CN116703230A - High-throughput sequencing laboratory flow quality control management system and method - Google Patents
High-throughput sequencing laboratory flow quality control management system and method Download PDFInfo
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Abstract
The invention relates to a high-throughput sequencing laboratory flow quality control management system and method, which are used for carding from the aspects of experimental flow, experimental data and the like based on high-throughput sequencing related detection projects, dividing a wet experimental flow into five modules, including a nucleic acid extraction module, a library construction module, a hybridization capture module, a Pooling module and an on-machine module, and carrying out quality control management on a high-throughput sequencing experiment by constructing a digital full-flow high-throughput sequencing laboratory management system based on an active workflow engine. The method has the advantages that the association mode among five test modules is reasonably set, the recording, circulation and quality control management methods of the wet experiment flow in the high-throughput sequencing experiment process are effectively solved, the whole flow of the high-throughput sequencing wet experiment part is traceable, and the informatization management of the quality control is realized in five aspects of people, machines, materials, methods and rings of the high-throughput sequencing wet experiment to meet the real-time quality control and management in the high-throughput sequencing wet experiment process.
Description
Technical Field
The invention relates to an information management technology, in particular to a high-throughput sequencing laboratory flow quality control management system and method.
Background
The quality control of each link of the current high-throughput sequencing wet test adopts a mode of filling in a paper form of the link and the circulation of the link is all manual handover. It is difficult to accurately grasp the starting and finishing time nodes of each link, and the risk of missing error detection and detection exists due to untimely information exchange. Because the wet test links are complex to operate and involve more operators, all data are filled in paper when the sample quality is controlled disqualification and tracing reasons are met, the wet test links are difficult to store, easy to lose and difficult to find, and a large amount of manpower and material resources are required to be consumed. Because high-throughput sequencing is strictly required for quality control, experimental data and operation record of experimental links, the current main mode is to record and manage by manpower, and because the manual operation is easy to cause errors and the processing speed is slow, a more efficient and accurate high-throughput sequencing experimental flow management method is needed.
Disclosure of Invention
Aiming at improving the record, circulation electronization and quality control management level of wet experiment flow in the high-throughput sequencing experiment process, a high-throughput sequencing laboratory flow quality control management system and method are provided.
The technical scheme of the invention is as follows: the high-throughput sequencing laboratory flow quality control management system is characterized by comprising a nucleic acid extraction module, a library construction module, a hybridization capture module, a Pooling module and an on-machine module, wherein the transfer relation among the modules is set according to the requirements of a wet experiment flow, and the task list generation or cancellation, quality inspection judgment and operation split after quality inspection judgment are realized in each module:
the nucleic acid extraction module: the extraction kit is used for generating or canceling an extraction task list according to a specific sample selection and an experimental method, carrying out quality inspection on an input experimental result, supporting to send the sample with normal quality control to a next experiment, and supporting to re-extract and resample the sample with abnormal quality control;
the library construction module: the method is used for generating or canceling a library task list according to a library kit and detection requirements corresponding to detection items, performing quality inspection on input detection results, supporting to send down to a next experiment for samples with normal quality control, and supporting to rebuild and re-extract samples with abnormal quality control, and re-sampling; the hybrid capture module: the method comprises the steps of generating or canceling a sundry capture task list according to a sundry capture kit and detection requirements corresponding to a detection item, performing quality inspection on an input detection result, supporting to issue to a next experiment for a sample with normal quality control, and supporting to re-sundry capture, re-warehouse establishment, re-extraction and re-sampling for the sample with abnormal quality control;
the Pooling module: and supporting generation or cancellation of a Pooling task list, supporting transmission to a next experiment for samples with normal quality control, and supporting re-library establishment, re-extraction and re-sampling for samples with abnormal quality control.
The machine loading module is used for: and generating or canceling the on-line task list according to an on-line platform corresponding to the detection item of the system configuration, or combining a plurality of Pooling to generate or cancel the on-line task list, directly performing on-line sequencing on samples with normal experiments, and supporting re-extraction and re-sampling on samples with abnormal quality control.
Preferably, the nucleic acid extraction module: different sample types of different detection projects have different nucleic acid extraction methods, aiming at different nucleic acid extraction kits, an operation manual of an experiment is supported to be checked on line, meanwhile, the experimental result of each task list is recorded, if the extraction methods used for the same sample types crossing the detection projects are the same, the same sample types are supported to be put together to generate one nucleic acid extraction task list, the real operation is carried out in batches, meanwhile, the system automatically calculates the total amount of nucleic acid according to the recorded nucleic acid concentration and elution volume, and quality control judgment is carried out by combining DIN and DV200 indexes.
Preferably, the library construction module: different detection projects correspond to different library kits, support to view an operation manual of an experiment online, and record an experiment result of each task list at the same time; simultaneously, the loading volume and the water supplementing volume of the nucleic acid are automatically calculated according to the nucleic acid concentration, the dilution times and the loading quantity, the Index of the library is recorded, the molar concentration is automatically calculated by the system according to the pre-library concentration and the average fragment length, and quality control judgment is carried out by combining a plurality of indexes of the molar concentration.
Preferably, the hybrid capture module: different detection projects correspond to different miscellaneous capture kits, support to check an operation manual of an experiment online, and record an experiment result of each task list at the same time; meanwhile, the Pooling loading volume and the water supplementing volume are automatically calculated according to the pre-library concentration and the Pooling loading volume in the heterocatcher, meanwhile, the molar concentration is automatically calculated according to the pre-library concentration and the average fragment length, and quality control judgment is carried out by combining a plurality of indexes of the molar concentration.
Preferably, the Pooling module: the method comprises the steps of supporting to put libraries of different detection projects into a reaction system for sequencing, distinguishing samples through different indexes, distributing different libraries according to the data size of each lane, and automatically judging whether the Index repetition exists in each lane and the data size of each lane, so that intelligent early warning and quality control judgment are carried out; index refers to a short base sequence added in the library building experimental step, read for distinguishing different samples in subsequent raw message analysis, and lane refers to a flow channel on a sequencing chip.
Preferably, the on-machine module: and supporting to combine a plurality of Pooling to generate an on-line task list according to an on-line platform corresponding to a detection item of system configuration, automatically judging whether Index repetition exists in each lane, and recording information related to on-line.
A method for establishing a high-throughput sequencing laboratory flow quality control management system comprises the following steps: modeling and connecting various steps and tasks by using a graphical editor provided by Activiti: based on a high-throughput sequencing related detection project, combing from the aspect of experimental flow and experimental data, dividing a wet experimental flow into five modules, including a nucleic acid extraction module, a library construction module, a hybridization capture module, a Pooling module and an on-machine module, defining each module as a user task, editing an associne or a candateUsers in the user task to control the executive people and participants of the user task, automatically controlling the authority problem of the task, controlling whether to submit and go to the next step of flow by the related participants, defining each possible flow as a directional line sequence flow among the tasks, editing a conditionExpression in the sequence flow to control the flow to automatically flow according to parameters, defining the starting point, the ending point and each step and task in the experimental flow, and designating the related participants, the executive conditions and the flow control by each step and task;
dynamic form design: in the step of requiring user interaction, a dynamic form design technology is used and a corresponding input form is generated, wherein the form is dynamically generated according to experimental requirements, and the experimenters are allowed to input related data; defining flow variables and flow parameters for transferring data and controlling flow circulation between different steps and tasks;
deployment BPMN flow chart: using a reposititoryService object of a ProcessEngine to deploy a BPMN file into an action engine, analyzing the BPMN file by a deployment process and storing the BPMN file in a process storage library of the action, and recording that a depoymentId is associated with a detection item and an experimental process;
as a system core is an experimental task management module, scheduling each resource to realize an experimental task; according to the depoymentId recorded at the start-up, a required ProcessDefinition is found, a run time service object of a processEngine is used, a process instance is started, by providing a process definition identifier, the engine analyzes the BPMN file, creates a new process instance, records the id of the ProcessInstance, and stores the id in a service system for later submission and flow after completing tasks.
A high-throughput sequencing laboratory flow quality control management method comprises the following operation steps:
1) Establishing the high throughput sequencing laboratory process quality control management system of claim 6;
2) The newly added application form, the application form manager inputs the detection requirements of clinical or scientific research into an application form list, wherein the application form list comprises basic requirement information, opening information, clinical information and sample type related information of a detector, and meanwhile supports printing of sample bar codes and signing of informed consent;
3) Sample collection management, wherein a sample receiving operator receives samples and then receives the samples, and the corresponding wet experiment flow is allocated from a database according to sample call;
4) The method comprises the steps of distributing and starting experiment tasks of an experiment workstation, distributing corresponding experiment operators and specific experiment modes by a laboratory manager according to detection projects, and then starting the experiment tasks;
5) Firstly, according to the experimental tasks allocated to the experimenter, selecting an extraction kit and samples with the same experimental mode in a system, generating an extraction task list and a corresponding operation manual by a nucleic acid extraction module, then, after the experimenter completes the experiment according to the corresponding operation manual, recording experimental results in the extraction task list, performing quality evaluation on the experiment by the nucleic acid extraction module, if the quality control is unqualified, re-extracting or resampling the selected samples after the selected samples are supported by the nucleic acid extraction module, and if the quality control is qualified, notifying the samples to be twisted to a library construction module by the nucleic acid extraction module;
6) The method comprises the steps that an experimenter of a library construction experiment receives samples, firstly, a library construction kit and the samples are selected in a system according to experiment tasks allocated to the experimenter, the library construction module generates a library construction task list and a corresponding operation manual, then the experimenter performs experiments according to the corresponding operation manual, after the experiments are completed, the experimenter performs recording of experimental results in the library construction task list, the library construction module performs quality evaluation on the experiments, if quality control is unqualified, the library construction module performs library reconstruction, re-extraction or re-sampling after supporting the selected samples, and if the quality control is qualified, the library construction module notifies the samples to be twisted to a Pooling module;
if the target detection item is the target detection item, after hybridization capture is needed, continuing the corresponding experiment, and recording the corresponding experiment result;
7) The method comprises the steps that an experimenter of a hybridization capture experiment receives a sample, firstly, a hybridization capture kit and the sample are selected in a system according to an experiment task allocated to the experimenter, a library construction task list and a corresponding operation manual are generated by the hybridization capture module, then the experimenter performs experiments according to the corresponding operation manual, after the experiments are completed, the experimenter performs recording of experimental results in the library construction task list, the hybridization capture module performs quality evaluation, if quality control is unqualified, the hybridization capture module performs re-hybridization capture, library reconstruction and re-extraction or re-sampling after supporting the selected sample, and if the quality control is qualified, the hybridization capture module notifies the sample to be twisted to a Pooling module;
8) The method comprises the steps that firstly, a sample is selected according to an experimental task distributed to an experimenter, the Pooling module generates a Pooling task list and a corresponding operation manual, one Pooling task list supports to select different detection items for Pooling, then the experimenter selects an on-machine platform and a chip type, the Pooling module distributes a lane where each sample is located, the experimenter performs experiments according to an operation manual corresponding to the experimenter, after the experiments are completed, the Pooling module performs recording of experimental results on the Pooling task list, performs quality evaluation, if quality control is not qualified, the Pooling module supports to re-Pooling, re-extraction or re-sampling after the selected sample is supported, if quality control is qualified, the Pooling module submits the task list for auditing, and the post-auditing module informs that the sample is twisted to the on-machine module;
9) The method comprises the steps that firstly, an experimenter for the on-line experiment selects an on-line platform, a chip type and a sample in a system according to an experiment task distributed to the experimenter, an on-line module generates an on-line task list, the experimenter fills in information related to the on-line, submits the on-line task list for auditing, and the on-line experiment can be carried out after the auditing passes;
10 After the experiment is completed, the sample record may be sent to an analysis or reporting workstation.
The invention has the beneficial effects that: the invention discloses a high-throughput sequencing laboratory flow quality control management system and a method, which adopt a SpringCloud micro-service framework to construct a high-availability, high-performance and high-expansion business flow system, realize the whole flow traceability of a high-throughput sequencing wet experiment part, and realize the informationized management of quality control in five aspects of personnel, machines, materials, methods and loops of a high-throughput sequencing wet experiment.
Drawings
FIG. 1 is a design flow chart of an experimental procedure for designing and deploying the invention;
FIG. 2 is an event diagram of the invention opening a specific experimental task;
FIG. 3 is a flow chart of the quality control management system of the high throughput sequencing laboratory process of the present invention.
Detailed Description
The invention will now be described in detail with reference to the drawings and specific examples. The present embodiment is implemented on the premise of the technical scheme of the present invention, and a detailed implementation manner and a specific operation process are given, but the protection scope of the present invention is not limited to the following examples.
A quality control management system for a high-throughput sequencing laboratory process is used for performing quality control management on a high-throughput sequencing experiment by constructing a digital full-flow high-throughput sequencing laboratory management system based on an actiti workflow engine. The method has the advantages of high availability, high performance and high expansion of a business process system, and reasonable arrangement of the association mode among five test modules, and effectively solves the recording, circulation and quality control management methods of the wet test process in the high-throughput sequencing experiment process, so as to meet the real-time quality control and management in the high-throughput sequencing wet test process.
The experimental flow management comprises links of experiment creation, release, execution, monitoring and the like. Definition, automatic execution and state tracking of the experimental flow are realized by combining the workflow engine Activiti and the dynamic form. Therefore, an experimenter can conduct experiments according to a predefined flow, relevant data is input through the dynamic form, and the system can automatically manage the execution and recording of the experiments, so that a convenient and efficient experimental operation and management means are provided for the experimenter. The workflow engine Activiti and the dynamic form are utilized to realize experimental flow management, so that various molecular pathology experimental flows can be better dealt with. The workflow engine Activiti is used for defining each step, task and participant of the experimental flow and automatically managing the execution and state tracking of the experimental flow.
FIG. 1 is a design flow chart showing an experimental procedure for designing and deploying, specifically as follows: 1. graphical design workflow: based on the high-throughput sequencing related detection project, combing is performed from the aspects of experimental flow, experimental data and the like, and the wet experimental flow is divided into five modules, including a nucleic acid extraction module, a library construction module, a hybridization capture module, a Pooling module and an on-machine module. Each experimental module is defined as a user task, an assignment or a candateUsers in the user task is edited to control an executive and a participant of the user task, the authority problem of the task is automatically controlled, whether the task is submitted and forwarded to the next step of circulation is controlled by the related participant, each possible circulation is defined as a directional line sequence flow among the tasks, and a control flow in the sequence flow is edited to control the automatic circulation according to parameters, so that the error of manual circulation is reduced.
The flow chart of the experimental procedure was designed and defined in a visual manner using a graphical editor provided by Activiti. The graphical editor supports drag-and-drop modeling and connecting the various steps and tasks. In the flow chart, the start point, end point, and various steps and tasks therein of the experimental procedure will be defined. Each step and task will specify the relevant participant, execution conditions and flow control.
2. Dynamic form design: in steps requiring user interaction, dynamic form design techniques will be used and corresponding input forms generated. These forms will be dynamically generated according to the experimental requirements, allowing the experimenter to input relevant data. Flow variables and flow parameters will be defined for transferring data and controlling flow of flow between the different steps and tasks.
3. Deployment BPMN flow diagram (workflow designer): a ProcessEngine instance is created using a ProcessEngine configuration object. ProcessEngine is the core object of the Activiti engine, which is responsible for managing flow definitions, executing flow instances, and interacting with databases. The BPMN file is deployed into the Activiti engine using the reposititoryService object of the ProcessEngine. The deployment process will parse the BPMN file and store it in the active's flow store. Record replymentid is associated with test item and experimental procedure.
4. As a system core is an experimental task management module, each resource is scheduled to realize an experimental task, and as shown in fig. 1 and 2, the system comprises the following steps:
distribution operators: the task allocation page required by each project is configured through the dynamic form, and the task responsible person of each node of the task can be determined according to the selected information after allocation, and the data record list and the operation manual required by each node can be determined.
The starting process is as follows: according to the depoymentId recorded at the start-up, the required ProcessDefinitions are found, and a process instance is started by using the RuntimeService object of the ProcessEngine. By providing the identifier of the flow definition (typically the ID of the BPMN file), the engine will parse the BPMN file and create a new flow instance, process instance, record the ID of the process instance, store it in the business system for later submission and flow circulation after completion of the task.
Form design of recording forms and operating manuals: the record list and the operation manual used at each node of the experimental procedure are determined according to the conditions of the experimental mode, sample type, library type and the like selected during the distribution. The record list can record the data produced in the experiment, the reagent consumptive material of use, the sequencing that uses goes up machine platform, go up machine chip etc. open with the stock simultaneously, after every circulation, can automatic update stock, reduce personnel's manual operation, can be used to the traceability of experimental procedure and reagent consumptive material.
The flow is: after the process instance is started, the TaskService object of the processEngine is used to manage the process tasks. By inquiring the task list to be handled, the task which needs to be executed currently can be obtained, and then corresponding operation is executed according to task definition. After the operation is completed, the completion method of the task service object is executed to complete the step, and then the input parameters and the defined flow to the next step.
Exception handling: when abnormal conditions occur in the experimental process, such as insufficient samples, equipment faults, abnormal data and the like, the abnormal conditions can be processed according to an abnormal processing scheme defined in a process model, and meanwhile, an active workflow engine can automatically send reminding notification to related personnel so as to process in time, so that stability and reliability of the NGS experimental process are guaranteed.
Real-time monitoring and optimizing: real-time monitoring and optimizing are carried out on the NGS experiment flow by using the real-time monitoring and analyzing function provided by the active workflow engine. For example, problems in the process may be discovered and resolved in time by monitoring metrics such as execution time of the process, quality of task processing, delay of task processing, etc. In addition, the flow can be deeply analyzed and optimized by methods such as data analysis and the like, so that the efficiency and quality of NGS experiment flow management are improved.
The specific page operation flow will be described in detail below, for each module to-be-tested sample list, firstly, selecting an experiment flow (including a reagent kit and an experiment mode) and the same sample, automatically generating a task list, wherein different sample types and library building types are different in the experiment flow, for example, the nucleic acid extraction of paraffin tissue is different from the nucleic acid extraction method of peripheral blood, even if the same sample type is different in operation, different reagent kits and different extraction methods (including automatic, semi-automatic and manual methods) are different in operation, therefore, when each module generates a corresponding experiment task list, the module needs to perform logic judgment of the same experiment flow, after generating the task list, an experimenter performs wet experiment operation according to an operation manual or SOP (standard operation instruction), after the experiment is completed, the experimenter inputs the experiment result of each sample in the experiment task list, then performs quality control qualification and disqualification judgment according to the quality control of each module, supports the transfer to the next module, and supports re-extraction or resampling of the current nodes for the quality control disqualification sample. Meanwhile, for the experimental result of each sample in each module, the system can automatically store the experimental result in the corresponding database, so that the subsequent quality control data query, screening and tracing are facilitated.
The method comprises the steps of setting the transfer relation among all modules according to the requirements of a wet experiment flow, and realizing the generation or cancellation of a task sheet, quality inspection judgment and operation split after the quality inspection judgment in each module, wherein the five modules are as follows:
nucleic acid extraction module: according to the extraction kit and the experimental method selected by the specific sample, an extraction task list is generated/cancelled, quality inspection is carried out on the input experimental result, the sample with normal quality control is supported to be issued to the next experiment, and the sample with abnormal quality control is supported to be re-extracted and re-sampled.
Library construction module: according to the library kit and detection requirements corresponding to the detection items, a library task list is generated/cancelled, quality inspection is carried out on the input detection result, the sample with normal quality control is supported to be issued to the next experiment, and the sample with abnormal quality control is supported to be rebuilt, re-extracted and re-sampled.
Hybridization capture module: the method is used for generating/canceling a sundry capture task list according to the sundry capture kit and detection requirements corresponding to detection items, performing quality inspection on input detection results, supporting to send down to a next experiment for samples with normal quality control, and supporting to re-sundry capture, re-warehouse building, re-extraction and re-sampling for samples with abnormal quality control.
A Pooling module: the method is used for placing a library of detection items into a reaction system to carry out sequencing and sequencing requirements, generating/canceling a Pooling task list, distributing current resources, inputting all distributed resource detection results and carrying out quality inspection, supporting to send to a next experiment for samples with normal quality control, and supporting to rebuild libraries, re-extract and re-sample samples with abnormal quality control.
And (5) an upper machine module: and generating/canceling the on-line task list according to an on-line platform corresponding to the detection item of the system configuration, or combining a plurality of Pooling to generate/cancel the on-line task list, directly performing on-line sequencing on samples with normal experiments, and supporting re-extraction and re-sampling on samples with abnormal quality control.
The high-throughput laboratory wet test flow implementation quality management method based on the system comprises the following steps of:
the informationized management of quality control is realized in five aspects of human, machine, material, method and loop of high-throughput sequencing wet test.
The system has different roles corresponding to corresponding account numbers and authorities, a quality administrator issues a task list to the experimenters responsible for detecting wet test links by different high-throughput sequencing, each link experimenter performs operation detection of the corresponding link according to the requirements of the issued task, each experimental link can provide an operation manual of the corresponding experimental link, the experimenter confirms the instrument and records of the operation while finishing the operation according to the manual content, the experimenter checks in the system, confirms and fills out the experiment record after the operation is finished, and the system is transferred to the next experimental link after the completion of the operation. In the process, the system can automatically calculate the usage amount of the reagent, register the usage amount in the reagent inventory and count the residual reagent amount, and an experimenter can record the temperature of the refrigerator used and the environment temperature and humidity of an experiment area by means of the system, so that the experimenter can record and check the residual reagent amount in time conveniently.
The following are quality control criteria for different experimental links:
nucleic acid extraction module: different sample types of different detection projects have different nucleic acid extraction methods, aiming at different nucleic acid extraction kits, an operation manual of an experiment is supported to be checked on line, meanwhile, the experimental result of each task list is recorded, for some sample types which are the same across the detection projects, if the extraction methods are the same, the sample types are supported to be put together to generate one nucleic acid extraction task list, the actual operation is carried out in batches, meanwhile, the system automatically calculates the total amount of nucleic acid according to the recorded nucleic acid concentration and elution volume, and quality control judgment is carried out by combining DIN, DV200 and other indexes. For example, the total amount of nucleic acids is 40ng or more, DIN is 2.2 or more, and DV200 is 30% or more.
Library construction module: different detection projects correspond to different library kits, support to view an operation manual of an experiment on line, and record an experiment result of each task sheet. Meanwhile, the system automatically calculates the loading volume and the water supplementing volume of the nucleic acid according to the numerical values of the concentration, dilution times, loading amount and the like of the nucleic acid, records Index of the library, automatically calculates the molar concentration according to the pre-library concentration and the average fragment length, and combines a plurality of indexes such as the molar concentration to carry out quality control judgment. For example, the pre-library concentration is greater than or equal to 70, the average fragment length is 300-600bp, and the molar concentration is greater than 1nM.
Hybridization capture module: different detection projects correspond to different miscellaneous capture kits, support to check an operation manual of an experiment on line, and record an experiment result of each task list. Meanwhile, the system automatically calculates the Pooling loading volume and the water supplementing volume according to the pre-library concentration and the Pooling loading volume in the miscellaneous trapping number, and simultaneously automatically calculates the molar concentration according to the pre-library concentration and the average fragment length and performs quality control judgment by combining a plurality of indexes such as the molar concentration. Such as molar concentrations greater than 1nM.
A Pooling module: the library supporting different detection projects is placed into a reaction system to be sequenced, samples are distinguished through different indexes, different libraries are distributed according to the data size of each lane, and the system automatically judges whether the Index repetition exists in each lane and the data size of each lane, so that intelligent early warning and quality control judgment are carried out. Index refers to a short base sequence added in the library building experimental step, read for distinguishing different samples in subsequent raw message analysis, and lane refers to a flow channel on a sequencing chip.
And (5) an upper machine module: and supporting to combine a plurality of Pooling to generate an on-line task list according to an on-line platform corresponding to a detection item of system configuration, automatically judging whether Index repetition exists in each lane by the system, and recording information related to on-line.
The high throughput sequencing laboratory flow quality control management system flow chart shown in fig. 3 comprises the following operation steps:
the first step, newly adds the application form, the application form manager inputs the detection requirement of clinic or scientific research into the application form list, including the basic requirement information, the opening information, the clinical information, the sample type and other related information of the detector, and simultaneously supports the printing of sample bar codes, the signing of informed consent and the like.
And secondly, sample collection management, wherein after a sample is received by a sample collector, the sample is received, and a corresponding wet experiment flow is allocated from a database according to sample call.
And thirdly, distributing and starting experiment tasks of the experiment workstation, distributing corresponding experiment operators and specific experiment modes by a laboratory manager according to the detection items, and then starting the experiment tasks.
Fourth, the experimenter of the nucleic acid extraction experiment firstly selects an extraction kit and samples with the same experimental mode in the system according to the experimental task allocated to the experimenter, the nucleic acid extraction module generates an extraction task list and a corresponding operation manual, then the experimenter performs experiments according to the corresponding operation manual, after the experiments are completed, the experimenter performs record of experimental results in the extraction task list, the nucleic acid extraction module performs quality evaluation on the experiments, if the quality control is unqualified, the nucleic acid extraction module performs re-extraction or re-sampling after supporting the selected samples, and if the quality control is qualified, the nucleic acid extraction module notifies the samples to be twisted to the library construction module.
And fifthly, receiving samples by an experimenter of a library construction experiment, firstly selecting a library construction kit and the samples in a system according to the experiment tasks allocated to the experimenter, generating a library construction task list and a corresponding operation manual by the library construction module, then performing experiments according to the corresponding operation manual by the experimenter, recording experimental results in the library construction task list after the experiments are completed, performing quality evaluation on the experiments by the library construction module, and performing library reconstruction, re-extraction or re-sampling after the selected samples are supported by the library construction module if quality control is unqualified, and notifying the samples to be twisted to a Pooling module by the library construction module if the quality control is qualified.
If the target detection item is the target detection item, after hybridization capture is needed, continuing the corresponding experiment, and recording the corresponding experiment result.
Step six, the experiment personnel of the hybridization capture experiment receive the sample, firstly select the hybridization capture kit and the sample in the system according to the experiment task allocated to the experiment personnel, the hybridization capture module generates a library construction task list and a corresponding operation manual, then the experiment personnel carries out the experiment according to the corresponding operation manual, after the experiment is completed, the experiment result is recorded in the library construction task list, the hybridization capture module carries out quality evaluation, if the quality control is unqualified, the hybridization capture module carries out re-hybridization capture, re-library construction, re-extraction or re-sampling after supporting the selected sample, and if the quality control is qualified, the hybridization capture module notifies the sample to be twisted to the Pooling module.
Seventh, the experimenter of the Pooling experiment receives samples, firstly selects the samples according to the experimental tasks allocated to the experimenter, the Pooling module generates a Pooling task list and a corresponding operation manual, one Pooling task list supports to select different detection items for Pooling, then the experimenter selects a loading platform and a chip type, the Pooling module allocates a lane where each sample is located, the experimenter performs experiments according to the operation manual corresponding to the experimenter, after the experiments are completed, the Pooling module performs quality evaluation, if quality control is not qualified, the Pooling module performs repoling, re-extraction or re-sampling after supporting the selected samples, if quality control is qualified, the Pooling module submits the task list for auditing, and after the auditing is passed, the Pooling module notifies that the samples are twisted to the loading module.
And eighth, an experimenter of the on-line experiment selects an on-line platform, a chip type and a sample in the system according to the experiment task allocated to the experimenter, the on-line module generates an on-line task list, the experimenter fills in information related to the on-line, submits the on-line task list for auditing, and the on-line experiment can be performed after the auditing passes.
And ninth, after the experiment is completed, the sample record can be sent to an analysis or report workstation.
The above examples illustrate only a few embodiments of the invention, which are described in detail and are not to be construed as limiting the scope of the invention. It should be noted that it will be apparent to those skilled in the art that several variations and modifications can be made without departing from the spirit of the invention, which are all within the scope of the invention. Accordingly, the scope of protection of the present invention is to be determined by the appended claims.
Claims (8)
1. The high-throughput sequencing laboratory flow quality control management system is characterized by comprising a nucleic acid extraction module, a library construction module, a hybridization capture module, a Pooling module and an on-machine module, wherein the transfer relation among the modules is set according to the requirements of a wet experiment flow, and the task list generation or cancellation, quality inspection judgment and operation split after quality inspection judgment are realized in each module:
the nucleic acid extraction module: the extraction kit is used for generating or canceling an extraction task list according to a specific sample selection and an experimental method, carrying out quality inspection on an input experimental result, supporting to send the sample with normal quality control to a next experiment, and supporting to re-extract and resample the sample with abnormal quality control;
the library construction module: the method is used for generating or canceling a library task list according to a library kit and detection requirements corresponding to detection items, performing quality inspection on input detection results, supporting to send down to a next experiment for samples with normal quality control, and supporting to rebuild and re-extract samples with abnormal quality control, and re-sampling; the hybrid capture module: the method comprises the steps of generating or canceling a sundry capture task list according to a sundry capture kit and detection requirements corresponding to a detection item, performing quality inspection on an input detection result, supporting to issue to a next experiment for a sample with normal quality control, and supporting to re-sundry capture, re-warehouse establishment, re-extraction and re-sampling for the sample with abnormal quality control;
the Pooling module: and supporting generation or cancellation of a Pooling task list, supporting transmission to a next experiment for samples with normal quality control, and supporting re-library establishment, re-extraction and re-sampling for samples with abnormal quality control.
The machine loading module is used for: and generating or canceling the on-line task list according to an on-line platform corresponding to the detection item of the system configuration, or combining a plurality of Pooling to generate or cancel the on-line task list, directly performing on-line sequencing on samples with normal experiments, and supporting re-extraction and re-sampling on samples with abnormal quality control.
2. The high throughput sequencing laboratory flow quality control management system of claim 1, wherein said nucleic acid extraction module: different sample types of different detection projects have different nucleic acid extraction methods, aiming at different nucleic acid extraction kits, an operation manual of an experiment is supported to be checked on line, meanwhile, the experimental result of each task list is recorded, if the extraction methods used for the same sample types crossing the detection projects are the same, the same sample types are supported to be put together to generate one nucleic acid extraction task list, the real operation is carried out in batches, meanwhile, the system automatically calculates the total amount of nucleic acid according to the recorded nucleic acid concentration and elution volume, and quality control judgment is carried out by combining DIN and DV200 indexes.
3. The high throughput sequencing laboratory flow quality control management system of claim 2, wherein said library construction module: different detection projects correspond to different library kits, support to view an operation manual of an experiment online, and record an experiment result of each task list at the same time; simultaneously, the loading volume and the water supplementing volume of the nucleic acid are automatically calculated according to the nucleic acid concentration, the dilution times and the loading quantity, the Index of the library is recorded, the molar concentration is automatically calculated by the system according to the pre-library concentration and the average fragment length, and quality control judgment is carried out by combining a plurality of indexes of the molar concentration.
4. The high throughput sequencing laboratory flow quality control management system of claim 3, wherein said hybridization capture module: different detection projects correspond to different miscellaneous capture kits, support to check an operation manual of an experiment online, and record an experiment result of each task list at the same time; meanwhile, the Pooling loading volume and the water supplementing volume are automatically calculated according to the pre-library concentration and the Pooling loading volume in the heterocatcher, meanwhile, the molar concentration is automatically calculated according to the pre-library concentration and the average fragment length, and quality control judgment is carried out by combining a plurality of indexes of the molar concentration.
5. The high throughput sequencing laboratory process quality control management system of claim 4, wherein said Pooling module: the method comprises the steps of supporting to put libraries of different detection projects into a reaction system for sequencing, distinguishing samples through different indexes, distributing different libraries according to the data size of each lane, and automatically judging whether the Index repetition exists in each lane and the data size of each lane, so that intelligent early warning and quality control judgment are carried out; index refers to a short base sequence added in the library building experimental step, read for distinguishing different samples in subsequent raw message analysis, and lane refers to a flow channel on a sequencing chip.
6. The high throughput sequencing laboratory process quality control management system of claim 5, wherein said on-board module: and supporting to combine a plurality of Pooling to generate an on-line task list according to an on-line platform corresponding to a detection item of system configuration, automatically judging whether Index repetition exists in each lane, and recording information related to on-line.
7. The method for establishing the high-throughput sequencing laboratory flow quality control management system is characterized in that a graphical editor provided by Activiti is used for modeling and connecting each step and task: based on a high-throughput sequencing related detection project, combing from the aspect of experimental flow and experimental data, dividing a wet experimental flow into five modules, including a nucleic acid extraction module, a library construction module, a hybridization capture module, a Pooling module and an on-machine module, defining each module as a user task, editing an associne or a candateUsers in the user task to control the executive people and participants of the user task, automatically controlling the authority problem of the task, controlling whether to submit and go to the next step of flow by the related participants, defining each possible flow as a directional line sequence flow among the tasks, editing a conditionExpression in the sequence flow to control the flow to automatically flow according to parameters, defining the starting point, the ending point and each step and task in the experimental flow, and designating the related participants, the executive conditions and the flow control by each step and task;
dynamic form design: in the step of requiring user interaction, a dynamic form design technology is used and a corresponding input form is generated, wherein the form is dynamically generated according to experimental requirements, and the experimenters are allowed to input related data; defining flow variables and flow parameters for transferring data and controlling flow circulation between different steps and tasks;
deployment BPMN flow chart: using a reposititoryService object of a ProcessEngine to deploy a BPMN file into an action engine, analyzing the BPMN file by a deployment process and storing the BPMN file in a process storage library of the action, and recording that a depoymentId is associated with a detection item and an experimental process;
as a system core is an experimental task management module, scheduling each resource to realize an experimental task; according to the depoymentId recorded at the start-up, a required ProcessDefinition is found, a run time service object of a processEngine is used, a process instance is started, by providing a process definition identifier, the engine analyzes the BPMN file, creates a new process instance, records the id of the ProcessInstance, and stores the id in a service system for later submission and flow after completing tasks.
8. The quality control management method for the high-throughput sequencing laboratory process is characterized by comprising the following operation steps of:
1) Establishing the high throughput sequencing laboratory process quality control management system of claim 6;
2) The newly added application form, the application form manager inputs the detection requirements of clinical or scientific research into an application form list, wherein the application form list comprises basic requirement information, opening information, clinical information and sample type related information of a detector, and meanwhile supports printing of sample bar codes and signing of informed consent;
3) Sample collection management, wherein a sample receiving operator receives samples and then receives the samples, and the corresponding wet experiment flow is allocated from a database according to sample call;
4) The method comprises the steps of distributing and starting experiment tasks of an experiment workstation, distributing corresponding experiment operators and specific experiment modes by a laboratory manager according to detection projects, and then starting the experiment tasks;
5) Firstly, according to the experimental tasks allocated to the experimenter, selecting an extraction kit and samples with the same experimental mode in a system, generating an extraction task list and a corresponding operation manual by a nucleic acid extraction module, then, after the experimenter completes the experiment according to the corresponding operation manual, recording experimental results in the extraction task list, performing quality evaluation on the experiment by the nucleic acid extraction module, if the quality control is unqualified, re-extracting or resampling the selected samples after the selected samples are supported by the nucleic acid extraction module, and if the quality control is qualified, notifying the samples to be twisted to a library construction module by the nucleic acid extraction module;
6) The method comprises the steps that an experimenter of a library construction experiment receives samples, firstly, a library construction kit and the samples are selected in a system according to experiment tasks allocated to the experimenter, the library construction module generates a library construction task list and a corresponding operation manual, then the experimenter performs experiments according to the corresponding operation manual, after the experiments are completed, the experimenter performs recording of experimental results in the library construction task list, the library construction module performs quality evaluation on the experiments, if quality control is unqualified, the library construction module performs library reconstruction, re-extraction or re-sampling after supporting the selected samples, and if the quality control is qualified, the library construction module notifies the samples to be twisted to a Pooling module;
if the target detection item is the target detection item, after hybridization capture is needed, continuing the corresponding experiment, and recording the corresponding experiment result;
7) The method comprises the steps that an experimenter of a hybridization capture experiment receives a sample, firstly, a hybridization capture kit and the sample are selected in a system according to an experiment task allocated to the experimenter, a library construction task list and a corresponding operation manual are generated by the hybridization capture module, then the experimenter performs experiments according to the corresponding operation manual, after the experiments are completed, the experimenter performs recording of experimental results in the library construction task list, the hybridization capture module performs quality evaluation, if quality control is unqualified, the hybridization capture module performs re-hybridization capture, library reconstruction and re-extraction or re-sampling after supporting the selected sample, and if the quality control is qualified, the hybridization capture module notifies the sample to be twisted to a Pooling module;
8) The method comprises the steps that firstly, a sample is selected according to an experimental task distributed to an experimenter, the Pooling module generates a Pooling task list and a corresponding operation manual, one Pooling task list supports to select different detection items for Pooling, then the experimenter selects an on-machine platform and a chip type, the Pooling module distributes a lane where each sample is located, the experimenter performs experiments according to an operation manual corresponding to the experimenter, after the experiments are completed, the Pooling module performs recording of experimental results on the Pooling task list, performs quality evaluation, if quality control is not qualified, the Pooling module supports to re-Pooling, re-extraction or re-sampling after the selected sample is supported, if quality control is qualified, the Pooling module submits the task list for auditing, and the post-auditing module informs that the sample is twisted to the on-machine module;
9) The method comprises the steps that firstly, an experimenter for the on-line experiment selects an on-line platform, a chip type and a sample in a system according to an experiment task distributed to the experimenter, an on-line module generates an on-line task list, the experimenter fills in information related to the on-line, submits the on-line task list for auditing, and the on-line experiment can be carried out after the auditing passes;
10 After the experiment is completed, the sample record may be sent to an analysis or reporting workstation.
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