CN113241177A - Method, device and equipment for evaluating immunity level and storage medium - Google Patents
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
- G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
- G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
- G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
Abstract
The invention provides a method, a device, equipment and a storage medium for evaluating immunity level. The method comprises the following steps: (1) collecting sequencing data of a B cell antigen receptor variable region and/or a T cell antigen receptor variable region of a lymphocyte sample, comparing the sequencing data with data in a public database, and calculating a D value; (2) distinguishing a healthy sample and a sub-healthy sample according to the distribution graph of the D values, fitting the D values of the healthy samples by adopting multiple Gaussian distributions, and determining a standard D value; (3) fitting the D values of the sub-health sample and the disease sample by adopting a Gaussian distribution function to obtain a Gaussian distribution function A and a Gaussian distribution function B; (4) and evaluating the immunity level of the unknown sample according to the standard D value, the Gaussian distribution function A and the Gaussian distribution function B. The method provided by the invention analyzes the sequencing result and fits multiple Gaussian distributions, and realizes the effect of accurately, comprehensively and efficiently evaluating the immunity of the sample.
Description
Technical Field
The invention belongs to the technical field of immunity, and relates to a method, a device, equipment and a storage medium for evaluating immunity level.
Background
At present, the immune function analysis methods applied clinically mainly include five items of immunity, blood routine and lymphocyte subpopulation analysis. Wherein, the five immune items adopt a one-way immunodiffusion method, an enzyme-linked immunosorbent assay (ELISA), a Radioimmunoassay (RIA), an immune fixed electrophoresis or an immunoturbidimetry to detect the content of IgG, IgA, IgM, complement C3 and C4 in blood; the conventional blood cell counting method is used for analyzing the number of white blood cells in peripheral blood and judging whether inflammatory reaction exists in vivo; lymphocyte subpopulation analysis the number and relative proportion of different leukocyte subpopulations in peripheral blood are analyzed using flow cytometry or PCR techniques.
However, these methods have various degrees of drawbacks. Five immune items are only directed against humoral immunity and cannot comprehensively evaluate cellular immunity; in assessing humoral immunity, only the overall levels of IgG, IgA, IgM, and complements C3, C4 were detected, and no in-depth analysis was possible at the molecular sequence level. Blood routine can only roughly judge the level of cellular immunity, cannot perform immunoassay for specific diseases, and cannot judge the classification and diversity of immune cells at the gene level. Though the lymphocyte subpopulation analysis can realize comprehensive analysis, the operation is complicated, the cost is high, the period is long, and the application range is limited.
CN110246539A discloses a method and a device for evaluating immunity level, which comprises separating lymphocytes from a sample of a subject, extracting RNA of the lymphocytes and carrying out reverse transcription, obtaining BCR and/or TCR variable region polynucleotides by utilizing specific primers, sequencing the polynucleotides to obtain sequence information, calculating D of the BCR and/or TCR variable region sequences50Value, thereby determining the immunity level of the subject. But the accuracy is to be further improved.
Therefore, most of the existing immunity detection methods can only carry out rough evaluation, and lack comprehensiveness, sensitivity and accuracy, and a new immunity evaluation method is needed to be established.
Disclosure of Invention
In response to the shortcomings of the prior art and the actual need, the present invention provides a method, apparatus, device and storage medium for assessing immunity levels. In the evaluation method of the immunity level, the sequencing result of the sample is analyzed, compared and fitted with multiple Gaussian distributions, so that the aim of accurately, comprehensively and efficiently evaluating the immunity of the sample is fulfilled.
In order to achieve the purpose, the invention adopts the following technical scheme:
in a first aspect, the present invention provides a method of assessing the level of immunity for the purpose of non-disease diagnosis, the method comprising:
(1) collecting sequencing data of a B cell antigen receptor variable region and/or a T cell antigen receptor variable region of a lymphocyte sample, comparing the sequencing data with data in a public database, and calculating a D value;
(2) distinguishing a healthy sample and a sub-healthy sample according to the distribution graph of the D values, fitting the D values of the healthy samples by adopting multiple Gaussian distributions, and determining a standard D value;
(3) fitting the D values of the sub-health sample and the disease sample by adopting a Gaussian distribution function to obtain a Gaussian distribution function A and a Gaussian distribution function B;
(4) and evaluating the immunity level of the unknown sample according to the standard D value, the Gaussian distribution function A and the Gaussian distribution function B.
The invention provides a method for evaluating immunity level, which can be used for evaluating the immunity level of health samples (including human beings or animals), sub-health samples and disease samples, in other words, the method can obtain the general classification of unknown samples according to the evaluation result of immunity, simply evaluate the health condition of the unknown samples, predict hidden samples with diseases in advance and remind the sample owners of whether to carry out further diagnosis and treatment; the method can also be used for the purposes of scientific research experiments and the like, and has a wide application range.
In the present invention, the method comprises:
collecting sequencing data of antigen receptor variable regions of B cells or T cells in lymphocyte samples (the samples comprise normal samples and disease samples, wherein the normal samples comprise healthy samples and sub-healthy samples), comparing the sequencing data with data in a public database, and calculating a D value; according to the distribution diagram of the D values, firstly distinguishing the healthy samples from the sub-healthy samples, adopting multiple Gaussian distributions to fit the D values of the healthy samples, and determining standard D values; fitting the D values of the sub-health sample and the disease sample by adopting a Gaussian distribution function to obtain a Gaussian distribution function A and a Gaussian distribution function B; the immunity level of the unknown sample is evaluated according to the standard D value, the gaussian distribution function a and the gaussian distribution function B, for example, by substituting the D value of the unknown sample into the gaussian distribution function a and the gaussian distribution function B, respectively, and comparing the magnitude of the obtained value with the magnitude of the judgment value, thereby evaluating the immunity level of the unknown sample.
Preferably, the D value calculation method includes the steps of:
(1) comparing the sequencing data of the B cell antigen receptor variable region and/or the T cell antigen receptor variable region with a public database to obtain the total amount and type of sequences of the variable region and the copy number of each sequence;
(2) counting the number of types with the proportion of the sequence copy number in the total sequence amount not less than 50%, and the proportion of the number of types in the total sequence amount is a D value.
Preferably, the lymphocyte cell sample in step (1) comprises a normal sample and a disease sample.
Wherein the normal sample comprises a healthy sample and a sub-healthy sample.
Preferably, the method for evaluating the immunity level of the unknown sample in the step (4) specifically comprises the following steps:
if the D value of the unknown sample is larger than or equal to the standard D value, the immunity of the unknown sample is normal;
and if the D value of the unknown sample is less than the standard D value, the immunity of the unknown sample is low or the immunity of the unknown sample is low.
When the D value of an unknown sample is smaller than the standard D value, substituting the D value of the unknown sample into the Gaussian distribution function A and the Gaussian distribution function B to obtain a judgment value A and a judgment value B;
if the judgment value A is larger than or equal to the judgment value B, the immunity of the unknown sample is lower;
and if the judgment value A is smaller than the judgment value B, the immunity of the unknown sample is low.
In a second aspect, the present invention provides a device for assessing the level of immunity for the purpose of non-disease diagnosis, the device comprising:
the sequencing module is used for sequencing the B cell antigen receptor variable region and/or the T cell antigen receptor variable region of the lymphocyte sample;
the D value calculation module is used for calculating a D value according to sequencing data of the B cell antigen receptor variable region and/or the T cell antigen receptor variable region of the lymphocyte sample;
the standard D value determining module is used for determining a healthy sample and a sub-healthy sample according to a D value distribution diagram of the lymphocyte sample, fitting the D value of the healthy sample by adopting multiple Gaussian distributions and determining a standard D value;
the fitting module is used for fitting the D values of the sub-health sample and the disease sample to obtain a Gaussian distribution function;
and the immunity evaluation module is used for evaluating the immunity level of the unknown sample according to the standard D value, the Gaussian distribution function A and the Gaussian distribution function B.
Preferably, the D value calculating module includes:
the sequencing data analysis unit is used for comparing the sequencing data of the B cell antigen receptor variable region and/or the T cell antigen receptor variable region with a public database to obtain the total amount and type of sequences of the variable region and the copy number of each sequence;
and the D value analysis unit is used for counting the number of types of which the proportion of the sequence copy number to the total sequence amount is not less than 50%, and calculating the proportion to the total type amount.
Preferably, the evaluation condition of the immunity evaluation module is as follows:
if the D value of the unknown sample is larger than or equal to the standard D value, the immunity of the unknown sample is normal;
and if the D value of the unknown sample is less than the standard D value, substituting the D value of the unknown sample into the Gaussian distribution function A and the Gaussian distribution function B to obtain a judgment value A and a judgment value B:
if the judgment value A is larger than or equal to the judgment value B, the immunity of the unknown sample is lower;
and if the judgment value A is smaller than the judgment value B, the immunity of the unknown sample is low.
In a third aspect, the present invention also provides a computer apparatus, the apparatus comprising:
one or more processors;
a storage device for storing one or more programs which, when executed by the one or more processors, cause the one or more processors to carry out the method of assessing an immunity level as described in the first aspect.
In a fourth aspect, the invention also comprises a computer storage medium having stored thereon a computer program which, when executed by a processor, carries out the method of assessing an immunity level as described in the first aspect.
Compared with the prior art, the invention has the following beneficial effects:
according to the method, the sequencing result is analyzed, the standard D value of the healthy sample is determined by combining multiple Gaussian distribution fitting according to the normal sample in the sample, the immunity level of the sample is conveniently and totally classified, namely whether the immunity level belongs to the normal level, if the immunity level does not belong to the normal level, the immunity level is further judged by combining the fitting result of the Gaussian distribution function, so that the patients with the normal and abnormal levels are more accurately classified, the accuracy of immunity evaluation is improved, the immunity of the patients is not simply evaluated once according to the standard value, and the effect of accurately, comprehensively and efficiently evaluating the immunity of the sample is realized.
Drawings
FIG. 1 is a schematic flow chart of a method for assessing an immunity level according to the present invention.
Fig. 2 is a schematic structural diagram of the device for evaluating immunity level provided by the invention.
FIG. 3 is a diagram of D-value distributions of healthy and sub-healthy samples according to an embodiment of the present invention.
FIG. 4 is a Gaussian distribution function obtained by fitting a sub-healthy sample to a diseased sample according to an embodiment of the present invention.
Detailed Description
To further illustrate the technical means adopted by the present invention and the effects thereof, the present invention is further described below with reference to the embodiments and the accompanying drawings. It is to be understood that the specific embodiments described herein are merely illustrative of the invention and are not limiting of the invention.
The examples do not show the specific techniques or conditions, according to the technical or conditions described in the literature in the field, or according to the product specifications. The reagents or apparatus used are conventional products commercially available from normal sources, not indicated by the manufacturer.
In the present invention, there is provided a method for assessing immunity levels for the purpose of non-disease diagnosis, said method comprising the steps of:
s1, comparing the sequencing data with the data in the public database, and counting the D value
Collecting sequencing data of B cell antigen receptor variable regions and/or T cell antigen receptor variable regions of a sample (the sample comprises a normal sample and a disease sample, wherein the normal sample comprises a healthy sample and a sub-healthy sample), and comparing the sequencing data with a public database to obtain the total amount and type amount of sequences of the variable regions and the copy number of each sequence;
counting the number of types with the sequence copy number accounting for not less than 50% of the total sequence amount, wherein the ratio of the number of types to the total sequence amount is a D value;
s2, distinguishing the healthy sample from the sub-healthy sample through the D value distribution of the normal sample, and determining the standard D value of the healthy sample
In the invention, the D value of the sequencing data of the collected normal sample is converted into a D value distribution diagram, and two obvious peaks appear in the D value distribution diagram can be obtained; if the D value is higher, the sample is judged to be a healthy sample, and if the D value is lower, the sample is judged to be a sub-healthy sample;
and fitting by adopting multiple Gaussian distributions according to the D value of the healthy sample to determine the standard D value of the healthy sample.
S3, fitting D values of the sub-health sample and the disease sample by adopting Gaussian distribution function
1) Fitting the D value of the sub-health sample by using a Gaussian distribution function to obtain a Gaussian distribution function A;
2) fitting the D value of the tumor patient by using a Gaussian distribution function to obtain a Gaussian distribution function B;
s4, evaluating the immunity level of the unknown sample
Respectively substituting the D value of the unknown sample (and the D value is smaller than the standard D value) into a Gaussian distribution function A and a Gaussian distribution function B to obtain judgment values A and B;
for an unknown sample, if the D value of the unknown sample is smaller than the standard D value, substituting the unknown sample into A Gaussian distribution functions B for calculation; if A is larger than B, the sample is judged to be a sub-health sample, and the immunity level is poor; if A is less than B, then the sample is judged to be a disease sample with low immunity level, and the unknown sample may be from a subject with a certain disease.
The device for evaluating the immunity level with the aim of non-disease diagnosis can detect different samples including human and animal models and the like, can be applied to various scenes such as the scientific research field, and can also detect the constitution of a normal human body.
The device is shown in fig. 2 and comprises: the device comprises a sequencing module, a D value calculating module, a standard D value determining module, a fitting module and an immunity evaluating module.
The sequencing module is used for sequencing the B cell antigen receptor variable region and/or the T cell antigen receptor variable region of the lymphocyte sample;
the D value calculation module is connected with the sequencing module and used for calculating a D value according to the sequencing data of the sequencing module;
the standard D value determining module is used for determining a healthy sample and a sub-healthy sample according to a D value distribution diagram of the lymphocyte sample, fitting the D value of the healthy sample by adopting multiple Gaussian distributions and determining a standard D value;
the fitting module is used for fitting the D values of the sub-health sample and the disease sample to obtain a Gaussian distribution function;
and the immunity evaluation module is used for evaluating the immunity level of the unknown sample according to the standard D value, the Gaussian distribution function A and the Gaussian distribution function B.
In a specific embodiment, sequencing data of the B cell antigen receptor variable regions of the sub-healthy sample and the tumor sample are collected and compared with a public database to obtain the total amount and type of the variable region sequences and the copy number of each sequence;
counting the number of types with the proportion of the sequence copy number in the total sequence amount not less than 50%, and the proportion of the number of types in the total sequence amount is a D value.
Classifying the healthy sample and the unhealthy sample according to the D value, converting the D value of the sequencing data of the collected normal sample into a D value distribution diagram, and obtaining two obvious peaks appearing in the D value distribution diagram, as shown in FIG. 3: samples with higher D values are classified as healthy samples, while samples with lower D values are sub-healthy samples;
fitting the data of the healthy sample with multiple gaussian distributions, and finding that the D value thereof is 0.043 (standard D value);
therefore, when the D value of the unknown sample is more than or equal to 0.043, the sample is a healthy sample;
when the D value of the unknown sample is < 0.043, the sample needs to be further classified, possibly a sub-healthy sample or a sample with a certain disease.
In another specific example, the D values of the sub-healthy and tumor samples were fitted, and the resulting curve is shown in FIG. 4:
(1) fitting the D values of the sub-healthy population with a Gaussian distribution function to obtain a Gaussian distribution function A with a mean value (mu) of 0.03063 and a mean square error (sigma) of 0.01178:
wherein the content of the first and second substances,
μ＝0.03063，σ＝0.01178；
(2) fitting the D value of the tumor patient by using a Gaussian distribution function to obtain a Gaussian distribution function B with the average value (mu) of 0.02796 and the mean square error (sigma) of 0.02568;
wherein the content of the first and second substances,
μ＝0.02796，σ＝0.02568；
in a specific embodiment, the method of the present invention is used to determine the immunity level of an unknown sample, and the D value is less than 0.043;
and respectively substituting the D value of the unknown sample into a Gaussian distribution function A and a Gaussian distribution function B to obtain judgment values A and B, judging the unknown sample to be a sub-health sample if A is larger than B, otherwise judging the unknown sample to be a disease sample with low immunity level, wherein the unknown sample may be from a subject with a certain disease.
In a specific example, the method of the present invention was used to determine the immunity level of 99 samples (11 cancer samples and 88 healthy samples) provided in CN110246539A, with an accuracy of 90.9%, wherein 9 errors, 2 tumor samples and 7 healthy people; the calculation method recorded in the method predicts the immunity of the tumor sample and the healthy sample to be only 77.8 percent.
The applicant states that the present invention is illustrated in detail by the above examples, but the present invention is not limited to the above detailed methods, i.e. it is not meant that the present invention must rely on the above detailed methods for its implementation. It should be understood by those skilled in the art that any modification of the present invention, equivalent substitutions of the raw materials of the product of the present invention, addition of auxiliary components, selection of specific modes, etc., are within the scope and disclosure of the present invention.
Claims (10)
1. A method for assessing the level of immunity for the purpose of non-disease diagnosis, said method comprising the steps of:
(1) collecting sequencing data of a B cell antigen receptor variable region and/or a T cell antigen receptor variable region of a lymphocyte sample, comparing the sequencing data with data in a public database, and calculating a D value;
(2) distinguishing a healthy sample and a sub-healthy sample according to the distribution graph of the D values, fitting the D values of the healthy samples by adopting multiple Gaussian distributions, and determining a standard D value;
(3) fitting the D values of the sub-health sample and the disease sample by adopting a Gaussian distribution function to obtain a Gaussian distribution function A and a Gaussian distribution function B;
(4) and evaluating the immunity level of the unknown sample according to the standard D value, the Gaussian distribution function A and the Gaussian distribution function B.
2. The method according to claim 1, wherein the D value in step (1) is calculated by:
comparing the sequencing data of the B cell antigen receptor variable region and/or the T cell antigen receptor variable region with a public database to obtain the total amount and type of sequences of the variable region and the copy number of each sequence;
counting the number of types with the proportion of the sequence copy number in the total sequence amount not less than 50%, and the proportion of the number of types in the total sequence amount is a D value.
3. The method according to claim 1, wherein the lymphocyte cell sample of step (1) comprises a normal sample and a disease sample;
wherein the normal sample comprises a healthy sample and a sub-healthy sample.
4. The method according to claim 1, characterized in that the method of evaluating the immunity level of an unknown sample of step (4) comprises in particular:
if the D value of the unknown sample is larger than or equal to the standard D value, the immunity of the unknown sample is normal;
and if the D value of the unknown sample is less than the standard D value, the immunity of the unknown sample is low or the immunity of the unknown sample is low.
5. The method of claim 4, further comprising: substituting the D value of the unknown sample into the Gaussian distribution function A and the Gaussian distribution function B to obtain a judgment value A and a judgment value B, wherein the D value of the unknown sample is smaller than the standard D value;
if the judgment value A is larger than or equal to the judgment value B, the immunity of the unknown sample is lower;
and if the judgment value A is smaller than the judgment value B, the immunity of the unknown sample is low.
6. An apparatus for assessing immunity levels for non-disease diagnosis purposes, the apparatus comprising:
the sequencing module is used for sequencing the B cell antigen receptor variable region and/or the T cell antigen receptor variable region of the lymphocyte sample;
the D value calculation module is used for calculating a D value according to sequencing data of the B cell antigen receptor variable region and/or the T cell antigen receptor variable region of the lymphocyte sample;
the standard D value determining module is used for determining a healthy sample and a sub-healthy sample according to a D value distribution diagram of the lymphocyte sample, fitting the D value of the healthy sample by adopting multiple Gaussian distributions and determining a standard D value;
the fitting module is used for fitting the D values of the sub-health sample and the disease sample to obtain a Gaussian distribution function;
and the immunity evaluation module is used for evaluating the immunity level of the unknown sample according to the standard D value, the Gaussian distribution function A and the Gaussian distribution function B.
7. The apparatus of claim 6, wherein the D-value computation module comprises:
the sequencing data analysis unit is used for comparing the sequencing data of the B cell antigen receptor variable region and/or the T cell antigen receptor variable region with a public database to obtain the total amount and type of sequences of the variable region and the copy number of each sequence;
and the D value analysis unit is used for counting the number of types of which the proportion of the sequence copy number to the total sequence amount is not less than 50%, and calculating the proportion to the total type amount.
8. The apparatus of claim 6, wherein the evaluation condition of the immunity evaluation module is:
if the D value of the unknown sample is larger than or equal to the standard D value, the immunity of the unknown sample is normal;
and if the D value of the unknown sample is less than the standard D value, substituting the D value of the unknown sample into the Gaussian distribution function A and the Gaussian distribution function B to obtain a judgment value A and a judgment value B:
if the judgment value A is larger than or equal to the judgment value B, the immunity of the unknown sample is lower;
and if the judgment value A is smaller than the judgment value B, the immunity of the unknown sample is low.
9. A computer device, the device comprising:
one or more processors;
a storage device for storing one or more programs which, when executed by the one or more processors, cause the one or more processors to carry out a method of assessing an immunity level as claimed in any one of claims 1 to 5.
10. A computer storage medium having a computer program stored thereon, which program, when being executed by a processor, is adapted to carry out the method of assessing an immunity level of any one of claims 1 to 5.
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