CN113470776A - Genetic diagnosis system integrating data acquisition, analysis and report generation - Google Patents

Genetic diagnosis system integrating data acquisition, analysis and report generation Download PDF

Info

Publication number
CN113470776A
CN113470776A CN202110595234.5A CN202110595234A CN113470776A CN 113470776 A CN113470776 A CN 113470776A CN 202110595234 A CN202110595234 A CN 202110595234A CN 113470776 A CN113470776 A CN 113470776A
Authority
CN
China
Prior art keywords
data
module
medical history
clinical
report
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
CN202110595234.5A
Other languages
Chinese (zh)
Other versions
CN113470776B (en
Inventor
周家健
李雪飞
张永军
陈旭光
吴铁强
杨斌
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Dermatology Hospital Of Southern Medical University Guangdong Provincial Dermatology Hospital Guangdong Skin Disease Prevention Center China Leprosy Control Research Center
Original Assignee
Dermatology Hospital Of Southern Medical University Guangdong Provincial Dermatology Hospital Guangdong Skin Disease Prevention Center China Leprosy Control Research Center
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Dermatology Hospital Of Southern Medical University Guangdong Provincial Dermatology Hospital Guangdong Skin Disease Prevention Center China Leprosy Control Research Center filed Critical Dermatology Hospital Of Southern Medical University Guangdong Provincial Dermatology Hospital Guangdong Skin Disease Prevention Center China Leprosy Control Research Center
Priority to CN202110595234.5A priority Critical patent/CN113470776B/en
Publication of CN113470776A publication Critical patent/CN113470776A/en
Application granted granted Critical
Publication of CN113470776B publication Critical patent/CN113470776B/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H15/00—ICT specially adapted for medical reports, e.g. generation or transmission thereof
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/22—Indexing; Data structures therefor; Storage structures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/24—Querying
    • G06F16/245—Query processing
    • G06F16/2457—Query processing with adaptation to user needs
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/50—Mutagenesis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/60—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Epidemiology (AREA)
  • Evolutionary Biology (AREA)
  • Data Mining & Analysis (AREA)
  • General Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Public Health (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • Databases & Information Systems (AREA)
  • Primary Health Care (AREA)
  • General Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Genetics & Genomics (AREA)
  • Computational Linguistics (AREA)
  • Software Systems (AREA)
  • Molecular Biology (AREA)
  • Medical Treatment And Welfare Office Work (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The application relates to a genetic diagnosis system integrating data acquisition, analysis and report generation. The system comprises: a clinical module, a medical history module, an association module and a reporting module; the medical history module is loaded with medical history data of a patient and a plurality of groups of family data distinguished based on family labels, a plurality of identity labels are linked under the family labels, and each identity label forms association pairwise through family attributes; the correlation module is respectively connected with the clinical module and the medical history module, and the clinical data and the medical history data of the patient are correlated through the identity tags, so that a family data network can be formed by outwards expanding the family attributes with the identity tags of the patient as the center and linking the individual clinical data and the medical history data of corresponding members through the identity tags of different family members, a multi-dimensional family data network is formed, and comprehensive and accurate genetic diagnosis is realized.

Description

Genetic diagnosis system integrating data acquisition, analysis and report generation
Technical Field
The application relates to the technical field of genetic diagnosis, in particular to a genetic diagnosis system integrating data acquisition, analysis and report generation.
Background
After the human genome project of 2001 is completed, the international haplotype project and the thousand human genome project are developed successively and accumulate massive genetic variation data, particularly the thousand human genome project started in 2008, and draw the most detailed and most valuable human genome genetic polymorphism map so far. The genetic variation data provides detailed basic data for deeper understanding of genetic differences among races and individuals and correlation analysis of various diseases, and greatly promotes group genetics, human disease research, comparative genomics, pharmacogenomics and other researches. The results of human genetics research, which is focused on human genome mapping, and various advanced technical means are strongly driving the rapid development of the whole life science.
With the popularization of genetic screening technology in the medical health field, there is an increasing demand for automated report generation systems after genetic mutation review. In the existing gene detection field, each data generation and analysis result and manual review module are relatively independent, and the generation of a final report needs to be realized through manual integration. The report generation mode needs to manually look up data of each independent system, is difficult to unify in standard, complicated in rule, high in integration difficulty, easy to make mistakes, and lack of effective management, and cannot support the requirement of generating large-batch gene detection reports.
In the related art, patent document CN107220885A discloses a gene test product reporting system and method, wherein a subject selects a gene test product in the system and places an order, the front end of the system collects basic information of the subject and binds the basic information with an order, sample collection of the subject is completed by sending a sample box, sample test is completed in a laboratory, and a test result is stored in a designated storage location, so that a report generating system reads the basic information of the subject and the corresponding sample test result to generate a gene test report, and sends the gene test report to a report receiver designated by the order.
The above solution has the following drawbacks:
1. the sample sending process has the problems that the sample is damaged or the matching of the sample and the detected person is wrong;
2. the gene detection report takes single clinical data as a diagnosis basis, and has low data integration level and low diagnosis accuracy;
3. the scheme does not collect family history information of a detected person, and is difficult to diagnose genetic diseases with family aggregation tendency.
Disclosure of Invention
In order to overcome the problems in the related art, the application provides a genetic diagnosis system integrating data acquisition, analysis and report generation, and the system can utilize a correlation module to form a data network by using clinical data, medical history data and information of relatives of patients, thereby realizing comprehensive and accurate genetic diagnosis.
In a first aspect, the present application provides a genetic diagnosis system integrating data acquisition, analysis and report generation, comprising:
a clinical module, a medical history module, an association module and a reporting module;
the clinical module is used for collecting and processing clinical data of a patient; the clinical data includes: identity tags and biometric information;
the medical history module is provided with a medical history database of the patient; the medical history database comprises medical history data of the patient; the medical history data includes: the identity label, family attribute and historical diagnosis report;
the medical history database comprises a plurality of groups of family data, the family data are distinguished based on the family tags, a plurality of identity tags are linked under the family tags, and the identity tags form association in pairs through the family attributes; the family attributes include: the number of generations or relatives of blood relatives;
the report module is respectively connected with the clinical module and the medical history module, and the report module calls the clinical data and the medical history data to generate a genetic diagnosis report;
the correlation module is respectively connected with the clinical module and the medical history module and is used for correlating the clinical data with the medical history data of the patient through the identity tag.
In one embodiment, the clinical module comprises: the system comprises a clinical acquisition unit, a gene sequencing unit and a clinical data unit;
the clinical acquisition unit is used for acquiring clinical data of a patient and storing the clinical data to the clinical data unit;
the gene sequencing unit is used for carrying out gene sequence analysis on the biological information of the patient to obtain a gene sequencing result; the patient biological information includes: genetic data, phenotypic information, and patient profile;
the clinical data unit is used for storing the clinical data and the gene sequencing result to a preset position to form association.
In one embodiment, the reporting module includes: the data calling unit and the report analyzing unit;
the data calling unit calls the clinical data, the gene sequencing result and the medical history data from the clinical module and the medical history module based on the identity label and transmits the clinical data, the gene sequencing result and the medical history data to the report analysis module;
the report analysis unit forms a genetic diagnosis report based on the clinical data, the genetic sequencing results, and the medical history data, and generates a report tag associated with the genetic diagnosis report.
In one embodiment, the data invoking unit is further configured to invoke medical history data of the patient relative in combination with the identity tag, the family tag, and the family attribute.
In one embodiment, the report analysis unit performs a comprehensive analysis of the clinical and medical history data of the patient and the medical history data of the patient's relatives to focus on multigenic diseases with a propensity to family clustering.
In one embodiment, the report tag comprises: report date and report number;
the report module is connected with the correlation module, and the correlation module transmits the genetic diagnosis report to the medical history database and correlates the genetic diagnosis report with the medical history data of the patient through the identity tag.
In one embodiment, the clinical data unit stores a database of reference genomes and genetic resources;
the gene sequencing unit comprises: a data quality control subunit, a variation identification subunit and a variation annotation subunit;
the data quality control subunit evaluates the base sequencing quality in the gene data according to a window with a fixed length, and moves the window to find a preset quality control threshold position so as to obtain target sequencing data; the target sequencing data are obtained by filtering based on a preset quality control threshold;
the variation identification subunit performs sequence comparison on the target sequencing data based on a reference gene group to generate a comparison result, and performs variation identification according to the comparison result to obtain a variation site; the reference genome, comprising: hg19 genome;
and the variation annotation subunit annotates the variation sites based on a genetic resource database to obtain the gene sequencing result.
In one embodiment, the clinical data unit further stores a normal person frequency database;
the gene sequencing unit further comprises: a variant filter subunit;
the mutation filtering subunit screens out the mutation sites based on a normal person frequency database, filters out the mutation sites higher than a frequency threshold in the normal person frequency database, scores and grades the mutation sites, and filters out the mutation sites rated as a preset grade.
In one embodiment, the clinical data unit further stores a skin condition database; the skin disease database includes: a gene set related to skin diseases and corresponding skin disease gene mutation sites;
the variation filter subunit can also compare the variation sites based on the skin disease database and perform key marking on the variation sites matched with the skin disease gene mutation sites.
In one embodiment, the integrated genetic diagnostic system for data collection, analysis and report generation further comprises: an interactive front end;
the interactive front end is connected with the clinical module and the report module respectively; for receiving instructions from a user to import clinical information, query medical history data, and download a genetic diagnosis report.
The technical scheme provided by the application can comprise the following beneficial effects:
according to the scheme, the clinical data in the clinical module and the medical history data in the medical history module are associated by the association module through the patient identity tag, so that the report module can simultaneously call the current clinical data and the historical diagnosis information of the patient according to the identity tag and accurately match the identity of the patient with the biological information of the patient, thereby enlarging the data quantity and data dimensionality which can be used as a basis for genetic diagnosis and further improving the accuracy of a genetic diagnosis report; in addition, a plurality of groups of family data are stored in the medical history database, the family data are distinguished based on family tags, a plurality of identity tags are linked under the family tags, and the identity tags are pairwise correlated through family attributes, so that a family data network can be formed by outwards expanding the family attributes with the identity tags of patients as the center, the identity tags of different family members are different data nodes, and the personal clinical data and the medical history data of the corresponding members are under the different data nodes, so that the multidimensional family data network is formed; by utilizing the multidimensional family data network, any node in the data network, namely the comprehensive information of any family member, can be quickly inquired through an identity label, so that the problems that a doctor repeatedly inquires the information of a patient in the diagnosis process and the information acquisition is blocked due to inconvenience in communication of the patient are effectively avoided, the diagnosis efficiency of the doctor is improved, and the communication cost between the doctor and the patient is reduced.
It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the application.
Drawings
The foregoing and other objects, features and advantages of the application will be apparent from the following more particular descriptions of exemplary embodiments of the application, as illustrated in the accompanying drawings wherein like reference numbers generally represent like parts throughout the exemplary embodiments of the application.
FIG. 1 is a schematic structural diagram of a genetic diagnostic system integrated with data collection, analysis and report generation according to an embodiment of the present application;
FIG. 2 is a schematic diagram of a clinical module shown in an embodiment of the present application;
fig. 3 is a schematic structural diagram of a reporting module according to an embodiment of the present application.
Detailed Description
Preferred embodiments of the present application will be described in more detail below with reference to the accompanying drawings. While the preferred embodiments of the present application are shown in the drawings, it should be understood that the present application may be embodied in various forms and should not be limited to the embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the disclosure to those skilled in the art.
The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the application. As used in this application and the appended claims, the singular forms "a", "an", and "the" are intended to include the plural forms as well, unless the context clearly indicates otherwise. It should also be understood that the term "and/or" as used herein refers to and encompasses any and all possible combinations of one or more of the associated listed items.
It should be understood that although the terms "first," "second," "third," etc. may be used herein to describe various information, these information should not be limited to these terms. These terms are only used to distinguish one type of information from another. For example, first information may also be referred to as second information, and similarly, second information may also be referred to as first information, without departing from the scope of the present application. Thus, a feature defined as "first" or "second" may explicitly or implicitly include one or more of that feature. In the description of the present application, "a plurality" means two or more unless specifically limited otherwise.
In the existing gene detection field, each data generation and analysis result and manual review module are relatively independent, and the generation of a final report needs to be realized through manual integration. The report generation mode needs to manually look up data of each independent system, is difficult to unify in standard, complicated in rule, high in integration difficulty, easy to make mistakes, and lack of effective management, and cannot support the requirement of generating large-batch gene detection reports.
The patent with the publication number of CN107220885A protects a gene detection product reporting system and a method thereof, wherein, the sample is damaged or the matching of the sample and a detected person is wrong; the data integration level and the diagnosis accuracy are low; and the defect that the diagnosis of the genetic diseases with the tendency of family aggregation is difficult without collecting the family history information of the examinee.
Example one
In view of the above problems, embodiments of the present application provide a genetic diagnosis system with integration of data acquisition, analysis and report generation, which can perform comprehensive and accurate genetic diagnosis by using multidimensional information.
The technical solutions of the embodiments of the present application are described in detail below with reference to the accompanying drawings.
Fig. 1 is a schematic structural diagram of a genetic diagnosis system integrating data acquisition, analysis, and report generation according to an embodiment of the present application.
Referring to fig. 1, the data collection, analysis and report generation integrated genetic diagnosis system includes:
a clinical module, a medical history module, an association module and a reporting module;
the clinical module is used for collecting and processing clinical data of a patient; the clinical data includes: identity tags and biometric information;
the medical history module is provided with a medical history database of the patient; the medical history database comprises medical history data of the patient; the medical history data includes: the identity label, family attribute and historical diagnosis report;
the medical history database comprises a plurality of groups of family data, the family data are distinguished based on the family tags, a plurality of identity tags are linked under the family tags, and the identity tags form association in pairs through the family attributes; the family attributes include: the number of generations or relatives of blood relatives;
the report module is respectively connected with the clinical module and the medical history module, and the report module calls the clinical data and the medical history data to generate a genetic diagnosis report;
the correlation module is respectively connected with the clinical module and the medical history module and is used for correlating the clinical data with the medical history data of the patient through the identity tag.
In the embodiment of the present application, one or more of the identification number, iris information, fingerprint information and face information of the patient may be used as the identification tag of the patient, so that the corresponding patient can be accurately and uniquely identified according to the identification tag, and other information of the patient, including but not limited to personal basic information, biological information, medical history data and clinical data and medical history data of relatives thereof, may be linked through the identification tag of the patient.
In an embodiment of the present application, the clinical module collects biological information of the patient in the current genetic diagnosis process, including but not limited to genetic data, patient phenotype information, and patient chief complaints, and in the practical application process, the biological information may further include: a preliminary diagnosis result; wherein the genetic data is derived from a biological sample of the patient, such as: interstitial fluid or body fluid.
In the embodiment of the present application, the association module associates the biological information of the patient in the current genetic diagnosis process with the medical history data of the patient stored in the medical history module through the identity tag, that is, the current clinical data of the patient can be read through the identity tag of the patient, and the medical history data of the patient in the medical history database can also be called, where the medical history data includes, but is not limited to, a family tag, family attributes, and a historical diagnosis report; the family label is an identity of a family where the patient is located, and is embodied as a family number in the embodiment of the application, the family number forms a mapping relation with a plurality of identity labels, and the identity labels are family members corresponding to the family number; the family attribute is the embodiment of the relationship between different identity tags under the same family number, specifically, the family attribute can be the blood affinity generation number of different identity tags or the relationship between two identity tags.
In an embodiment of the present application, the medical history database is stored in the medical history module, the medical history database includes medical history data of a patient, and family data of a family where the patient is located, and the family data includes, but is not limited to, a family tag and medical history data of all family members under the family. In the medical history database, different families are distinguished by different family labels. Based on the medical history database, the family label of the family of the patient can be retrieved by utilizing the identity label of the patient, then the identity label of any relative of the patient is retrieved, and then the medical history data of the relative is read, so that the calling of the family medical history related information of the patient is realized.
Based on the medical history database, the identity label of the patient is used as a data node, the data node can be linked to a plurality of identity labels through one identity label to form a radiation-type data network, the data network is essentially a family data network, the data nodes, namely the identity labels, of the data network form association through family attributes, and the data nodes can also be linked to clinical data and medical history data of the patient corresponding to the identity labels through the identity labels, so that a multi-dimensional family data network is formed, and the network integrates the data of a plurality of dimensions of a plurality of members under one family.
In an embodiment of the present application, the report module is used for generating a genetic diagnosis report according to clinical data and medical history data of a patient, wherein the genetic diagnosis report includes, but is not limited to, personal basic information, gene sequencing results and genetic diagnosis results of the patient.
Furthermore, the report module can be connected with the association module, and the association module associates the genetic diagnosis report and the historical diagnosis report generated at the current time through the identity tag of the patient and stores the genetic diagnosis report and the historical diagnosis report into the medical history database, so that the medical history data of the patient in the medical history database is updated, and the reliability of the data in the medical history database is improved.
Further, when a genetic diagnosis report is generated, the date of generation of the report is used as a label to distinguish the genetic diagnosis reports.
Further, in an embodiment of the present application, the integrated genetic diagnosis system for data collection, analysis and report generation further includes: an interactive front end;
the interactive front end is connected with the clinical module and the report module respectively; for receiving instructions from a user to import clinical information, query medical history data, and download a genetic diagnosis report.
In the embodiment of the application, a user inputs the identity tag of the patient through the interactive front end, and selects a corresponding operation instruction on the interactive front end, and in the actual application process, the user instruction can be obtained by setting a virtual key on the interactive front end.
Furthermore, the interactive front end can be further provided with a camera for acquiring face information of a user and scanning a bar code or a two-dimensional code carrying a patient identity label; or a diagnosis and treatment card induction area is arranged, and the identity label of the patient is obtained by sensing the diagnosis and treatment card of the patient, so that the corresponding module is instructed to execute the corresponding action according to the identity label and a user instruction.
It should be noted that the above description of the functional implementation of the interactive front end is only an example in the embodiment of the present application, and should not be taken as a limitation to the present invention.
In the embodiment of the application, storage units are separately arranged in the clinical module, the medical history module, the association module and the report module so as to realize storage and calling of various data; in the practical application process, a data storage module can be independently arranged, and the unified management of various data is realized in a local storage or cloud storage mode.
According to the scheme shown in the embodiment of the application, the clinical data in the clinical module and the medical history data in the medical history module are associated by the association module through the patient identity tag, so that the report module can simultaneously call the current clinical data and the historical diagnosis information of the patient according to the identity tag and accurately match the identity of the patient with the biological information of the patient, the data volume and the data dimension which can be used as the basis of genetic diagnosis are enlarged, and the accuracy of a genetic diagnosis report is improved; in addition, a plurality of groups of family data are stored in the medical history database, the family data are distinguished based on family tags, a plurality of identity tags are linked under the family tags, and the identity tags are pairwise correlated through family attributes, so that a family data network can be formed by outwards expanding the family attributes with the identity tags of patients as the center, the identity tags of different family members are different data nodes, and the personal clinical data and the medical history data of the corresponding members are under the different data nodes, so that the multidimensional family data network is formed; by utilizing the multidimensional family data network, any node in the data network, namely the comprehensive information of any family member, can be quickly inquired through an identity label, so that the problems that a doctor repeatedly inquires the information of a patient in the diagnosis process and the information acquisition is blocked due to inconvenience in communication of the patient are effectively avoided, the diagnosis efficiency of the doctor is improved, and the communication cost between the doctor and the patient is reduced.
Example two
The embodiment of the present application describes the structure of the clinical module in the system shown in the first embodiment.
Fig. 2 is a schematic structural diagram of a clinical module according to an embodiment of the present application.
Referring to fig. 2, the clinical module includes: the system comprises a clinical acquisition unit, a gene sequencing unit and a clinical data unit;
the clinical acquisition unit is used for acquiring clinical data of a patient and storing the clinical data to the clinical data unit;
the gene sequencing unit is used for carrying out gene sequence analysis on the biological information of the patient to obtain a gene sequencing result; the patient biological information includes: genetic data, phenotypic information, and patient profile;
the clinical data unit is used for storing the clinical data and the gene sequencing result to a preset position to form association.
In an embodiment of the present application, the clinical acquisition module may acquire clinical data of a patient by using a form entry or a picture upload.
In an embodiment of the present application, the gene sequencing unit performs gene sequence analysis on the gene data of the patient based on one or more of Sanger sequencing technology and full exon sequencing technology, so as to obtain a gene sequencing result.
Further, in the embodiment of the present application, the gene sequencing unit can perform quality detection, data de-noising, and sequencing data analysis on the data, so as to output candidate pathogenic mutation sites and corresponding gene data as a gene sequencing result.
Illustratively, in the present embodiments, the gene sequencing unit comprises: a data quality control subunit, a variation identification subunit and a variation annotation subunit;
the data quality control subunit evaluates the base sequencing quality in the gene data according to a window with a fixed length, and moves the window to find a preset quality control threshold position so as to obtain target sequencing data; the target sequencing data are obtained by filtering based on a preset quality control threshold;
the variation identification subunit performs sequence comparison on the target sequencing data based on a reference gene group to generate a comparison result, and performs variation identification according to the comparison result to obtain a variation site; the reference genome, comprising: hg19 genome;
and the variation annotation subunit annotates the variation sites based on a genetic resource database to obtain the gene sequencing result.
In an embodiment of the application, the reference genome and the database of genetic resources are stored in a clinical data unit. In the practical application process, the reference genome adopted includes but is not limited to Hg19 genome, and GRCH37 genome or ensembl 75 genome can also be adopted; the genetic resource database employed may be one or more of an OMIM database, a COSMIC database, and a 1000genome database.
It will be appreciated that the above selection of reference genomic and genetic resource databases is merely an example in the examples of the present application and should not be taken as a limitation of the present invention.
In the examples of the present application, the quality control threshold is a criterion for evaluating the quality of base sequencing in gene data, and bases larger than the quality control threshold are identified as high-quality base sequences. It should be noted that the preset quality control threshold is a parameter set in advance by a user in the system, and is a preset value that can be adjusted according to actual requirements; in the present embodiment, Q20 is used as the quality standard for base sequencing, and the preset quality control threshold is 95%.
It should be understood that the preset quality control threshold is only an example given in the embodiments of the present application, and should not be taken as a limitation on the present invention.
Further, the clinical data unit also stores a normal human frequency database;
the gene sequencing unit further comprises: a variant filter subunit;
the mutation filtering subunit screens out the mutation sites based on a normal person frequency database, filters out the mutation sites higher than a frequency threshold in the normal person frequency database, scores and grades the mutation sites, and filters out the mutation sites rated as a preset grade.
In the embodiment of the present invention, the value of the frequency threshold is 0.01, and in the actual application process, the value of the frequency threshold may be adjusted according to actual requirements, that is, the value of the frequency threshold should not be taken as a limitation to the present invention.
In the embodiment of the present application, the mutation filtering subunit can score and grade the mutation sites by using the ACMG score of intervar, and classify the mutation sites into five types of mutation sites that are pathogenic, possibly pathogenic, mild, possibly mild, and unknown.
Further, the clinical data unit also stores a skin disease database; the skin disease database includes: a gene set related to skin diseases and corresponding skin disease gene mutation sites;
the variation filter subunit can also compare the variation sites based on the skin disease database and perform key marking on the variation sites matched with the skin disease gene mutation sites.
According to the scheme shown in the embodiment of the application, the clinical data of the patient are acquired by the clinical acquisition unit and transmitted to the gene sequencing unit, so that the gene sequence analysis is performed on the gene data of the patient to obtain a gene sequencing result, the result is stored in the clinical data unit, the result is bound with the patient through the identity label of the patient, the system can complete the calling and analysis of large-scale data through simple parameter submission, and the automation degree of the detection process is high; besides the data quality control subunit, the variation identification subunit and the variation annotation subunit, the gene sequencing unit also comprises a variation filtering subunit, so that the quality detection, data denoising and sequencing data analysis of the patient gene data can be realized, candidate pathogenic mutation sites and related genes are output, and accurate basis is provided for clinical genetic diagnosis.
EXAMPLE III
The embodiment of the present application describes a reporting module in the first embodiment.
Fig. 3 is a schematic structural diagram of a reporting module according to an embodiment of the present application.
Referring to fig. 3, the reporting module includes: the data calling unit and the report analyzing unit;
the data calling unit calls the clinical data, the gene sequencing result and the medical history data from the clinical module and the medical history module based on the identity label and transmits the clinical data, the gene sequencing result and the medical history data to the report analysis module;
the report analysis unit forms a genetic diagnosis report based on the clinical data, the genetic sequencing results, and the medical history data, and generates a report tag associated with the genetic diagnosis report.
In the examples of the present application, the above-mentioned report tags are used to distinguish genetic diagnosis reports formed at different times in the same patient.
Further, the report tag includes: report date and report number;
the report module is connected with the correlation module, and the correlation module transmits the genetic diagnosis report to the medical history database and correlates the genetic diagnosis report with the medical history data of the patient through the identity tag.
That is, in the medical history database, all the genetic diagnosis reports of the patient can be retrieved through the identity tags of the patient, the genetic diagnosis reports are distinguished according to the report date and the report number, and according to the report date or the report number, the user can screen all the genetic diagnosis reports of the patient in the system.
Further, the data calling unit is further configured to call medical history data of the patient relative in combination with the identity tag, the family tag, and the family attribute.
In the system, the family of the patient can be obtained through the identity tag of the patient, the data in the family data network is read through the family tag of the patient, and then the family data is linked to the medical history data of any family member according to the family attribute, so that the related information of the family medical history of the patient is obtained and provided for a subsequent report analysis unit.
Further, the report analysis unit can also perform comprehensive analysis by combining the clinical data and the medical history data of the patient and the medical history data of the relatives of the patient, and perform key analysis on the polygenic diseases with the family aggregation tendency.
In an embodiment of the present application, the report analyzing unit can analyze the potential diseases and the corresponding mutation sites that appear at high frequency in the family of the patient according to the related information of the family history of the patient, so as to perform a diagnosis focusing on the potential diseases and the corresponding mutation sites.
Furthermore, the potential diseases and the corresponding variation sites which exist in the detection result of the patient and appear or do not appear frequently in the family are marked with emphasis, and factors which may cause the potential diseases are analyzed and displayed in the genetic diagnosis report.
The scheme shown in the embodiment of the application provides a report module, which can automatically generate a genetic diagnosis report of a patient based on clinical data, medical history data and a gene sequencing result of the patient, and a user can query or download the genetic diagnosis report of the patient only by inputting an identity label of the patient into a system during operation, so that the link of report generation is simplified, the efficiency of genetic diagnosis is optimized, and the experience of the patient in the genetic diagnosis process is improved; for doctors, the speed of obtaining the information related to the patients is increased, the comprehensiveness of the obtained information is enhanced, and the communication with the patients and the diagnosis of the patients are facilitated.
With regard to the apparatus in the above-described embodiment, the specific manner in which each module performs the operation has been described in detail in the embodiment related to the method, and will not be elaborated here.
The aspects of the present application have been described in detail hereinabove with reference to the accompanying drawings. In the above embodiments, the descriptions of the respective embodiments have respective emphasis, and for parts that are not described in detail in a certain embodiment, reference may be made to related descriptions of other embodiments. Those skilled in the art should also appreciate that the acts and modules referred to in the specification are not necessarily required in the present application. In addition, it can be understood that the steps in the method of the embodiment of the present application may be sequentially adjusted, combined, and deleted according to actual needs, and the modules in the device of the embodiment of the present application may be combined, divided, and deleted according to actual needs.
Furthermore, the method according to the present application may also be implemented as a computer program or computer program product comprising computer program code instructions for performing some or all of the steps of the above-described method of the present application.
Alternatively, the present application may also be embodied as a non-transitory machine-readable storage medium (or computer-readable storage medium, or machine-readable storage medium) having stored thereon executable code (or a computer program, or computer instruction code) which, when executed by a processor of an electronic device (or electronic device, server, etc.), causes the processor to perform part or all of the various steps of the above-described method according to the present application.
Those of skill would further appreciate that the various illustrative logical blocks, modules, circuits, and algorithm steps described in connection with the applications disclosed herein may be implemented as electronic hardware, computer software, or combinations of both.
The flowchart and block diagrams in the figures illustrate the architecture, functionality, and operation of possible implementations of systems and methods according to various embodiments of the present application. In this regard, each block in the flowchart or block diagrams may represent a module, segment, or portion of code, which comprises one or more executable instructions for implementing the specified logical function(s). It should also be noted that, in some alternative implementations, the functions noted in the block may occur out of the order noted in the figures. For example, two blocks shown in succession may, in fact, be executed substantially concurrently, or the blocks may sometimes be executed in the reverse order, depending upon the functionality involved. It will also be noted that each block of the block diagrams and/or flowchart illustration, and combinations of blocks in the block diagrams and/or flowchart illustration, can be implemented by special purpose hardware-based systems which perform the specified functions or acts, or combinations of special purpose hardware and computer instructions.
Having described embodiments of the present application, the foregoing description is intended to be exemplary, not exhaustive, and not limited to the disclosed embodiments. Many modifications and variations will be apparent to those of ordinary skill in the art without departing from the scope and spirit of the described embodiments. The terminology used herein is chosen in order to best explain the principles of the embodiments, the practical application, or improvements made to the technology in the marketplace, or to enable others of ordinary skill in the art to understand the embodiments disclosed herein.

Claims (10)

1. A genetic diagnostic system that integrates data acquisition, analysis, and report generation, comprising:
a clinical module, a medical history module, an association module and a reporting module;
the clinical module is used for collecting and processing clinical data of a patient; the clinical data includes: identity tags and biometric information;
the medical history module is provided with a medical history database of the patient; the medical history database comprises medical history data of the patient; the medical history data includes: the identity label, family attribute and historical diagnosis report;
the medical history database comprises a plurality of groups of family data, the family data are distinguished based on the family tags, a plurality of identity tags are linked under the family tags, and the identity tags form association in pairs through the family attributes; the family attributes include: the number of generations or relatives of blood relatives;
the report module is respectively connected with the clinical module and the medical history module, and the report module calls the clinical data and the medical history data to generate a genetic diagnosis report;
the correlation module is respectively connected with the clinical module and the medical history module and is used for correlating the clinical data with the medical history data of the patient through the identity tag.
2. The integrated data collection, analysis and report generation genetic diagnostic system of claim 1,
the clinical module, comprising: the system comprises a clinical acquisition unit, a gene sequencing unit and a clinical data unit;
the clinical acquisition unit is used for acquiring clinical data of a patient and storing the clinical data to the clinical data unit;
the gene sequencing unit is used for carrying out gene sequence analysis on the biological information of the patient to obtain a gene sequencing result; the patient biological information includes: genetic data, phenotypic information, and patient profile;
the clinical data unit is used for storing the clinical data and the gene sequencing result to a preset position to form association.
3. The integrated data collection, analysis and report generation genetic diagnostic system of claim 1,
the reporting module includes: the data calling unit and the report analyzing unit;
the data calling unit calls the clinical data, the gene sequencing result and the medical history data from the clinical module and the medical history module based on the identity label and transmits the clinical data, the gene sequencing result and the medical history data to the report analysis module;
the report analysis unit forms a genetic diagnosis report based on the clinical data, the genetic sequencing results, and the medical history data, and generates a report tag associated with the genetic diagnosis report.
4. The integrated data collection, analysis and report generation genetic diagnostic system of claim 3,
the data calling unit is further used for calling the medical history data of the patient relatives by combining the identity tag, the family tag and the family attribute.
5. The integrated data collection, analysis and report generation genetic diagnostic system of claim 4,
the report analysis unit is used for carrying out comprehensive analysis on the clinical data and the medical history data of the patient and the medical history data of the relatives of the patient, and carrying out key analysis on the polygenic diseases with family aggregation tendency.
6. The integrated data collection, analysis and report generation genetic diagnostic system of claim 3,
the report tag includes: report date and report number;
the report module is connected with the correlation module, and the correlation module transmits the genetic diagnosis report to the medical history database and correlates the genetic diagnosis report with the medical history data of the patient through the identity tag.
7. The integrated data collection, analysis and report generation genetic diagnostic system of claim 2,
the clinical data unit stores a reference genome and a genetic resource database;
the gene sequencing unit comprises: a data quality control subunit, a variation identification subunit and a variation annotation subunit;
the data quality control subunit evaluates the base sequencing quality in the gene data according to a window with a fixed length, and moves the window to find a preset quality control threshold position so as to obtain target sequencing data; the target sequencing data are obtained by filtering based on a preset quality control threshold;
the variation identification subunit performs sequence comparison on the target sequencing data based on a reference gene group to generate a comparison result, and performs variation identification according to the comparison result to obtain a variation site; the reference genome, comprising: hg19 genome;
and the variation annotation subunit annotates the variation sites based on a genetic resource database to obtain the gene sequencing result.
8. The integrated data collection, analysis and report generation genetic diagnostic system of claim 7,
the clinical data unit also stores a normal human frequency database;
the gene sequencing unit further comprises: a variant filter subunit;
the mutation filtering subunit screens out the mutation sites based on a normal person frequency database, filters out the mutation sites higher than a frequency threshold in the normal person frequency database, scores and grades the mutation sites, and filters out the mutation sites rated as a preset grade.
9. The integrated data collection, analysis and report generation genetic diagnostic system of claim 8,
the clinical data unit also stores a skin disease database; the skin disease database includes: a gene set related to skin diseases and corresponding skin disease gene mutation sites;
the variation filter subunit can also compare the variation sites based on the skin disease database and perform key marking on the variation sites matched with the skin disease gene mutation sites.
10. The data collection, analysis and report generation integrated genetic diagnostic system of claim 1, further comprising: an interactive front end;
the interactive front end is connected with the clinical module and the report module respectively; for receiving instructions from a user to import clinical information, query medical history data, and download a genetic diagnosis report.
CN202110595234.5A 2021-05-28 2021-05-28 Genetic diagnosis system integrating data acquisition, analysis and report generation Active CN113470776B (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
CN202110595234.5A CN113470776B (en) 2021-05-28 2021-05-28 Genetic diagnosis system integrating data acquisition, analysis and report generation

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
CN202110595234.5A CN113470776B (en) 2021-05-28 2021-05-28 Genetic diagnosis system integrating data acquisition, analysis and report generation

Publications (2)

Publication Number Publication Date
CN113470776A true CN113470776A (en) 2021-10-01
CN113470776B CN113470776B (en) 2024-07-16

Family

ID=77871872

Family Applications (1)

Application Number Title Priority Date Filing Date
CN202110595234.5A Active CN113470776B (en) 2021-05-28 2021-05-28 Genetic diagnosis system integrating data acquisition, analysis and report generation

Country Status (1)

Country Link
CN (1) CN113470776B (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN118380053A (en) * 2024-06-24 2024-07-23 首都医科大学附属北京天坛医院 Method for screening novel hereditary susceptibility genes of medulloblastoma

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR20070038925A (en) * 2005-10-07 2007-04-11 가부시끼가이샤 도시바 Computer readable medium containing a marker selection program for genetic diagnosis, and marker selection apparatus and system, and genetic diagnosing function creation apparatus and system
CN101449161A (en) * 2006-05-03 2009-06-03 人口诊断公司 Evaluating genetic disorders
WO2015123600A1 (en) * 2014-02-13 2015-08-20 The Childrens's Mercy Hospital Method and process for whole genome sequencing for genetic disease diagnosis
CN108549795A (en) * 2018-03-13 2018-09-18 刘吟 Genetic counselling information system based on pedigree chart frame
CN109086571A (en) * 2018-08-03 2018-12-25 国家卫生计生委科学技术研究所 A kind of method and system that monogenic disease hereditary variation is intelligently interpreted and reported
CN109585019A (en) * 2018-11-22 2019-04-05 广州市金圻睿生物科技有限责任公司 Genetic test management system, method and device, computer storage medium

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR20070038925A (en) * 2005-10-07 2007-04-11 가부시끼가이샤 도시바 Computer readable medium containing a marker selection program for genetic diagnosis, and marker selection apparatus and system, and genetic diagnosing function creation apparatus and system
CN101449161A (en) * 2006-05-03 2009-06-03 人口诊断公司 Evaluating genetic disorders
WO2015123600A1 (en) * 2014-02-13 2015-08-20 The Childrens's Mercy Hospital Method and process for whole genome sequencing for genetic disease diagnosis
CN108549795A (en) * 2018-03-13 2018-09-18 刘吟 Genetic counselling information system based on pedigree chart frame
CN109086571A (en) * 2018-08-03 2018-12-25 国家卫生计生委科学技术研究所 A kind of method and system that monogenic disease hereditary variation is intelligently interpreted and reported
CN109585019A (en) * 2018-11-22 2019-04-05 广州市金圻睿生物科技有限责任公司 Genetic test management system, method and device, computer storage medium

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN118380053A (en) * 2024-06-24 2024-07-23 首都医科大学附属北京天坛医院 Method for screening novel hereditary susceptibility genes of medulloblastoma

Also Published As

Publication number Publication date
CN113470776B (en) 2024-07-16

Similar Documents

Publication Publication Date Title
US20130238363A1 (en) Medical examination assistance system and method of assisting medical examination
US8412541B2 (en) Method and system for intelligent qualitative and quantitative analysis for medical diagnosis
CN109686439B (en) Data analysis method, system and storage medium for genetic disease gene detection
CN110991536B (en) Training method of early warning model of primary liver cancer
CN110291555B (en) Systems and methods for facilitating computational analysis of health conditions
US20060184489A1 (en) Genetic knowledgebase creation for personalized analysis of medical conditions
CN102947832A (en) Identity matching of patient records
CN105096225A (en) Analysis system, apparatus and method for assisting disease diagnosis and treatment
US11094403B2 (en) Method and apparatus for collecting test data from use of a disposable test kit
CN113077875B (en) CT image processing method and device
CN112309566A (en) Remote automatic diagnosis system and method for intelligent image recognition and intelligent medical reasoning
CN109063747A (en) Intestinal pathology sectioning image discriminance analysis system and method based on deep learning
CN111180027B (en) Patient portrait correlation rule screening method and device based on medical big data
CN110473636B (en) Intelligent medical advice recommendation method and system based on deep learning
US20140046694A1 (en) Systems and methods for synoptic element structured reporting
CN113470776B (en) Genetic diagnosis system integrating data acquisition, analysis and report generation
RU2481631C2 (en) System and method for analysis consolidation of series ecg and prescription of ecg
JP5616859B2 (en) Medical support system and program
EP3467770B1 (en) Method for analysing a medical imaging data set, system for analysing a medical imaging data set, computer program product and a computer-readable medium
Zhang et al. Multistep Automated Data Labelling Procedure (MADLaP) for thyroid nodules on ultrasound: An artificial intelligence approach for automating image annotation
CN116824670A (en) Micro-expression-based inquiry assisting method, device, equipment and medium
CN115274091A (en) Medical information analysis method and system
JP2010061389A (en) Interactive interface for medical diagnostic support
RU120799U1 (en) INTEREST AREA SEARCH SYSTEM IN THREE-DIMENSIONAL MEDICAL IMAGES
CN111192679A (en) Method and device for processing image data exception and storage medium

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
GR01 Patent grant
GR01 Patent grant