinical related information, obtain meeting institute in the variation comment file
State the variation annotation result of screening and filtering condition.
Optionally, the genetic test reporting modules include hereditary tumor genetic test report template and tumour medication base
Because of examining report template.
The embodiment of the present invention also provides a kind of device for automatically generating genetic test report, comprising:
Loading module, for obtaining the hereditary information and sample information of subject, the sample information includes variation annotation
File, the variation comment file includes gene annotation information；
Module is chosen, for choosing genetic test template；
Setup module, for screening and filtering condition to be arranged；
Enquiry module inquires Service functions according to the screening and filtering condition, to obtain annotation query result,
The variation comment file is inquired, variation annotation result is obtained；
Report generation module, for being annotated according to the annotation query result and the variation as a result, according to the gene
Examining report template automatically generates genetic test report.
Optionally, the screening and filtering condition include: phenotype, hereditary pattern, the pathogenic, Service functions of variation,
The assortment of genes, variation type, gene.
Optionally, the Service functions include dbSNP database, ClinVar database, public crowd's frequency number
According to library, HPO database；
The HPO database is used to filter out corresponding pathogenic base from the variation comment file according to the phenotype
Cause；
According to the screening and filtering condition, the HPO database, dbSNP database, ClinVar database, public is inquired
Crowd's frequency database therefrom obtains the genetic mutation-clinical related information for meeting the screening and filtering condition；
According to the Disease-causing gene and genetic mutation-clinical related information, obtain meeting institute in the variation comment file
State the variation annotation result of screening and filtering condition.
Optionally, the genetic test reporting modules include hereditary tumor genetic test report template and tumour medication base
Because of examining report template.
The embodiment of the present invention also provides a kind of electronic equipment, including memory, processor and storage are on a memory and can
The computer program run on a processor, the processor realize the method when executing described program.
From the above it can be seen that the method and device provided by the invention for automatically generating genetic test report, electronics
Equipment chooses genetic test report template by obtaining the hereditary information and sample information of subject；Screening and filtering item is set
Part；According to screening and filtering condition, Service functions are inquired, annotation query result is obtained from Service functions, is looked into
Variation comment file is ask, the variation annotation result for meeting screening and filtering condition is obtained；According to annotation query result and variation annotation
As a result, automatically generating genetic test report according to selected genetic test report template.The present invention can automatically generate cancer gene
Examining report, science are accurate.
Detailed description of the invention
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 technical description to be briefly described, it should be apparent that, the accompanying drawings in the following description is only this
Some embodiments of invention for those of ordinary skill in the art without creative efforts, can be with
It obtains other drawings based on these drawings.
Fig. 1 is the method flow schematic diagram of the embodiment of the present invention；
Fig. 2 is the apparatus structure schematic diagram of the embodiment of the present invention.
Specific embodiment
To make the objectives, technical solutions, and advantages of the present invention clearer, below in conjunction with specific embodiment, and reference
Attached drawing, the present invention is described in more detail.
It should be noted that all statements for using " first " and " second " are for differentiation two in the embodiment of the present invention
The non-equal entity of a same names or non-equal parameter, it is seen that " first " " second " only for the convenience of statement, does not answer
It is interpreted as the restriction to the embodiment of the present invention, subsequent embodiment no longer illustrates this one by one.
Fig. 1 is the method flow schematic diagram of the embodiment of the present invention.As shown, provided in an embodiment of the present invention automatically generate
The method of genetic test report, comprising:
S10: the hereditary information and sample information of subject are obtained；
Hereditary information refers to biology to replicate inhereditary material identical with oneself, passing to filial generation or each cell by parental generation
Pass to the information of cell when division by cell every time, i.e., the putting in order of base-pair (or refers to the deoxynucleotide of DNA molecular
It puts in order).
Sample information includes the personal essential information of subject, detection essential information, detection sample information etc..It is personal basic
Information includes the personal essential information such as name, gender, age, clinical diagnosis, treatment history, family history.Detecting essential information includes
Essential information detects in detection time, testing agency etc..
Detection sample information is the gene annotation information of oncogene detection pattern detection result, and oncogene detects sample
After the completion of detection, the variation comment file of gene annotation information is generated using gene annotation tool, is recorded in the comment file that makes a variation
The annotation information of the variant sites of sample, annotation information include but is not limited to phred mass value, allele status, equipotential base
Because of frequency, variation classification, hereditary pattern classification, genetic marker, transcript mark, (HGVSc indicates human gene to HGVSc mark
Tissue variation association name DNA reference sequences), HGVSp (HGVSp indicate human genome variation association name protein reference
Sequence), exon initial position, exon final position, exon number, introne initial position, introne final position,
Introne number number, father/mother's detecting state, ACMG hereditary variation classifying rules etc..
S11: genetic test report template is chosen；
In the embodiment of the present invention, genetic test reporting modules include that hereditary tumor genetic test report template and tumour are used
The report templates such as medicine genetic test report template.
Wherein, hereditary tumor genetic test report template is divided into several report subtemplates according to disease type, such as
Hereditary breast cancer ovarian cancer syndrome genetic test report template, heredity colorectal cancer genetic test report template, heredity
Property gastric cancer genetic test report template etc., each template generally comprises variation testing result table, and the meter reading of variation solution, genetic mutation are general
Want the contents such as table, indicating risk content, sample Quality Control result.
Tumour medication genetic test report template is divided into several report subtemplates according to disease type, and each template is generally wrapped
Include the contents such as variation testing result table, targeted drug table, chemotherapeutics table, prognosis evaluation table, sample Quality Control table.
S12: setting screening and filtering condition；
Screening and filtering condition includes: phenotype, hereditary pattern, make a variation pathogenic, Service functions, the assortment of genes
(Panel), variation type, gene etc..
Phenotype condition is for selecting specific disease type.Such as breast cancer, the then genetic test generated may be selected in phenotype
Report only carries out analysis interpretation to the related genes variants of breast cancer.
Hereditary pattern condition is for selecting hereditary pattern, including autosomal recessive, compound recessive, the chain dominant, X of X to connect
Lock recessiveness etc..Such as: the sample of analysis HSD10 mitochondrial disease, hereditary pattern select X chain dominant, may filter that other something lost
Information of the arq mode without concern, directly obtains the chain dominant genetic mutation of X, saves user and interprets sample time.
The pathogenic condition that makes a variation is to utilize the variation intelligent decision based on ACMG hereditary variation classification standard and guide exploitation
System carries out pathogenic filtering to the variation for meeting Mendelian inheritance disease sample.The pathogenic condition that makes a variation includes pathogenic, possible
It is pathogenic, equivocal, may be benign and benign etc..
Service functions include dbSNP database, ClinVar database, public crowd's frequency database.Wherein,
DbSNP database, ClinVar database, public crowd's frequency database are to disclose more authoritative database, database tool
Hold in vivo without being described in detail.
DbSNP database, ClinVar database and public crowd's frequency database include multiple classifying type databases,
Specific classifying type database is selected, the interpretation that can be made a variation in aid sample.For example, public crowd's frequency database includes thousand people
The genome whole world, thousand human genome East Asia, the whole world ESP6500, ExAC database, the whole world gnomAD, the East Asia gnomAD, gnomAD
The databases such as South Asia can be carried out the setting of variation crowd's frequency by above public crowd's frequency database, filter out and compare
Variation in crowd or general population, helps to assess the potential pathogenic of the variation.
Assortment of genes condition is used to select the assortment of genes of concern, to filter out target area or the concern base of user's concern
Cause.
Variation type condition is for selecting variation type, to filter out the variation type of concern.Variation type includes but not
It is limited to acceptor splicing site variation, donor splicing site variation, frameshift mutation, terminator codon acquisition, terminator codon missing, initiation codon
Son missing, missense mutation, nonsense mutation, same sense mutation, encoder block insertion, encoder block missing, montage region mutagenesis, 5 ' _ UTR become
It is different, 3 ' _ UTR variation, introne variation, upstream gene variation, downstream gene variation etc..
Gene condition is used to select the gene of concern, to filter out the gene type of concern.
S13: according to screening and filtering condition, inquiring Service functions, and annotation is obtained from Service functions and is looked into
It askes as a result, inquiry variation comment file, the variation that acquisition meets screening and filtering condition from variation comment file annotate result；
Service functions except include dbSNP database, ClinVar database, in addition to public crowd's frequency database,
It further include human phenotype standard term alliance's (HPO) database reconciliation read from database, wherein HPO database is well known data
Library.
HPO database is used to be filtered out from a large amount of variant sites in variation comment file according to the phenotype condition of setting
Disease-causing gene variation relevant to disease described in phenotype condition.
According to the phenotype of setting, hereditary pattern, make a variation pathogenic, the assortment of genes, variation type, gene condition, inquires HPO
Database, dbSNP database, ClinVar database, public crowd's frequency database etc. therefrom obtain and meet screening and filtering item
Genetic mutation-clinical related information of part.The genetic test report being subsequently generated only embodies base relevant to screening and filtering condition
Because of variation information and its interpret information and clinical information.
According to HPO database, dbSNP database, ClinVar database, public crowd's frequency database query result,
The annotation information for meeting every screening and filtering condition in variation comment file is obtained, which includes but is not limited to gene mark
The information such as knowledge, variation mark, genetic mutation mark.
Disease-is preserved in unscrambling data library introduces tables of data, gene-disease-bibliography tables of data, gene-disease-
Indicating risk tables of data, variation tables of data, variation-proof data table, variation-targeted drug tables of data, variation-targeted drug are treated
Imitate tables of data, variation-chemotherapeutics tables of data, variation chemotherapeutics-sensitive data table, variation chemotherapeutics-side effect number
According to table, variation-prognosis evaluation tables of data etc..Disease mark and ACMG variation intelligent decision in tables of data can be introduced according to disease-
Genetic marker query gene-disease-the risk for the result (it is pathogenic or doubtful pathogenic for making a variation) that system judges genetic mutation mentions
Show tables of data, carries the corresponding disease risks suggestion content of certain genetic mutation to obtain certain disease；According to disease mark and base
Because variation identifies query gene-disease-bibliography tables of data, to obtain reference corresponding with the genetic mutation of certain disease mark
Literature content.Inquiry variation tables of data is identified according to variation, to obtain corresponding variation record；Inquiry variation-is identified according to variation
Proof data table identifies corresponding variation grade proof data to obtain and make a variation；Inquiry variation-targeting medicine is identified according to variation
Object tables of data identifies corresponding targeted drug title to obtain and make a variation；Become according to variation mark and targeted drug mark inquiry
Iso- targeting medicament curative effect tables of data identifies corresponding clinical drug curative effect content to obtain and make a variation；According to variation mark inquiry
Variation-chemotherapeutics tables of data identifies corresponding chemotherapeutics title to obtain and make a variation；According to variation mark and chemotherapeutics
Mark inquiry chemotherapeutics-sensitive data table, to obtain prediction sensibility corresponding with chemotherapeutics；According to variation mark and
Chemotherapeutics mark inquiry chemotherapeutics-side effect tables of data, to obtain prediction side effect content corresponding with chemotherapeutics；Root
Inquiry variation-prognosis evaluation tables of data is identified according to variation, identifies corresponding prognosis evaluation content to obtain and make a variation；
Individually below to the data of hereditary tumor genetic test report template and tumour medication genetic test report template
Source is illustrated.
1, hereditary tumor genetic test report template
The template includes variation testing result table, variation solution meter reading, genetic mutation summary table, indicating risk content, sample
Quality Control result etc..
1) variation testing result table includes gene, variation, mode of inheritance, gene subprovince, heterozygosis/homozygosis, family members' verifying knot
The data item such as fruit, variation type.Wherein, the data content of gene data item is infused according to the variation for meeting every screening and filtering condition
The genetic marker of annotations part (the variation comment file for meeting every screening and filtering condition is each meant with lower variation comment file) obtains
It takes；The data content for the data item that makes a variation is identified according to the variation of variation comment file and is obtained；In the data of mode of inheritance data item
Hold and is obtained according to the hereditary pattern condition of setting；The data content of gene subprovince data item according to variation comment file exon
Initial position, exon final position, total exon number, introne initial position, introne final position include subnumber etc. and obtain
It takes；Heterozygosis/homozygosis data item data content is obtained according to the allele status of variation comment file；Family members' verification result number
Determined according to the data content of item according to father/mother detecting state of variation comment file (if father/mother's detecting state not detect,
Family members' verification result is that father/mother does not detect；If father/mother's detecting state is not detect the variation, family members' verification result is father/mother
The variation is not carried；If father/mother's detecting state is to detect the variation, family members' verification result is the change of father/mother's heterozygosis or homozygosis
Metachromatic state)；The data content of variation type data item is classified according to the variation of variation comment file to be obtained.
2) meter reading of variation solution includes variation, the data item such as the doubtful Zhi Bing clinical meaning of of causing a disease.Wherein, make a variation data item
Data content is identified according to the variation of variation comment file and is obtained；Cause a disease it is doubtful it is pathogenic clinical meaning data item data content
According to the ACMG hereditary variation classification rule acquisition of variation comment file.
3) genetic mutation summary table include gene, cause a disease, it is doubtful cause a disease, clinical meaning is unknown, the doubtful number such as benign, benign
According to item.Wherein, the data content of gene data item is obtained according to the genetic marker of variation comment file, pathogenic, doubtful to cause a disease, face
Bed meaning is unknown, doubtful benign, benign data content is classified according to the variation of variation comment file obtains.
4) indicating risk content includes the introduction of disease generality, genetic mutation prompt disease risks content, in bibliography
Hold.Wherein, the introduction of disease generality is to identify inquiry disease-according to disease to introduce tables of data acquisition disease description content；Gene
Variation prompt disease risks content be according in genetic mutation summary table it is pathogenic doubtful pathogenic data item query gene-disease-
Indicating risk tables of data obtain, if cause a disease doubtful pathogenic data item be zero, that is, be not necessarily to query gene-disease-indicating risk data
The genetic test report of table, generation does not embody genetic mutation suggestion content；Bibliography content is inquired according to gene data item
Gene-disease-bibliography tables of data obtains corresponding bibliography content.
5) sample Quality Control is the result is that obtain sample Quality Control as a result, for assessing using analysis tool based on gene sequencing result
The quality of sequencing result, Quality Control result will affect downstream data analysis.
2, tumour medication genetic test report template
The template includes variation testing result table, targeted drug table, chemotherapeutics table, prognosis evaluation table etc..
1) variation testing result table includes the data item such as gene, variation, gene subprovince, frequency.Wherein, gene data item
Data content is obtained according to the genetic marker of variation comment file；The data content for the data item that makes a variation is according to variation comment file
Variation mark obtains；Exon initial position of the data content of gene subprovince data item according to variation comment file, exon
Final position, total exon number, introne initial position, introne final position include the acquisition such as subnumber；Frequency data item
Data content is obtained according to the gene frequency item of variation comment file.
2) targeted drug table include gene, variation, prediction sensibility, targeted drug, clinical efficacy parsing, Evidence grade,
The data item such as bibliography.Wherein, the data content of gene data item is obtained according to the genetic marker item of variation comment file；Become
The data content of different data item is identified according to the variation of variation comment file and is obtained；Predicting the data content of sensitive data item is
It is obtained according to the data content of variation data item and disease data item inquiry variation-targeting medicament curative effect tables of data；Targeted drug
The data content of data item is obtained according to data content inquiry variation-targeted drug tables of data of variation data item；Clinic is treated
The data content of effect parsing data item is treated according to the data content and disease mark inquiry variation-targeted drug of variation data item
Tables of data is imitated to obtain；The data content of Evidence grade data item inquires variation-evidence according to variation data item and disease data item
Tables of data obtains；Bibliography is obtained according to the data content query gene-variation-bibliography tables of data of variation data item
It takes.
3) chemotherapeutics table includes gene, variation, chemotherapeutics, prediction sensibility, prediction side effect, Evidence grade, ginseng
Examine the data item such as document.Wherein, the data content of gene data item is obtained according to the genetic marker of variation comment file；Variance
It is identified and is obtained according to the variation of variation comment file according to the data content of item；The data content of chemotherapeutics data item is according to change
Data content inquiry variation-chemotherapeutics tables of data of different data item obtains；The data content for predicting sensitive data item is root
It is obtained according to the data content and disease data item inquiry chemotherapeutics-sensitive data table of variation data item；Predict side effect number
Data content according to item is the data content and disease data item inquiry chemotherapeutics-side effect tables of data according to variation data item
It obtains；The data content of Evidence grade data item is obtained according to variation data item and disease data item inquiry variation-proof data table
It takes；Bibliography is obtained according to the data content query gene-variation-bibliography tables of data of variation data item.
4) prognosis evaluation table includes the data item such as gene, variation, prognosis evaluation, Evidence grade, bibliography.Wherein, base
Because the data content of data item is obtained according to the genetic marker of variation comment file；The data content for the data item that makes a variation is according to variation
The variation of comment file, which identifies, to be obtained；The data content of prognosis evaluation data item is inquired according to the data content of variation data item to be become
Iso- prognosis evaluation tables of data obtains；The data content of Evidence grade data item is inquired according to variation data item and disease data item
Variation-proof data table obtains；Bibliography is data content query gene-variation-bibliography according to variation data item
Tables of data obtains.
S14: it is annotated according to the variation of the annotation query result of each Service functions and variation comment file as a result, pressing
According to selected genetic test report template, genetic test report is automatically generated.
The annotation inquiry of the variation annotation result and inquiry Service functions that are obtained according to inquiry variation comment file
As a result, the selected genetic test of the corresponding importing of the annotation query result of variation annotation result and Service functions is reported
Template automatically generates genetic test report；The report content of the genetic test report of generation includes testing result and its interpretation, target
To drug and chemotherapeutics interpretation, disease risks prompt and preventive suggestions etc., for subject and reference for clinicians.
Fig. 2 is the apparatus structure schematic diagram of the embodiment of the present invention.As shown, provided in an embodiment of the present invention automatically generate
The device of genetic test report, comprising:
Loading module, for obtaining the hereditary information and sample information of subject；
Sample information includes the personal essential information of subject, detection essential information, detection sample information etc..Detect sample
Information is the gene annotation information of oncogene detection pattern detection result, after the completion of oncogene detects pattern detection, is utilized
Gene annotation tool generates the variation comment file of the gene annotations information such as including genotype information, records in the comment file that makes a variation
The gene annotation information of the variant sites of sample.
Module is chosen, for choosing genetic test template；
In the embodiment of the present invention, genetic test reporting modules include that hereditary tumor genetic test report template and tumour are used
The report templates such as medicine genetic test report template.
Setup module, for screening and filtering condition to be arranged；
The screening and filtering condition includes: phenotype, hereditary pattern, make a variation pathogenic, Service functions, genome
Conjunction, variation type, gene etc..
Enquiry module inquires Service functions, from biomedical data for the screening and filtering condition according to setting
Annotation query result is obtained in library, inquiry variation comment file obtains from variation comment file and meets screening and filtering condition
Variation annotation result；
The Service functions include dbSNP database, ClinVar database, public crowd's frequency database,
HPO database conciliates read from database.HPO database is used for according to the phenotype condition of setting from the big quantitative change in variation comment file
Disease-causing gene relevant to disease described in phenotype condition is filtered out in ectopic sites.
According to every screening and filtering condition of setting, HPO database, dbSNP database, ClinVar database, public affairs are inquired
Crowd's frequency database altogether therefrom obtains the genetic mutation-clinical related information for meeting screening and filtering condition.The base being subsequently generated
Because examining report only embodies genetic mutation information relevant to screening and filtering condition and its interprets information and clinical information.
According to HPO database, dbSNP database, ClinVar database, public crowd's frequency database query result,
The annotation information for meeting every screening and filtering condition in variation comment file is obtained, which includes but is not limited to gene mark
The information such as knowledge, variation mark, genetic mutation mark.
Report generation module, for the change for annotating query result and the comment file that makes a variation according to each Service functions
Different annotation is as a result, automatically generate genetic test report according to selected genetic test report template.
Based on above-mentioned purpose, the embodiment of the present invention also proposed the side that genetic test report is automatically generated described in a kind of execution
One embodiment of the device of method.Described device includes:
One or more processors and memory.
The device that the method for genetic test report is automatically generated described in the execution can also include: input unit and output
Device.
Processor, memory, input unit and output device can be connected by bus or other modes.
Memory as a kind of non-volatile computer readable storage medium storing program for executing, can be used for storing non-volatile software program,
Non-volatile computer executable program and module, such as the method for automatically generating genetic test report in the embodiment of the present invention
Corresponding program instruction/module.Processor is by running non-volatile software program, instruction and mould stored in memory
Block, thereby executing the various function application and data processing of server, that is, that realizes above method embodiment automatically generates base
Because of the method for examining report.
Memory may include storing program area and storage data area, wherein storing program area can storage program area, extremely
Application program required for a few function；Storage data area can be stored automatically generates genetic test report according to execution
The device of method uses created data etc..In addition, memory may include high-speed random access memory, can also wrap
Include nonvolatile memory, for example, at least a disk memory, flush memory device or other non-volatile solid state memories
Part.In some embodiments, it includes the memory remotely located relative to processor that memory is optional, these remote memories can
To pass through network connection to member user's behavior monitoring device.The example of above-mentioned network includes but is not limited to internet, in enterprise
Portion's net, local area network, mobile radio communication and combinations thereof.
Input unit can receive the number or character information of input, and generates and automatically generate genetic test report with execution
Method device user setting and function control related key signals input.Output device may include the display such as display screen
Equipment.
One or more of module storages in the memory, are executed when by one or more of processors
When, execute the method for automatically generating genetic test report in above-mentioned any means embodiment.It is automatically generated described in the execution
The embodiment of the device of the method for genetic test report, technical effect are same or similar with aforementioned any means embodiment.
The embodiment of the invention also provides a kind of non-transient computer storage medium, the computer storage medium is stored with
The place of the operation of the list items in above-mentioned any means embodiment can be performed in computer executable instructions, the computer executable instructions
Reason method.The embodiment of the non-transient computer storage medium, technical effect it is identical as aforementioned any means embodiment or
Person is similar.
Finally, it should be noted that those of ordinary skill in the art will appreciate that realizing the whole in above-described embodiment method
Or part process, it is that related hardware can be instructed to complete by computer program, the program can be stored in a calculating
In machine read/write memory medium, the program is when being executed, it may include such as the process of the embodiment of above-mentioned each method.Wherein, described
Storage medium can be magnetic disk, CD, read-only memory (Read-Only Memory, ROM) or random access memory
(Random Access Memory, RAM) etc..The embodiment of the computer program, technical effect and aforementioned any means
Embodiment is same or similar.
In addition, typically, device described in the disclosure, equipment etc. can be various electric terminal equipments, such as mobile phone, individual
Digital assistants (PDA), tablet computer (PAD), smart television etc. are also possible to large-scale terminal device, such as server, therefore this
Disclosed protection scope should not limit as certain certain types of device, equipment.Client described in the disclosure can be with electricity
The combining form of sub- hardware, computer software or both is applied in any one of the above electric terminal equipment.
In addition, being also implemented as the computer program executed by CPU, the computer program according to disclosed method
It may be stored in a computer readable storage medium.When the computer program is executed by CPU, executes and limited in disclosed method
Fixed above-mentioned function.
In addition, above method step and system unit also can use controller and for storing so that controller is real
The computer readable storage medium of the computer program of existing above-mentioned steps or Elementary Function is realized.
In addition, it should be appreciated that computer readable storage medium (for example, memory) as described herein can be it is volatile
Property memory or nonvolatile memory, or may include both volatile memory and nonvolatile memory.As example
And not restrictive, nonvolatile memory may include read-only memory (ROM), programming ROM (PROM), electrically programmable to son
ROM (EPROM), electrically erasable programmable ROM (EEPROM) or flash memory.Volatile memory may include arbitrary access
Memory (RAM), the RAM can serve as external cache.As an example and not restrictive, RAM can be with more
Kind form obtains, such as synchronous random access memory (DRAM), dynamic ram (DRAM), synchronous dram (SDRAM), double data rate SDRAM
(DDR SDRAM), enhancing SDRAM (ESDRAM), synchronization link DRAM (SLDRAM) and directly RambusRAM (DRRAM).Institute
The storage equipment of disclosed aspect is intended to the memory of including but not limited to these and other suitable type.
The device of above-described embodiment for realizing method corresponding in previous embodiment there is corresponding method to implement
The beneficial effect of example, details are not described herein.
It should be understood by those ordinary skilled in the art that: the discussion of any of the above embodiment is exemplary only, not
It is intended to imply that the scope of the present disclosure (including claim) is limited to these examples；Under thinking of the invention, above embodiments
Or can also be combined between the technical characteristic in different embodiments, step can be realized with random order, and be existed such as
Many other variations of the upper different aspect of the invention, for simplicity, they are not provided in details.
In addition, to simplify explanation and discussing, and in order not to obscure the invention, it can in provided attached drawing
It is connect with showing or can not show with the well known power ground of integrated circuit (IC) chip and other components.Furthermore, it is possible to
Device is shown in block diagram form, to avoid obscuring the invention, and this has also contemplated following facts, i.e., about this
The details of the embodiment of a little block diagram arrangements be height depend on will implementing platform of the invention (that is, these details should
It is completely within the scope of the understanding of those skilled in the art).Elaborating that detail (for example, circuit) is of the invention to describe
In the case where exemplary embodiment, it will be apparent to those skilled in the art that can be in these no details
In the case where or implement the present invention in the case that these details change.Therefore, these descriptions should be considered as explanation
Property rather than it is restrictive.
Although having been incorporated with specific embodiments of the present invention, invention has been described, according to retouching for front
It states, many replacements of these embodiments, modifications and variations will be apparent for those of ordinary skills.Example
Such as, discussed embodiment can be used in other memory architectures (for example, dynamic ram (DRAM)).
The embodiment of the present invention be intended to cover fall into all such replacements within the broad range of appended claims,
Modifications and variations.Therefore, all within the spirits and principles of the present invention, any omission, modification, equivalent replacement, the improvement made
Deng should all be included in the protection scope of the present invention.
Claims (9)
1. a kind of method for automatically generating genetic test report characterized by comprising
The hereditary information and sample information of subject are obtained, the sample information includes variation comment file, the variation annotation
File includes gene annotation information；
Choose genetic test report template；
Screening and filtering condition is set；
According to the screening and filtering condition, Service functions are inquired, to obtain annotation query result, inquire the variation note
Annotations part obtains variation annotation result；
According to the annotation query result and variation annotation as a result, automatically generating base according to the genetic test report template
Because of examining report.
2. the method according to claim 1, wherein the screening and filtering condition include: phenotype, hereditary pattern,
Make a variation pathogenic, Service functions, the assortment of genes, variation type, gene.
3. according to the method described in claim 2, it is characterized in that, the Service functions include dbSNP database,
ClinVar database, public crowd's frequency database, HPO database；
The HPO database is used to filter out corresponding Disease-causing gene from the variation comment file according to the phenotype；
According to the screening and filtering condition, the HPO database, dbSNP database, ClinVar database, public crowd are inquired
Frequency database therefrom obtains the genetic mutation-clinical related information for meeting the screening and filtering condition；
According to the Disease-causing gene and genetic mutation-clinical related information, obtain meeting the sieve in the variation comment file
The variation of filter condition is selected to annotate result.
4. according to the method described in claim 3, it is characterized in that, the genetic test reporting modules include hereditary tumor base
Because of examining report template and tumour medication genetic test report template.
5. a kind of device for automatically generating genetic test report characterized by comprising
Loading module, for obtaining the hereditary information and sample information of subject, the sample information includes variation comment file,
The variation comment file includes gene annotation information；
Module is chosen, for choosing genetic test template；
Setup module, for screening and filtering condition to be arranged；
Enquiry module inquires Service functions according to the screening and filtering condition, to obtain annotation query result, inquiry
The variation comment file obtains variation annotation result；
Report generation module, for being annotated according to the annotation query result and the variation as a result, according to the genetic test
Report template automatically generates genetic test report.
6. device according to claim 5, which is characterized in that the screening and filtering condition include: phenotype, hereditary pattern,
Make a variation pathogenic, Service functions, the assortment of genes, variation type, gene.
7. device according to claim 6, which is characterized in that the Service functions include dbSNP database,
ClinVar database, public crowd's frequency database, HPO database；
The HPO database is used to filter out corresponding Disease-causing gene from the variation comment file according to the phenotype；
According to the screening and filtering condition, the HPO database, dbSNP database, ClinVar database, public crowd are inquired
Frequency database therefrom obtains the genetic mutation-clinical related information for meeting the screening and filtering condition；
According to the Disease-causing gene and genetic mutation-clinical related information, obtain meeting the sieve in the variation comment file
The variation of filter condition is selected to annotate result.
8. device according to claim 7, which is characterized in that the genetic test reporting modules include hereditary tumor base
Because of examining report template and tumour medication genetic test report template.
9. a kind of electronic equipment including memory, processor and stores the calculating that can be run on a memory and on a processor
Machine program, which is characterized in that the processor realizes the side as described in Claims 1-4 any one when executing described program
Method.
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| CN110544508A (en) * | 2019-07-29 | 2019-12-06 | 北京荣之联科技股份有限公司 | Method and device for analyzing monogenic genetic disease genes and electronic equipment |
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