CN111627509A

CN111627509A - Method, device, equipment and storage medium for generating virus gene detection report

Info

Publication number: CN111627509A
Application number: CN202010378805.5A
Authority: CN
Inventors: 刘让蛟; 戴立忠; 周玮欢; 郭鑫武; 邓中平; 李勃
Original assignee: Sansure Biotech Inc
Current assignee: Sansure Biotech Inc
Priority date: 2020-05-07
Filing date: 2020-05-07
Publication date: 2020-09-04

Abstract

The embodiment of the application discloses a method, a device, equipment and a computer storage medium for generating a virus gene detection report, wherein the method comprises the following steps: acquiring object information of a biological sample; acquiring PCR detection information of the biological sample, wherein the PCR detection information comprises PCR detection information of at least one detection item; determining type information of a detection gene corresponding to the detection item based on operation information in the PCR detection information and a relation between the operation information and the type; determining the positive and negative detection information of the detection gene based on the reaction result in the PCR detection information and the relation between the reaction result and the positive and negative detection result; generating a virus gene detection report of the biological sample based on the object information, the type information and the negative and positive detection information. Thus, the target information and the detection information of the viral gene are integrated, and the work efficiency of generating a viral gene detection report is improved.

Description

Method, device, equipment and storage medium for generating virus gene detection report

Technical Field

The present application relates to biological information technology, and in particular, to a method, an apparatus, a device, and a computer storage medium for generating a virus gene detection report.

Background

More than 130 Human Papillomaviruses (HPV) are currently isolated, at least 15 HPV subtypes can increase the risk of cervical cancer of women, 95 percent of cervical cancer is caused by 8 high-risk HPV subtypes, HPV16 and HPV18 are two most common oncogenic HPV, and more than 70 percent of cervical cancer and more than 50 percent of cervical intraepithelial neoplasia are caused by the two HPV subtypes. Therefore, judgment of the types of multiple viral genes is required in the HPV detection project for cervical cancer screening. Meanwhile, in order to save detection time and resources, multiple samples are simultaneously subjected to HPV detection.

Since HPV is integrated, replicated and proliferated in cervical epithelial cells to cause precancerous lesion, namely cervical intraepithelial neoplasia, and finally develops into cervical invasive carcinoma, HPV subtypes can be detected by adopting a nucleic acid detection method, such as fluorescence quantitative Polymerase Chain Reaction (PCR) detection. However, the results obtained from the fluorescent quantitative PCR assay are usually numerical, for example, the results obtained from the fluorescent quantitative PCR assay are Cycle Threshold (CT). Therefore, the PCR detection result needs to be interpreted according to the instruction of the kit, so as to obtain the detection results of multiple HPV subtypes of the sample. If the detection of HPV is to be done in multiple samples, it takes a lot of time. And the generation process of the detection report is long, and the finished detection report lacks a uniform standard.

Disclosure of Invention

The embodiment of the application provides a method, a device and equipment for generating a virus gene detection report and a computer storage medium.

In a first aspect, the embodiments of the present application provide a method for generating a viral gene detection report, the method includes:

acquiring object information of a biological sample;

acquiring PCR detection information of the biological sample, wherein the PCR detection information comprises PCR detection information of at least one detection item;

determining type information of a detection gene corresponding to the detection item based on operation information in the PCR detection information and a relation between the operation information and the type; wherein the detection gene comprises a virus gene and an internal standard gene;

determining the positive and negative detection information of the detection gene based on the reaction result in the PCR detection information and the relation between the reaction result and the positive and negative detection result;

generating a virus gene detection report of the biological sample based on the object information, the type information and the negative and positive detection information.

In some embodiments, the obtaining PCR detection information of the biological sample includes:

reading a file containing PCR detection information in a target storage area according to the PCR file identification in the object information;

and determining the PCR detection information according to the file containing the PCR detection information.

In some embodiments, the operation information includes position information of the reaction well and information of the fluorescence channel, and the determining type information of the detection gene corresponding to the detection item based on the operation information in the PCR detection information and a relationship between the operation information and the type includes:

and determining the type of the detection gene corresponding to the fluorescence channel in each reaction hole based on the position information of the reaction hole and the information of the fluorescence channel in the information of the PCR detection and the relationship among the position information of the reaction hole, the information of the fluorescence channel and the type.

In some embodiments, the method further comprises:

determining a reaction result corresponding to each virus genotype in the detection genes and a reaction result corresponding to the internal standard gene in the detection genes according to a reaction result corresponding to the fluorescent channel in each reaction hole;

the determining the positive and negative detection information of the detection gene based on the reaction result in the PCR detection information and the relationship between the reaction result and the positive and negative detection result comprises:

and determining the positive and negative detection information of each virus genotype and the positive and negative detection information of the internal standard gene based on the reaction result corresponding to each virus genotype, the reaction result corresponding to the internal standard gene and the relationship between the reaction result and the positive and negative detection result.

In some embodiments, after the determining negative-positive detection information for the detected gene, the method further comprises:

determining at least one type of virus gene which is positive in the positive and negative detection information and a first internal standard gene which is positive in the positive and negative detection information according to the positive and negative detection information of the detection gene;

and determining the concentration of the at least one virus gene type according to the reaction result information of the at least one virus gene type and the relation between the reaction result of the virus gene type and the concentration of the virus gene.

And determining the concentration of the first internal standard gene according to the reaction result information of the first internal standard gene and the relation between the reaction result of the internal standard gene and the concentration of the internal standard gene.

In some embodiments, the method further comprises:

determining infection information for the at least one type of viral gene based on the concentration of the at least one type of viral gene and the concentration of the first internal standard gene, and adding the infection information to the viral gene detection report.

In some embodiments, the method further comprises:

generating clinical interpretation information for the viral genes based on the viral genotype and the relationship between the viral genotype and clinical risk annotations, and adding the clinical interpretation information to the viral gene detection report.

In a second aspect, an embodiment of the present application provides an apparatus for generating a virus gene detection report, the apparatus including: the system comprises a first acquisition module, a second acquisition module, a genotype type determination module, an information determination module and a generation module;

the first acquisition module is used for acquiring object information of a biological sample;

the second obtaining module is configured to obtain PCR detection information of the biological sample, where the PCR detection information includes PCR detection information of at least one detection item;

the genotype determination module is used for determining the genotype information of the detection gene corresponding to the detection item based on the operation information in the PCR detection information and the relationship between the operation information and the genotype; wherein the detection gene comprises a virus gene and an internal standard gene;

the information determination module is used for determining the positive and negative detection information of the detection gene based on the reaction result in the PCR detection information and the relation between the reaction result and the positive and negative detection result;

the generation module is used for generating a virus gene detection report of the biological sample based on the object information, the type information and the negative and positive detection information.

In a third aspect, an embodiment of the present application provides an apparatus, including a memory, a processor, and a computer program stored on the memory and executable on the processor, wherein the processor executes the program to implement the steps of the method for generating a virus gene detection report according to any embodiment of the present application.

In a fourth aspect, embodiments of the present application provide a computer storage medium, where a computer program is stored on the computer storage medium, and when the computer program is executed by a processor, the method for generating a virus gene detection report provided in any embodiment of the present application is implemented.

In the embodiment of the present application, object information of a biological sample is acquired. And acquiring PCR detection information of the biological sample, wherein the PCR detection information comprises PCR detection information of at least one detection item. And determining the type information of the detection gene corresponding to the detection item based on the operation information in the PCR detection information and the relationship between the operation information and the type, so that the type of the virus gene of the sample can be rapidly determined by utilizing the relationship between the operation information and the type. And determining the negative and positive detection information of the detection gene based on the reaction result in the PCR detection information and the relationship between the reaction result and the negative and positive detection result, so that the negative and positive of the virus genotype of the sample can be rapidly and accurately judged by utilizing the relationship between the reaction result and the negative and positive detection result. Generating a virus gene detection report of the biological sample based on the object information, the type information and the negative and positive detection information. Therefore, the object information and the detection information are integrated, the processes of data analysis of the viral genes and report generation are simplified, the detection reports of the viral genes can be generated quickly, the working efficiency of generating the detection reports is improved, and the defects of long time consumption are overcome. Meanwhile, the generated detection report comprises the object information, the type information and the positive and negative detection information, the information contained in the detection report is more comprehensive, and the generated detection report can provide more standardized information.

Drawings

FIG. 1 is a process flow diagram illustrating a method for generating a virus gene detection report according to an embodiment of the present application.

Fig. 2 is a schematic structural diagram of a device for generating a virus gene detection report according to an embodiment of the present application.

FIG. 3 is a schematic structural diagram of a system for generating a viral gene detection report according to an embodiment of the present application.

Fig. 4 is a schematic view of an application scenario of a system for generating a virus gene detection report according to another embodiment of the present application.

FIG. 5 is a schematic process flow diagram of a method for generating a viral gene detection report according to another embodiment of the present application.

FIG. 6 is a schematic diagram of a main interface of a system for generating a virus gene detection report according to an embodiment of the present application.

FIG. 7 is a schematic diagram of a sample information scanning interface of a system for generating a virus gene detection report according to an embodiment of the present application.

Fig. 8 is a schematic diagram of a sample information query interface of a system for generating a virus gene detection report according to an embodiment of the present application.

Fig. 9 is a schematic diagram of a PCR result query interface of a system for generating a virus gene detection report according to an embodiment of the present application.

FIG. 10 is a schematic diagram of a query interface of a PCR report of a system for generating a virus gene detection report according to an embodiment of the present application.

FIG. 11 is a schematic representation of a first type of HPV detection report in an embodiment of the present application.

FIG. 12 is a schematic representation of a second type of HPV detection report in an embodiment of the present application.

FIG. 13 is a schematic illustration of a statistical interface of a system for generating a viral gene detection report according to an embodiment of the present application.

FIG. 14 is a diagram illustrating a checklist query interface, according to an embodiment of the present application.

Fig. 15 is a first schematic diagram of a TCT detection interface according to an embodiment of the present disclosure.

Fig. 16 is a second schematic diagram of a TCT detection interface according to an embodiment of the present application.

Fig. 17 is a schematic structural diagram of an apparatus according to an embodiment of the present application.

Detailed Description

In order to make the objects, technical solutions and advantages of the embodiments of the present application clearer, the following will describe the specific technical solutions of the present application in further detail with reference to the accompanying drawings in the embodiments of the present application. The following examples are intended to illustrate the present application but are not intended to limit the scope of the present application.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs. The terminology used herein in the description of the present application is for the purpose of describing particular embodiments only and is not intended to be limiting of the application. As used herein, the term "and/or" includes any and all combinations of one or more of the associated listed items.

Before describing the method for generating a virus gene detection report provided in the examples of the present application in detail, HPV detection technology will be briefly described.

The existing HPV detection technology has a plurality of detection schemes, including 15 general high-risk HPV qualitative detections, 15 or 25 HPV typing detections, and 13 mixed high-risk HPV qualitative plus 'HPV 16' and 'HPV 18' typing detections.

The genotype of the virus is judged according to the nucleic acid detection result of the biological sample, such as the detection result of the fluorescent quantitative Polymerase Chain Reaction (PCR), so as to confirm the virus infection condition of the detected person. However, when the number of samples to be detected is large, a plurality of different systems are required to provide the target information and the nucleic acid detection result information of the samples. Therefore, the nucleic acid detection data cannot be directly bound to the target information of the sample, and a worker is usually required to check and bind the data item by item.

The detection result of HPV nucleic acid amplification is mostly expressed by the cycle number reaching the threshold value in the fluorescence amplification curve. And the digital results of the PCR detection of a large number of samples are subjected to virus genotype type interpretation, and the digital results of the PCR detection are compared with the positive interpretation threshold values of the respective virus genotype types, so that the negative and positive interpretation of the virus genotype types is completed. Therefore, the difficulty of judging and negative-positive judging of the virus genotype of a large number of samples by manually analyzing data is high, the time consumption is long, and the error rate is high. In addition, the detection report is generated by manually integrating the sample information and the analysis result in a large batch, so that the problems of complicated report generation process, long time consumption and high error rate exist. Thus, manual operations are difficult to achieve for high throughput cervical cancer screening involving complex data analysis and interpretation procedures. And the accuracy of detection result analysis cannot be guaranteed by manpower, and the detection report period required by clinic cannot be guaranteed.

Meanwhile, in order to further observe the disease of the sample subject, quantitative estimation of HPV is required. Since the quantitative estimation formula of each HPV typing detection reagent is not completely the same, it is difficult to accomplish quantitative estimation of a large number of samples by means of manual work.

It should be noted that, in the embodiment of the present application, the virus gene is not limited to HPV, but may also be other types of viruses, such as Hepatitis B Virus (HBV), HIV (human immunodeficiency virus), and the like. In the examples of the present application, the virus genotype corresponds to the virus subtype.

An embodiment of the present application provides a method for generating a viral gene detection report, and fig. 1 is a schematic processing flow diagram of the method for generating a viral gene detection report in an embodiment of the present application, where the method for generating a viral gene detection report includes:

step 11, object information of the biological sample is acquired.

Here, the biological sample includes a sample containing nucleic acid, such as a blood sample, cervical detached cells, or a secretion sample. The object information of the biological sample may include basic information of the acquisition object and basic information of the PCR detection. The detection items comprise HPV typing detection, and 15 high-risk HPV typing judgments are carried out by adopting a four-tube method as an example for explanation. Table 1 shows the subject information of the biological sample in an embodiment of the present application, and referring to table 1, the subject information of the biological sample may include basic information of the subject, type information of the biological sample, application item information, information of the detection operation of the biological sample, and time information. Here, the sample number represents identification information of an acquisition subject of the biological sample. The basic information of the subject may include name, gender, age, and contact address. The application item information includes a detection item. The PCR reaction file name identifies a file of PCR detection information corresponding to the biological sample. It should be noted that cervical exfoliated cells or cervical secretions can be used as a biological sample in HPV typing assays.

TABLE 1 object information of biological samples

The information of the detection operation of the biological sample includes the spotting coordinates. The spotting coordinates contain the order of spotting of the same batch of biological samples on the PCR detection disk. The spotting coordinates represent information on the position of the reaction well where the sample is located. Generally, a PCR detection plate includes 96 reaction wells. The sample number includes the number of the biological sample at the time of the examination. For example, in the HPV15 typing four-tube method, 15 high-risk HPV subtypes and 1 internal standard gene are detected by a combination of 4 fluorescence channels and 4 tube reaction wells, and thus, each biological sample includes 4 point-like coordinates. As in table 1, the spotting coordinates of one biological sample are a1, B1, C1 and D1.

Further, the subject information of the biological sample may also include censorship information of the biological sample. The submission information of the biological sample includes a detection instrument, submission time, submission mechanism, sampling time, sample collection time, and subject information transmission time.

And step 12, acquiring PCR detection information of the biological sample, wherein the PCR detection information comprises PCR detection information of at least one detection item.

Here, the PCR detection information may be detection information of fluorescent quantitative PCR. The PCR detection information includes operation information and reaction results. The operation information includes information on the fluorescent channel and information on the position of the reaction well. Wherein the reaction result comprises a cycle threshold of the amplification curve. The PCR detection information of the detection item is determined according to the sample application coordinate corresponding to the detection item in the object information. Taking the detection item as HPV15 typing four-tube method detection and the sample application coordinates corresponding to the biological sample as A1, B1, C1 and D1 as an example, PCR detection information corresponding to the reaction wells A1, B1, C1 and D1 is included in PCR detection information of HPV15 typing four-tube method detection of one biological sample. The PCR detection information corresponding to the reaction well A1 is described. Table 2 shows PCR detection information in an embodiment of the present application. Referring to Table 2, Well indicates positional information of reaction wells of the detection plate, and the Detector indicates detection of fluorescence channels. FAM represents carboxyfluorescein, HEX represents hexachlorofluorescein, ROX represents 6-carboxy-X-rhodamine succinimidyl ester, and CY5 represents anthocyanin 5. Ct represents the cycle threshold of the PCR amplification curve, and NoCt represents no Ct value. StdDev Ct represents the standard deviation of Ct values. Sample Name represents the Sample Name. Task denotes a Task.

TABLE 2 information on PCR detection

Well	Sample Name	Detector	Task	Ct	StdDev Ct
						A1	/	FAM	/	NoCt	/
A1	/	HEX	/	NoCt	/
						A1	/	ROX	/	NoCt	/
A1	/	CY5	/	NoCt	/

It should be noted that the PCR detection information of the detection item can be determined according to the spotting coordinates corresponding to the detection item in the object information. In the embodiment of the present application, the detection items include various virus detection items, such as hepatitis b virus detection, HPV typing detection, and the like.

And step 13, determining the type information of the detection gene corresponding to the detection item based on the operation information in the PCR detection information and the relationship between the operation information and the type. Wherein, the detection genes comprise virus genes and internal standard genes.

Here, the relationship between the operation information and the genotype is defined in the metadata. Therefore, based on the information of the PCR detection of the acquired biological sample and the metadata, the type information of the detection gene corresponding to the detection item is determined. Wherein the relationship between the operation information and the genotype comprises the position information of the reaction hole and the relationship between the fluorescence channel and the genotype. Here, the internal standard gene can be used to detect whether PCR operation conditions are normal and whether the biological sample meets the detection conditions. For example, the internal standard gene includes beta-globin. In the examples of the present application, the detection genes include different viral genes and different internal standard genes depending on the detection items. In the examples of the present application, the types and the numbers of the viral gene and the internal standard gene are not limited.

In some embodiments, step 14, the positive and negative detection information of the detection gene is determined based on the reaction result in the PCR detection information and the relationship between the reaction result and the positive and negative detection result.

Here, the threshold value of the CT value of the PCR positive interpretation is stored in the metadata. Thus, the relationship between the PCR reaction results for different genotypes and the negative and positive detection results is defined in the metadata. And determining the positive and negative detection information of various virus genotypes in the detection gene and the positive and negative detection information of the reference gene based on the reaction result and the metadata in the PCR detection information.

Taking the four-tube test with the test item HPV15 typing as an example, table 3 shows the relationship among the operation information, genotype, PCR reaction result and positive and negative test result in the metadata. In Table 3, the internal standard gene is β -Globulins (β -globulin). HPV type 56 represents the type name of HPV. FAM represents carboxyfluorescein, HEX represents hexachlorofluorescein, ROX represents carboxy-X-rhodamine succinimidyl ester, and CY5 represents anthocyanin 5. N is not, Y is. CT denotes the cycle threshold.

Table 3 shows the relationship among the operation information, genotype, PCR reaction results and the positive and negative detection results in the metadata

And step 15, generating a virus gene detection report of the biological sample based on the object information, the type information and the positive and negative detection information.

Here, the target information, the type information of the viral gene, and the negative/positive detection information corresponding to each type of viral gene are correlated with each other based on the sample number, and a viral gene detection report for the biological sample is generated.

In the embodiment of the present application, since the PCR detection information of a plurality of detection items can be obtained at the same time, the virus gene detection report may include detection information of different viruses and/or different subtypes of the same virus of a plurality of detection items. In this way, the method for generating a virus gene detection report can quickly complete the analysis of the PCR detection results of a plurality of detection items, and comprehensively grasp the physical health condition of a clinical subject.

In the embodiment of the present application, object information of a biological sample is acquired. And acquiring PCR detection information of the biological sample, wherein the PCR detection information comprises PCR detection information of at least one detection item. And determining the type information of the detection gene corresponding to the detection item based on the operation information in the PCR detection information and the relationship between the operation information and the type, so that the type of the virus gene of the sample can be rapidly determined by utilizing the relationship between the operation information and the type. And determining the negative and positive detection information of the detection gene based on the reaction result in the PCR detection information and the relationship between the reaction result and the negative and positive detection result, so that the negative and positive of the virus genotype of the sample can be rapidly and accurately judged by utilizing the relationship between the reaction result and the negative and positive detection result. Generating a virus gene detection report of the biological sample based on the object information, the type information and the negative and positive detection information. Therefore, the object information and the detection information are integrated, the processes of data analysis of the viral genes and report generation are simplified, the detection reports of the viral genes can be generated quickly, the working efficiency of generating the detection reports is improved, and the defects of long time consumption are overcome. The information in the generated detection report comprises the object information, the type information and the positive and negative detection information, the information contained in the detection report is more comprehensive, and the generated detection report can provide more standardized information.

In some embodiments, step 11, obtaining subject information of a biological sample comprises:

object information contained in the file stored in the target storage area is read.

Here, a file conforming to a preset format is stored in a designated target storage area. The preset format includes an Excel file or a Comma Separated Values (CSV) file. Automatically scanning the file of the designated storage area and identifying object information in the file. Reading the object information of the biological sample by checking the header name, and uploading the object information of the biological sample to a database. In addition, a timing scanning mode can be adopted to update the new object information into the database. Thus, the object information is reduced from being missed and mistakenly transmitted. And the object information of the samples can be obtained in batch, so that the time for obtaining the object information of the samples is saved.

In some embodiments, step 12, obtaining PCR detection information of the biological sample comprises:

and reading the file containing the PCR detection information in the target storage area.

And determining PCR detection information according to the PCR file identification in the object information.

Here, the target storage area is a designated storage area, such as a designated folder within a disk. Automatically scanning the file of the designated storage area and identifying PCR detection information in the file. Reading the PCR detection information in the file by checking the header name, and uploading the PCR detection information to a database. And quickly determining PCR detection information corresponding to the biological sample from the database by using the PCR file identification in the object information. Therefore, the file information is automatically scanned and read and the information is quickly matched, so that the time for obtaining the information is saved, and the accuracy of information matching is improved.

And determining PCR detection information in the PCR file corresponding to the PCR file identification. Thus, PCR detection information is quickly determined.

and reading the file containing the PCR detection information in the target storage area according to the PCR file identification in the object information.

And determining PCR detection information according to the file containing the PCR detection information.

Here, a file conforming to a preset format is stored in a designated target storage area. The preset format includes an Excel file or a Comma Separated Values (CSV) file. Automatically scanning the file of the designated storage area and identifying PCR detection information in the file. And matching the identification information of the file containing the PCR detection information according to the PCR file identification in the object information, and determining the file containing the PCR detection information corresponding to the PCR file identification. For example, table 4 is a file containing PCR detection information in an embodiment of the present application. FAM represents carboxyfluorescein, HEX represents hexachlorofluorescein, ROX represents carboxy-X-rhodamine succinimidyl ester, and CY5 represents anthocyanin 5. Ct represents the cycle threshold of the PCR amplification curve, and NoCt represents no Ct value. # FF0013FF denotes color identification.

Table 4 shows a file containing PCR detection information according to an embodiment of the present application

Here, the PCR detection information of the biological sample in the file is read by checking the header name, and the PCR detection information is uploaded to the database. In addition, a timing scanning mode can be adopted to update the new PCR detection information into the database. Thus, the PCR detection information is reduced from missing transmission and error transmission. And the method achieves the purpose of obtaining the PCR detection information of the samples in batches, and saves the time for obtaining the PCR detection information of the samples.

and acquiring object information from a third-party system.

Here, the subject information of the biological sample is generally stored in a pathology system and a laboratory information system. The third party system may include a pathology system and/or a laboratory information system. To reduce manual duplication of clinical information, the viral gene testing report generation system 30 interfaces with third party systems. According to at least one of: and querying a database of a third-party system to acquire the object information of the biological sample according to the basic information, the sample number and the detection items of the object. For example, the third party system is a pathology information system. And inquiring a pathological information system according to the serial number information of the biological sample to obtain the object basic information of the biological sample.

In some embodiments, to achieve free addition of the subject information, step 11, obtaining the subject information of the biological sample includes: subject information of the entered biological sample is received. Wherein, the sample number in the object information can be recorded by a bar code gun.

In some embodiments, the operational information includes information on the location of the reaction wells and information on the fluorescence channels. Step 13, determining type information of the detection gene corresponding to the detection item based on the operation information in the PCR detection information and the relationship between the operation information and the type, including:

Here, the relationship between the positional information of the reaction well, the information of the fluorescence channel, and the genotype is defined in the metadata. For example, as shown in Table 3, using the relationship among the positional information of the reaction well, the information of the fluorescence channel, and the genotype in the metadata, it is possible to identify the fluorescence channel FAM having the reaction well order of 1 in the PCR detection, and the corresponding type of the viral gene is HPV56 type.

Meanwhile, various genotypes can be determined by utilizing different combinations of reaction holes and fluorescence channels. Thus, each fluorescence channel in each reaction well in the metadata corresponds to a type of gene. For example, using a combination of 4 fluorescence channels and 4 reaction wells in the metadata, the types of 15 high-risk HPV subtypes and 1 internal standard gene were detected. The combination of 2 fluorescence channels and 8 reaction wells in the metadata can also be used to detect the types of 15 high-risk HPV subtypes and 1 internal standard gene. It should be noted that, depending on the detection method, the type of the detection gene is determined by using a combination of the fluorescence channel and the reaction well in the metadata.

In the above embodiment, the types of the detection genes corresponding to the reaction wells and the fluorescence channels in the information for PCR detection can be determined without fail by using the relationship among the position information of the reaction wells, the information of the fluorescence channels, and the types of the genes in the metadata. Thus, the speed and accuracy of judging a plurality of virus genotypes are improved.

In some embodiments, the method for generating a viral gene detection report further comprises:

and determining a reaction result corresponding to each virus genotype in the detection genes and a reaction result corresponding to an internal standard gene in the detection genes according to the reaction result corresponding to the fluorescence channel in each reaction hole.

Here, the detection gene includes a viral gene and an internal standard gene. After determining the type of the detection gene corresponding to each fluorescence channel in each reaction hole, correlating the reaction result with the type of the gene by using the position information of the reaction hole and the information of the fluorescence channel to obtain the reaction result corresponding to each virus type and the reaction result corresponding to the internal standard gene.

Step 14, determining the positive and negative detection information of the detection gene based on the reaction result in the PCR detection information and the relationship between the reaction result and the positive and negative detection result, including:

and determining the positive and negative detection information of each virus genotype and the positive and negative detection information of the internal standard gene based on the reaction result corresponding to the virus gene, the reaction result corresponding to the internal standard gene and the relationship between the reaction result and the positive and negative detection result.

Specifically, the positive and negative detection information of each virus genotype is determined based on the reaction result corresponding to each virus genotype and the relationship between the PCR reaction result and the positive and negative detection result of the virus genes of different types. And determining the negative and positive detection information of the internal standard genes based on the corresponding reaction results of the internal standard genes and the relationship between the internal standard genes of different types and the negative and positive detection results.

Here, the threshold value of the CT value of the PCR positive interpretation is stored in the metadata. Therefore, the relationship between the PCR reaction results and the positive and negative detection results for different types of viral genes, and the relationship between the internal standard genes and the positive and negative detection results for different types are defined in the metadata.

Specifically, the threshold value of PCR positive interpretation is stored in the metadata. And by comparing the PCR reaction results of the virus genes of different types with the positive judgment threshold value, the relationship between the PCR reaction results of the virus genes of different types and the positive and negative detection results is defined. And comparing the PCR reaction results of the internal standard genes of different types with the positive interpretation threshold value to define the relationship between the PCR reaction results of the internal standard genes of different types and the positive and negative detection results.

In some embodiments, the threshold for PCR positive calls comprises a threshold for CT values for PCR positive calls. And defining the relationship between the PCR reaction results of the virus genes of different types and the positive and negative detection results through the size relationship between the PCR reaction results of the virus genes of different types and the threshold value of the positive interpretation CT value.

For example, the detection item is HPV detection, and as shown in table 3, the threshold value of the CT value for PCR positive interpretation with the virus type HPV type 56 is 39, and the metadata defines the relationship between the PCR reaction result for HPV type 56 and the negative-positive detection result by the magnitude relationship between the PCR reaction result for HPV type 56 and the threshold value of the CT value for positive interpretation.

In some embodiments, the relationship between the PCR reaction results and the negative-positive detection results for different types of viral genes comprises:

and when the PCR reaction result of the viral genes of one type is not less than the threshold value of the positive reading CT value, judging that the viral genes of the type are positive.

And when the PCR reaction result of the viral genes of one type is smaller than the threshold value of the positive reading CT value, judging that the viral genes of the type are negative.

In some embodiments, the relationship between the PCR reaction results and the negative-positive detection results for different types of internal standard genes comprises:

and when the PCR reaction result of the internal standard gene of one type is not less than the threshold value of the positive interpretation CT value, judging that the internal standard gene of the type is positive.

And when the PCR reaction result of the internal standard gene of one type is smaller than the threshold value of the positive interpretation CT value, judging that the internal standard gene of the type is negative.

In the above examples, the threshold value for positive interpretation was different for each type of gene. Therefore, when an auditor performs positive interpretation of multiple type genes, the auditor needs to query the threshold of positive interpretation of a single type gene, so as to complete the positive interpretation of the single type gene. Therefore, it takes a long time to complete the positive interpretation of genes of a plurality of types, and the error rate of interpretation is relatively high. However, in the present application, the threshold for PCR positive interpretation is stored in the metadata, and the relationship between the reaction result and the genotype in the metadata is used to quickly and accurately determine the negative and positive of the gene of each genotype according to the actual reaction result of the gene of each genotype, thereby improving the efficiency and accuracy of negative and positive interpretation of multiple genotypes.

In some embodiments, in step 14, after determining the negative-positive detection information of the detected gene, the method for generating the viral gene detection report further comprises:

and determining at least one type of virus gene which is positive in the positive and negative detection information and a first internal standard gene which is positive in the positive and negative detection information according to the positive and negative detection information of the detection genes.

Here, the type of virus whose detection result is positive is obtained from the negative and positive detection information of the detection gene, and the type of virus may be various. And taking the internal standard gene with positive detection result as the first internal standard gene.

And determining the concentration of the at least one type of viral genes according to the information of the reaction result of the at least one type of viral genes and the relation between the reaction result of the viral genes and the concentration of the viral genes.

Here, the PCR reaction standard curve of the viral gene was determined by quantitative correction of the standard. The functional relationship between the reaction result of the viral gene and the concentration of the viral gene can be determined according to the PCR reaction standard curve of the viral gene.

Here, the standard curve of PCR reaction of the internal standard gene was determined by quantitative correction of the standard. And determining the functional relationship between the reaction result of the internal standard gene and the concentration of the internal standard gene according to the PCR reaction standard curve of the internal standard gene.

For example, the HPV15 typing four-tube method quantitative formula is as follows:

according to the standard curve of the virus gene PCR reaction, the functional relationship between the reaction result of the virus gene and the concentration of the virus gene is determined as follows:

Ct_v＝-3.36lg(C_v) +44.93 (equation 1)

The formula for calculating the concentration of the viral gene can be derived from formula 1:

according to the standard curve of the PCR reaction of the internal standard gene, determining the functional relationship between the reaction result of the internal standard gene and the concentration of the internal standard gene as follows:

Ct_ism＝-3.43lg(C_ism)+47.86. (formula 3)

From equation 3, a formula for calculating the concentration of the internal standard gene can be derived:

wherein Ct is_vCharacterization of the PCR reaction results of the viral genes, Ct_ismCharacterization of the PCR reaction results of the internal reference genes, C_vCharacterization of the concentration of the viral genes, C_ismThe concentration of the internal standard gene was characterized.

determining infection information of certain at least one type of viral gene based on the concentration of the at least one type of viral gene and the concentration of the first internal standard gene, and adding the infection information to the viral gene detection report.

Here, the infection information includes a viral load. Determining the viral load of at least one type of viral gene based on the concentration of at least one type of viral gene and the concentration of the first internal standard gene. Viral load can be expressed in relative amounts. For example, viral load characterizes the viral copy number of a certain viral subtype per 1 million cells.

Wherein the calculation formula of the virus load is as follows:

here, VL characterizes the viral load, C_vCharacterization of the concentration of the viral genes, C_ismThe concentration of the internal standard gene was characterized.

In addition, the human genome is diploid, and the concentration of the cells has a twofold relationship with the concentration of the internal standard gene. The cell concentration in the sample was:

C_cell＝C_ism/2 (formula 6)

Here, C_cellCharacterization of the concentration of cells, C_ismThe concentration of the internal standard gene was characterized.

In the above embodiment, the viral load is calculated by the standard curve, so as to accurately calculate the viral load of the sample. Meanwhile, the change of the viral load can be detected according to multiple HPV quantitative estimations, so that the development or the outcome of the pathological changes of the sample object can be predicted. In this manner, clinical management of the sample subject is facilitated, and screening and prevention of disease is facilitated. In addition, when the genotype of the virus is analyzed based on the PCR detection information, the virus load can be quantitatively estimated, thereby contributing to the judgment of the lesion status of the sample object.

In some embodiments, the infection information further includes an infection rate. The infection ratio is characterized by the ratio of the concentration of the viral gene of any one positive type to the total concentration of the viral genes of all positive types. Here, the formula for calculating the infection rate is as follows:

wherein i_vmCharacterizing the infection ratio of the m-type viral genes, k being the number of detected positive viral subtypes, C_vmThe concentration of the m-type viral genes was characterized.

generating clinical interpretation information of the viral genes based on the viral genotype and the relationship between the viral genotype and the clinical risk annotation, and adding the clinical interpretation information to the viral gene detection report.

Here, clinical risk annotations corresponding to the virus genotype are stored in the metadata. Thus, the metadata defines the relationship between the virus genotype and the clinical risk annotation. Thereby generating clinical interpretation information of the viral genes according to the viral genotype and the metadata. Therefore, the virus gene detection report contains the clinical interpretation information of the virus genes, so that the user can understand the detection result, and the doctor can perform clinical diagnosis on the user conveniently.

In some embodiments, when the positive-negative information of the biological sample includes a virus genotype with a positive detection result, the biological sample is subjected to a thin layer cell assay (TCT). Thus, whether the biological sample is diseased or not is further determined.

In some embodiments, step 15, generating a virus gene detection report of the biological sample based on the subject information, the type information, and the negative-positive detection information, comprises:

and replacing the content label to be replaced in the analysis report template by using the object information, the type information and the positive and negative detection information to generate a virus gene detection report of the biological sample.

Here, the Free Marker framework is used to define the content tag to be filled in each item in the detection report template. And replacing the content label to be replaced in the detection report template by using the object information, the type information and the negative and positive detection information, thereby generating a virus gene detection report of the biological sample. Therefore, the virus gene detection report is generated by replacing the label, and the generation of analysis reports in various formats can be supported. And the information in the generated detection report comprises the object information, the type information and the positive and negative detection information, the information contained in the detection report is more comprehensive, and the generated detection report can provide more standardized information.

and replacing the content label to be replaced in the analysis report template by using the object information, the type information, the positive and negative detection information and the infection information to generate a virus gene detection report of the biological sample.

Here, the Free Marker framework is used to define the content tag to be filled in each item in the detection report template. And replacing the object information, the type information, the positive and negative detection information and the infection information with the content label to be replaced in the detection report template to generate a virus gene detection report of the biological sample. Therefore, the virus gene detection report is generated by replacing the label, and the generation of analysis reports in various formats can be supported, so that the generation device of the analysis reports is suitable for different clinical application scenes.

In another aspect of the embodiments of the present application, a device for generating a virus gene detection report is also provided. Fig. 2 is a schematic structural diagram of a device for generating a virus gene detection report according to an embodiment of the present application, please refer to fig. 2, wherein the generating device 20 includes: a first acquisition module 21, a second acquisition module 22, a genotype determination module 23, an information determination module 24, and a generation module 25.

A first obtaining module 21, configured to obtain object information of a biological sample.

And a second obtaining module 22, configured to obtain PCR detection information of the biological sample, where the PCR detection information includes PCR detection information of at least one detection item.

And the genotype determination module 23 is configured to determine, based on the operation information in the PCR detection information and the relationship between the operation information and the genotype, the genotype information of the detection gene corresponding to the detection item, where the detection gene includes a virus gene and an internal standard gene.

And the information determining module 24 is used for determining the positive and negative detection information of the detection genotype based on the reaction result in the PCR detection information and the relationship between the reaction result and the positive and negative detection result.

And the generating module 25 is used for generating a virus gene detection report of the biological sample based on the object information, the type information and the negative and positive detection information.

In some embodiments, the first obtaining module 21 is configured to read the object information included in the file stored in the target storage area.

The second obtaining module 22 is configured to read a file containing PCR detection information in the target storage area according to the PCR file identifier in the object information; and determining PCR detection information according to the file containing the PCR detection information.

In some embodiments, the operational information includes information on the location of the reaction wells and information on the fluorescence channels. And a genotype determination module 23, configured to determine a genotype of the detection gene corresponding to the fluorescence channel in each reaction well based on the position information of the reaction well and the information of the fluorescence channel in the information detected by the PCR and a relationship among the position information of the reaction well, the information of the fluorescence channel and the genotype.

In some embodiments, the generating means 20 further comprises: and a result determination module. And the result determining module is used for determining a reaction result corresponding to each virus genotype in the detection genes and a reaction result corresponding to the internal standard gene in the detection genes according to the reaction result corresponding to the fluorescence channel in each reaction hole.

And an information determining module 24, configured to determine, based on the reaction result corresponding to each virus genotype, the reaction result corresponding to the internal standard gene, and a relationship between the reaction result and a positive/negative detection result, positive/negative detection information of each virus genotype and positive/negative detection information of the internal standard gene.

In some embodiments, the generating means 20 further comprises: a positive detection module and a concentration determination module.

And the positive detection module is used for determining at least one type of positive virus gene in the negative and positive detection information and a first internal standard gene which is positive in the negative and positive detection information according to the negative and positive detection information of the detection gene.

The concentration determination module is used for determining the concentration of the at least one type of virus genes according to the reaction result information of the at least one type of virus genes and the relation between the reaction result of the virus genes and the concentration of the virus genes; and determining the concentration of the first internal standard gene according to the reaction result information of the first internal standard gene and the relation between the reaction result of the internal standard gene and the concentration of the internal standard gene.

In some embodiments, the information determining module 24 is further configured to determine the infection information of the at least one type of viral gene based on the concentration of the at least one type of viral gene and the concentration of the first internal standard gene.

A generating module 25 for adding the infection information to the virus gene detection report.

In order to further understand the apparatus for generating a virus gene detection report provided in the embodiments of the present application, another system for generating a virus gene detection report is provided in one embodiment of the present application, and the system 30 for generating a virus gene detection report includes the apparatus 20 for generating a detection report. Fig. 3 is a schematic structural diagram of a system for generating a virus gene detection report in an embodiment of the present application, please refer to fig. 3, wherein the system 30 for generating a virus gene detection report includes a test order information module 31, a PCR result module 32, and a metadata module 33. The examination order information module 31 includes a first obtaining module, a genotype determination module, an information determination module, and a generation module, and the PCR result module 32 includes a second obtaining module, including the example.

The test order information module 31 includes a scanning unit 311, a sample information query unit 312, a PCR result information query unit 313, and a test order query unit 314. And a scanning unit 311 for reading object information and PCR detection information contained in the file stored in the target area. A sample information query unit 312 for querying information of the biological sample. The information of the biological sample includes object information of the biological sample and a detection report of the biological sample. And a PCR result information inquiring unit 313 for inquiring detection information of the biological sample, the detection information including type information of the gene and positive and negative detection information. And the test order query unit 314 is used for querying the detection report of the biological sample. The test sheet query unit 314 is further configured to filter the positive samples so as to screen out the positive samples in the biological sample. And querying positive samples for TCT detection information.

The PCR result module 32 may include a PCR result information uploading unit 321, a genotype analysis unit 322, a clinical annotation unit 323, a report generation unit 324, a PCR report query unit 325, and a PCR report statistics unit 326. A PCR result information uploading unit 321, configured to upload PCR result information. And a genotype analysis unit 322 for judging the genotype of the virus and the genotype of the internal standard. A clinical annotation unit 323 for reading viral genes. And a report generation unit 324 for generating a virus gene detection report. The PCR report query unit 325 is used for querying the detection report and deriving the detection report. And a PCR report statistic unit 326 for graphically displaying the number of samples and the detection rate of each genotype. Therefore, the PCR report statistic unit 326 can be used for calculating and displaying the distribution of virus subtypes in the detected population in real time, and parameters such as the detection time period of the sample can be adjusted, so that a tool for monitoring the detection rate in real time is provided for experimenters. In this way, the PCR report statistics unit 326 can quickly find the positive detection rate of single or multiple virus types, thereby monitoring the accuracy of the detection experiment result and using the statistical result as the index of regional epidemiology.

In some embodiments, the object information and the detection information already in the database can be queried through a sample number, basic information of the object, a detection item, or a detection time.

In some embodiments, the test report is downloaded or batch downloaded based on the sample number, basic information of the object, or file name.

The metadata module 33 includes a PCR threshold information unit 331 and a clinical annotation information unit 332. And a PCR threshold information unit 331 for storing genotypes corresponding to the fluorescence channel and the reaction well. And storing the PCR reaction threshold of the detection kit. And the clinical annotation information unit 333 is used for storing clinical annotation information corresponding to the virus genes.

In some embodiments, referring to fig. 3, the system 30 for generating a viral gene detection report further comprises a system setup module 34. The system setting module 34 includes a user management unit 341, a character management unit 342, a password modification unit 343, a random password unit 344, and a card information unit 345. The user management unit 341 is configured to edit a user account. A role management unit 342 for managing the authority roles of the users. A password modification unit 343, configured to modify the account password of the user. A random password unit 344 for automatically generating a random initial password for the new user. A card information unit 345 for managing user information.

In some embodiments, fig. 4 is a schematic view of an application scenario of a system for generating a virus gene detection report in an embodiment of the present application, and as shown in fig. 4, the system 30 for generating a virus gene detection report may log in by using a web page type user interface, for example, using a fox browser to open the user interface and log in the system. The background of the virus gene detection report generation system 30 is connected with the PCR database and the Linux server. The PCR database is a relational database, such as a structured query language (MySQL) database. The Linux server is a Tomcat (Tomcat) web application server.

In some embodiments, referring to FIG. 4, the viral gene testing report generation system 30 also interfaces with third party systems. The third party system includes a pathology system and/or a laboratory information system. The third-party system stores object information of the biological sample.

In order to further understand the method for generating a virus gene detection report provided in the embodiment of the present application, another method for generating a virus gene detection report is provided in an embodiment of the present application, and is applied to the system 30 for generating a virus gene detection report, and the PCR detection is a fluorescence quantitative PCR detection, and the detection item is an HPV typing four-tube method detection. Fig. 5 is a schematic processing flow chart of a method for generating a viral gene detection report according to another embodiment of the present application, please refer to fig. 5, wherein the method for generating a viral gene detection report includes:

step 41, reading the object information contained in the file stored in the target storage area.

Here, the object information of the biological sample may include basic information of the acquisition object and basic information of the PCR detection. The following will describe the detection items including HPV typing detection and HPV typing judgment by the four-tube method. The object information of the biological sample may include basic information of the object, type information of the biological sample, application item information, information of the detection operation of the biological sample, and time information. The sample number represents identification information of an acquisition subject of the biological sample. The basic information of the subject may include name, gender, age, and contact address. The application item information includes a detection item.

The information of the detection operation of the biological sample includes the spotting coordinates. The spotting coordinates contain the order of spotting of the same batch of biological samples on the PCR detection disk. The spotting coordinates represent information on the position of the reaction well where the sample is located. Generally, a PCR detection plate includes 96 reaction wells. The sample number includes the number of the biological sample at the time of the examination. Further, the subject information of the biological sample may also include censorship information of the biological sample. The submission information of the biological sample includes a detection instrument, submission time, submission mechanism, sampling time, sample collection time, and subject information transmission time.

Here, a file conforming to a preset format is stored in a designated target storage area. The preset format includes an Excel file or a Comma Separated Values (CSV) file. The system automatically scans the files of the designated storage area and identifies object information in the files. Reading the object information of the biological sample by checking the header name, and uploading the object information of the biological sample to a database. In addition, a timing scanning mode can be adopted to update the new object information into the database. Thus, the object information is reduced from being missed and mistakenly transmitted. And the object information of the samples can be obtained in batch, so that the time for obtaining the object information of the samples is saved.

Taking an example that the generation system of the viral gene detection report includes a cervical cancer screening report system, fig. 6 is a schematic diagram of a main interface of the generation system of the viral gene detection report in an embodiment of the present application. The generation of viral gene testing reports the menu list in the interface of system 30 includes test order information, PCR results, system settings and help information. FIG. 7 is a schematic diagram of a sample information scanning interface of a system for generating a virus gene detection report according to an embodiment of the present application. Referring to fig. 6 and 7, in the interface of the generation system 30 for detecting a virus gene detection report, the sample file is scanned under the inspection list information or the sample file is uploaded as the scanning result file is clicked, and the interface for scanning the sample information is entered.

In addition, the system 30 for generating a virus gene detection report queries sample information after detecting an instruction to query the sample information. Wherein, for the sample information already in the database, the system 30 for generating the virus gene detection report is based on at least one of the following: basic information, sample numbers, detection items and detection time of the objects, and sample information is inquired.

For example, fig. 8 is a schematic diagram of a sample information query interface of a system for generating a virus gene detection report according to an embodiment of the present application. Referring to fig. 6 and 8, in the interface of the system 30 for generating a virus gene detection report, the sample information query under the test ticket information is clicked and enters the interface of the sample information query, when the system 30 for generating a virus gene detection report detects that the virus gene detection report is generated. The system provides a query function of multi-condition screening sample information and a summary query function of a check sheet, and queries personnel information and detection results of the biological samples according to query conditions. Meanwhile, the sample number in the sample information can be input through a bar code gun.

In addition, after the system 30 for generating a virus gene detection report enters the interface for inquiring the sample information, the virus gene detection report of the biological sample can be downloaded individually or in batch.

And step 42, reading the PCR detection information contained in the file stored in the target storage area.

Here, a file conforming to a preset format is stored in a designated target storage area. The preset format includes an Excel file or a Comma Separated Values (CSV) file. Automatically scanning the file of the designated storage area and identifying PCR detection information in the file. And matching the identification information of the file containing the PCR detection information according to the PCR file identification in the object information, and determining the file containing the PCR detection information corresponding to the PCR file identification.

Here, the PCR detection information may be detection information of fluorescent quantitative PCR. The PCR detection information includes operation information and reaction results. The operation information includes information on the fluorescent channel and information on the position of the reaction well. Wherein the reaction result comprises a cycle threshold of the amplification curve. The system 30 for generating a virus gene detection report can accept result files exported by different PCR instrument software systems.

And 43, determining the type information of the virus gene corresponding to the detection item based on the operation information in the PCR detection information and the relationship between the operation information and the type in the metadata.

Here, the relationship between the operation information and the genotype is defined in the metadata. Therefore, based on the information of the PCR detection of the acquired biological sample and the metadata, the type information of the detection gene corresponding to the detection item is determined. Wherein the relationship between the operation information and the genotype comprises the position information of the reaction hole and the relationship between the fluorescence channel and the genotype.

And step 44, determining the positive and negative detection information of the virus genes based on the reaction result in the PCR detection information and the relationship between the reaction result and the positive and negative detection result in the metadata.

For example, fig. 9 is a schematic diagram of a PCR result query interface of a system for generating a virus gene detection report according to an embodiment of the present application. Taking the detection item as HPV typing detection as an example, the PCR result query interface is shown in FIG. 9. Referring to fig. 6 and 9, in the interface of the generation system 30 for generating a virus gene detection report, the PCR result query under the test report result information is clicked and enters the interface of the PCR result query, which is detected by the generation system 30 for a virus gene detection report.

And step 45, determining the virus load of the virus genes based on the reaction result in the PCR detection information and the relationship between the reaction result and the virus load in the metadata.

Here, at least one type of viral gene whose detection result is positive is specified based on the negative-positive detection information of the detection gene. And determining the viral load of the viral genes of at least one type according to the reaction result of the viral genes of at least one type and the relationship between the reaction result of the viral gene type and the viral load in the metadata.

And step 46, generating a virus gene detection report of the biological sample based on the object information, the type information of the virus genes, the negative and positive detection information and the virus load.

Here, the system 30 for generating a viral gene test report integrates the type information of viral genes, the negative and positive test information, and the viral load according to the sample number, and generates a viral gene test report of a biological sample.

For example, fig. 10 is a schematic diagram of a PCR report query interface of a system for generating a virus gene detection report according to an embodiment of the present application. Taking the detection item as HPV typing detection as an example, the PCR report query interface is shown in FIG. 10. Referring to fig. 6 and 10, in the interface of the generation system 30 for generating a virus gene detection report, the PCR report query is clicked under the PCR result, and the interface enters the PCR report query.

In some embodiments, step 43, determining type information of the virus gene corresponding to the detection item based on the operation information in the PCR detection information and the relationship between the operation information and the type in the metadata, includes:

In some embodiments, step 45, determining the viral load of the viral gene based on the reaction result in the PCR detection information and the relationship between the reaction result and the viral load in the metadata comprises:

step 451, determining the concentration of at least one type of viral gene based on the information on the reaction result of at least one type of viral gene and the relationship between the reaction result of the viral gene and the concentration of the viral gene.

And step 452, determining the concentration of the first internal standard gene according to the reaction result information of the first internal standard gene and the relation between the reaction result of the internal standard gene and the concentration of the internal standard gene.

Ct_v＝-3.36lg(C_v) +44.93 (equation 8)

From equation 8, the formula for calculating the concentration of the viral gene can be derived:

Ct_ism＝-3.43lg(C_ism)+47.86. (formula 10)

From equation 10, the formula for calculating the concentration of the internal standard gene:

At step 453, the viral load of the at least one viral genotype type is determined based on the concentration of the at least one viral gene type and the concentration of the first internal standard gene.

Here, the viral load can be expressed in relative amounts. For example, viral load characterizes the viral copy number of a viral subtype per 1 million cells.

Wherein the calculation formula of the virus load is as follows:

Furthermore, the cell concentration in the sample was:

C_cell＝C_ism/2 (formula 13)

In some embodiments, the method further comprises: the infection rate was determined based on the gene concentration of the positive virus genotype.

Here, the infection ratio represents the ratio of the concentration of any one type of positive viral gene to the total concentration of all types of positive viral genes. Here, the formula for calculating the infection rate is as follows:

In some embodiments, the method further comprises:

Here, clinical risk annotations corresponding to the virus genotype are stored in the metadata. Thus, the metadata defines the relationship between the virus genotype and the clinical risk annotation. Thus, based on the viral genes and the metadata, clinical interpretation information of the viral genes is generated. Therefore, the virus gene detection report contains the clinical interpretation information of the virus genes, so that the user can understand the detection result, and the doctor can perform clinical diagnosis on the user conveniently.

In some embodiments, step 46, generating a virogene detection report for the biological sample based on the subject information, the type information of the virogenes, the negative-positive detection information, and the viral load, comprises:

For example, FIG. 11 is a schematic representation of a first type of HPV detection report in an embodiment of the present application. For an example of the four-tube method for typing HPV15, please refer to FIG. 11 for the report of the virus gene detection of the biological sample.

and replacing the content labels to be replaced in the analysis report template by using the object information, the type information, the positive and negative detection information, the virus capacity and the infection rate to generate a virus gene detection report of the biological sample.

For example, FIG. 12 is a schematic representation of a second type of HPV detection report in an embodiment of the present application. For an example of the four-tube method for typing HPV15, please refer to FIG. 12 for the report of the virus gene detection of the biological sample.

Here, the Free Marker framework is used to define the content tag to be filled in each item in the detection report template. And replacing the content label to be replaced in the detection report template by using the object information, the type information and the positive and negative detection information so as to generate a first type of virus gene detection report of the biological sample.

In addition, on the basis of the object information, the type information and the positive and negative detection information, the content tags to be replaced in the detection report template can be replaced by the viral load and the infection rate, so that a second type of viral gene detection report of the biological sample is generated.

Therefore, the virus gene detection report is generated by replacing the label, and the generation of analysis reports in various formats can be supported, so that the generation device of the analysis reports is suitable for different clinical application scenes.

In some embodiments, the method for generating a viral gene detection report further comprises: the system 30 for generating a virus gene test report counts the number of samples and the detection rate for each virus genotype under the test items.

Here, the system 30 for generating a virus gene test report counts the number of samples and the detection rate for each virus genotype under the test items. The system 30 for generating a virus gene detection report can adjust parameters such as a detection time period of a biological sample, and provide an experimenter with a tool for monitoring a detection rate in real time. For example, fig. 13 is a schematic diagram of a statistical interface of a system for generating a virus gene detection report according to an embodiment of the present application. Therefore, the statistical result of the system can enable a detector to quickly find the positive detection rate of single or multiple compound virus types, and the accuracy of the detection experiment can also be used as the index of regional epidemiology.

In some embodiments, the method for generating a viral gene detection report further comprises: and when the yin-yang detection information of the biological sample contains the virus genotype with a positive detection result, carrying out TCT detection on the positive sample.

Here, the system 30 for generating a viral gene test report filters out positive samples and prompts TCT test for the positive samples. For example, fig. 14 is a schematic diagram of a checklist query interface in an embodiment of the present application. The generation system 30 of the virus gene detection report detects that the test order query is clicked under the test order information in the interface of the generation system 30 of the virus gene detection report, and the test order query enters the interface of the test order query. A TCT test flag may appear in a checklist query interface containing an entry for a positive sample.

For example, fig. 15 is a first schematic diagram of a TCT detection interface according to an embodiment of the present application. Fig. 16 is a second schematic diagram of a TCT detection interface according to an embodiment of the present application. When the generation system 30 of the virus gene detection report detects that the TCT detection flag in the interface of the checklist query is clicked, the TCT detection interface is entered.

In practical applications, it is not feasible in practice to manually interpret multiple virus types and estimate the viral load according to the instructions of the fluorescent quantitative PCR assay kit, thereby generating a high throughput assay report. For example, for the typing of 15 HPV, one sample takes 60 minutes manually for interpretation and report generation, and a 96-well reaction plate can take 24 samples in a batch, which takes 1 person 32 hours to work. However, with the generation system of the virus gene detection report, the analysis time and the auditing detection report time of the matched software of the PCR instrument are eliminated from one batch of 24 samples, the system completes the automatic scanning of the information of the screening personnel and the automatic analysis of the detection data, and the generation of the detection report of one batch of 24 samples only needs 3 minutes. Therefore, the screening efficiency can be improved aiming at the characteristic of large sample quantity of the detection items. And the mode of reading files by automatic scanning replaces the mode of manually inputting data by operators, so that the information input efficiency can be improved. The system is also provided with a database and a statistical tool, so that the later statistical analysis and data mining are facilitated, and the normalization and the repeatability of information are ensured.

Fig. 17 is a schematic structural diagram of an apparatus in an embodiment of the present application, and the apparatus 500 at least includes at least one processor 501 and at least one memory 502. Wherein the memory 502 is used for storing a computer program capable of running on the processor 501, and the processor 501 is used for executing the computer program and executing: a method for generating a viral gene detection report, the method comprising:

object information of a biological sample is acquired.

And acquiring PCR detection information of the biological sample, wherein the PCR detection information comprises the PCR detection information of at least one detection item.

Determining type information of a detection gene corresponding to the detection item based on operation information in the PCR detection information and a relation between the operation information and the type; wherein, the detection gene comprises a virus gene and an internal standard gene.

And determining the negative and positive detection information of the detection gene based on the reaction result in the PCR detection information and the relationship between the reaction result and the negative and positive detection result.

In some embodiments, the processor 501 is further configured to, when running the computer program, perform:

the acquiring PCR detection information of the biological sample comprises:

the operation information comprises position information of the reaction hole and information of the fluorescence channel, and type information of the detection gene corresponding to the detection item is determined based on the operation information in the PCR detection information and the relationship between the operation information and the type, and comprises the following steps:

and determining a reaction result corresponding to each virus genotype in the detection genes and a reaction result corresponding to an internal standard gene in the detection genes according to the reaction result corresponding to the fluorescent channel in each reaction hole.

Determining the positive and negative detection information of the detection gene based on the reaction result in the PCR detection information and the relationship between the reaction result and the positive and negative detection result, wherein the determination comprises:

after determining the positive and negative detection information of the detection genes, determining at least one type of virus gene which is positive in the positive and negative detection information and a first internal standard gene which is positive in the positive and negative detection information according to the positive and negative detection information of the detection genes.

determining infection information of the at least one type of viral gene based on the concentration of the at least one type of viral gene and the concentration of the first internal standard gene, and adding the infection information to a viral gene detection report.

generating a virus gene detection report of the biological sample based on the subject information, the type information, and the negative-positive detection information, including:

In some embodiments, the device further comprises a system bus 503, a user interface 504, and a communication interface 505. Wherein the system bus 503 is configured to enable connective communication between these components, the user interface 504 may include a display screen, and the communication interface 505 may include standard wired and wireless interfaces.

An embodiment of the present invention further provides a storage medium, where a computer program is stored on the storage medium, and when the computer program is executed by a processor, the steps of the method for generating a virus gene detection report provided in any embodiment of the present application are implemented.

It will be understood by those of ordinary skill in the art that all or some of the steps of the methods, systems, functional modules/units in the devices disclosed above may be implemented as software, firmware, hardware, and suitable combinations thereof. In a hardware implementation, the division between functional modules/units mentioned in the above description does not necessarily correspond to the division of physical components; for example, one physical component may have multiple functions, or one function or step may be performed by several physical components in cooperation. Some or all of the physical components may be implemented as software executed by a processor, such as a central processing unit, digital signal processor, or microprocessor, or as hardware, or as an integrated circuit, such as an application specific integrated circuit. Such software may be distributed on computer readable media, which may include computer storage media (or non-transitory media) and communication media (or transitory media). The term computer storage media includes volatile and nonvolatile, removable and non-removable media implemented in any method or technology for storage of information such as computer readable instructions, data structures, program modules or other data, as is well known to those of ordinary skill in the art. Computer storage media includes, but is not limited to, RAM, ROM, EEPROM, flash memory or other memory technology, CD-ROM, Digital Versatile Disks (DVD) or other optical disk storage, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage devices, or any other medium which can be used to store the desired information and which can accessed by a computer. In addition, communication media typically embodies computer readable instructions, data structures, program modules or other data in a modulated data signal such as a carrier wave or other transport mechanism and includes any information delivery media as known to those skilled in the art.

The above description is only for the specific embodiments of the present application, but the scope of the present application is not limited thereto, and any person skilled in the art can easily conceive of the changes or substitutions within the technical scope of the present application, and shall be covered by the scope of the present application. The protection scope of the present application shall be subject to the protection scope of the claims.

Claims

1. A method for generating a viral gene detection report, the method comprising:

acquiring object information of a biological sample;

2. The method of claim 1, wherein the obtaining PCR detection information of the biological sample comprises:

3. The method of claim 1, wherein the operation information includes position information of the reaction well and information of the fluorescence channel, and the determining type information of the detection gene corresponding to the detection item based on the operation information in the PCR detection information and a relationship between the operation information and the type comprises:

4. The method of claim 3, further comprising:

5. The method of claim 1, wherein after determining the negative-positive detection information of the detected gene, the method further comprises:

and determining the concentration of the at least one type of viral genes according to the reaction result information of the at least one type of viral genes and the relation between the reaction result of the viral genes and the concentration of the viral genes.

6. The method of claim 5, further comprising:

7. The method of claim 1, further comprising:

8. An apparatus for generating a virus gene detection report, the apparatus comprising: the system comprises a first acquisition module, a second acquisition module, a genotype type determination module, an information determination module and a generation module;

9. An apparatus comprising a memory, a processor and a computer program stored on the memory and executable on the processor, wherein the processor when executing the program performs the steps of the method for generating a viral gene detection report according to any of claims 1 to 7.

10. A computer storage medium, characterized in that the computer storage medium has stored thereon a computer program which, when executed by a processor, implements the steps of the method for generating a viral gene detection report according to any one of claims 1 to 7.