CN110993026B - Evaluation method and evaluation system for myelodysplastic syndrome - Google Patents
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Abstract
The invention relates to an evaluation method of myelodysplastic syndrome, comprising (1) collecting age data, collecting data required by an IPSS evaluation system, collecting EVI1 expression quantity data, and detecting whether NRAS, SF3B1 and TP53 genes are mutated; (2) assigning a value to Age according to the Age data; (3) assigning a value to the IPSS based on the packet from the IPSS assessment system; (4) assigning a value to the EVI1 according to the EVI1 expression quantity; (5) Assigning values to TP53, NRAS and SF3B1 according to whether the TP53, NRAS and SF3B1 genes are mutated or not; (6) According to the calculation result of Age×0.8+IPSS×0.6+EVI1×0.2+TP53×1+NRAS×0.7+SF3B1×0.9; (7) grouping according to the calculation result. The present invention evaluates relatively comprehensively and specifically, and provides positive guidance for subsequent treatment of the patient, thereby providing a relatively good prognosis for the patient. In addition, the evaluation method of the invention can predict event-free survival at the same time.
Description
Technical Field
The invention particularly relates to an evaluation method and an evaluation system for myelodysplastic syndrome.
Background
Myelodysplastic syndrome (myelodysplastic syndrome, MDS) is a clonal hematopoietic stem or progenitor disease driven by genetic abnormalities, often manifested by a high risk of whole blood cytopenia, pathologic hematopoiesis, and conversion to leukemia. Cytomorphological and cytogenetic abnormalities are currently the major parameters in establishing the diagnosis of MDS. In recent years, with rapid development and wide application of gene sequencing technology (especially, second generation sequencing technology), most MDS patients can detect gene mutation, and have profound effects on diagnosis, treatment, prognosis evaluation and the like of MDS. About 90% of patients have gene mutations, more than 50 of which are associated with pathogenesis, whiteing mechanisms, therapeutic response, and prognosis of survival of MDS. EVI1 expression levels also play an important role in MDS/AML disease progression, and based on the high risk of MDS to leukemia transformation, a plurality of prognostic integration systems including IPSS-R (the International Prognostic Scoring System-resolved), IPSS (the International Prognostic Scoring System) and WPSS are currently used internationally for prognosis risk assessment of MDS patients, and in particular, the prognostic assessment effect of the IPSS-R integration system is significantly better than that of the other two. However, the prognosis of IPSS and IPSS-R is evaluated by combining the primary blood image, bone marrow primitive cells and nuclear abnormal factors of patients; the WPSS evaluation system was combined with transfusion or not, WHO diagnosed the typing (mainly based on bone marrow primordial cells) and karyotype abnormalities. The prognosis evaluation of MDS patients at home and abroad at present is mainly carried out by using an IPSS and IPSS-R integral system, and the three evaluation systems mainly comprise patients in a relatively low-risk group (except for high-risk extremely high-risk), so that the current treatment strategies of the patients at home and abroad are mainly observation and waiting, and the small-dose chemotherapy of the demethylated drug can be used.
However, none of these three assessment systems involved age and genomic abnormalities in the initial diagnosis of the patient. Since 90% of patients with MDS can detect gene mutation, diagnosis, treatment, prognosis, etc. of MDS will be profoundly affected, and for some patients in the same or different risk groups of IPSS or IPSS-R stratification, gene mutation can provide prognostic factors independent of the IPSS-R system. In addition, age affects patient clonogenic hematopoiesis, therapeutic response, etc., and its prognostic role of independent IPSS, IPSS-R systems and gene mutations has been shown in several studies. The absence of the assessment system herein necessarily affects the precise and individualised differences in disease assessment of a portion of patients prior to treatment.
Disclosure of Invention
The invention aims to provide an evaluation method and an evaluation system for evaluating the disease of MDS patients before treatment at the initial diagnosis relatively comprehensively and specifically.
In order to solve the technical problems, the invention adopts the following technical scheme:
in one aspect, the present invention provides a method for assessing myelodysplastic syndrome, comprising the steps of:
(1) Collecting age data, collecting data required by an IPSS evaluation system, collecting EVI1 expression quantity data, and detecting whether NRAS, SF3B1 and TP53 genes are mutated or not;
(2) Age data collected in step (1) is less than 60 years old, age=0, and age=0.6 when Age data collected in step (1) is more than or equal to 60 years old;
(3) Performing integral grouping according to the data required by the IPSS evaluation system acquired in the step (1) and the IPSS evaluation system, wherein when the integral grouping is low-risk, the IPSS=0; ipss=0.6 when the integral packet is medium risk-1; ipss=1.2 when the integral packet is medium risk-2; ipss=1.8 when the integral packet is high-risk;
(4) When the expression level of EVI1 collected in the step (1) is less than 300 copies/10000 abl copies, evi1=0; when the EVI1 expression amount acquired in the step (1) is more than or equal to 300 copies/10000 abl copies, EVI1=0.2;
(5) When the TP53 gene detected in step (1) is not mutated, TP 53=0; when the TP53 gene detected in step (1) is mutated, TP 53=1;
(6) Nras=0 when no mutation occurs in the NRAS gene detected in step (1); nras=0.7 when the NRAS gene detected in step (1) is mutated;
(7) When the SF3B1 gene detected in step (1) is not mutated, sf3b1=0; when the SF3B1 gene detected in step (1) is mutated, sf3b1=0.9;
(8) Substituting the Age value obtained in the step (2), the IPSS value obtained in the step (3), the EVI1 value obtained in the step (4), the TP53 value obtained in the step (5), the NRAS value obtained in the step (6) and the SF3B1 value obtained in the step (7) into the following formulas to calculate, wherein the formulas are: age×0.8+ipss×0.6+evi1×0.2+tp53×1+nras×0.7+sf3b1×0.9;
(9) Grouping according to the result of the formula calculation in the step (8), wherein the calculation result <1.20 is a low-risk group; the calculated result is not less than 1.20 and not more than 3, and is a medium-risk group, and the calculated result is not less than 3 and is a high-risk group.
Further, a treatment regimen is recommended according to the grouping obtained by the evaluation method, and observation and waiting or administration of a small-dose demethylated dose treatment is recommended when the grouping is a low-risk group; when the groupings are medium-risk or high-risk, aggressive chemotherapy or transplantation is recommended.
Preferably, the EVI1 expression level data in the step (1) is detected by RT-PCR.
Another aspect of the present invention is to provide an evaluation system for reporting risk of myelodysplastic syndrome, said evaluation system comprising:
(a) At least one memory unit configured to receive a data input comprising age from a subject, IPSS assessing system packet data, EVI1 expression levels, NRAS, SF3B1, and TP53 genes are mutated;
(b) A computer processor operably coupled to the memory unit, wherein the computer processor is programmed to (i) assign Age to 0 when the input Age data is <60 years old and to assign Age to 0.6 when the input Age data is greater than or equal to 60 years old;
(ii) assigning 0 to the IPSS when the incoming IPSS evaluation system packet is low risk; when the input IPSS evaluation system group is medium-risk-1, assigning 0.6 to the IPSS; when the input IPSS evaluation system group is medium-risk-2, assigning 1.2 to the IPSS; when the input IPSS evaluation system packet is high-risk, assigning 1.8 to the IPSS;
(iii) assigning an EVI1 value of 0 when the input EVI1 expression level is <300 copies/10000 abl copies; when the input EVI1 expression quantity is more than or equal to 300 copies/10000 abl copies, the EVI1 is assigned to be 0.2;
(iv) assigning a value of 0 to TP53 when no mutation occurs in the inputted TP53 gene; when the input TP53 gene is mutated, assigning 1 to TP 53;
(v) assigning a value of 0 to NRAS when no mutation of the input NRAS gene has occurred; when the input NRAS gene is mutated, assigning 0.7 for NRAS;
(vi) assigning a value of 0 to SF3B1 when no mutation occurs in the input SF3B1 gene; when the input SF3B1 gene is mutated, assigning 0.9 to SF3B 1;
(vii) substituting the values assigned by Age, IPSS, EVI, TP53, NRAS and SF3B1 into the formula AgeX0.8+IPSS X0.6+EVI1×0.2+TP53×1+NRAS×0.7+SF3B1×0.9 to calculate to obtain a calculation result;
and (viii) generating an output, wherein when the calculation result is <1.20, the output is a low risk group; when the calculated result is more than or equal to 1.20 and less than or equal to 3, outputting the calculated result as a medium-risk group; when the calculated result is more than or equal to 3, outputting the calculated result as a high-risk group.
Further, the outputting further comprises recommending a treatment regimen based on the outputted groupings, wherein observing and waiting or administering a small dose of demethylated dose treatment is recommended when the groupings are low risk groups; when the groupings are medium-risk or high-risk, aggressive chemotherapy or transplantation is recommended.
Further, the assessment system includes a module for delivering the output to a user interface for display.
Due to the implementation of the technical scheme, compared with the prior art, the invention has the following advantages:
the invention combines the marks of age, EVI1 expression quantity, IPSS, molecular genetics and the like to formulate a new integral model for evaluating myelodysplastic syndrome, combines the gene mutation characteristics of Chinese population on the existing integral model of IPSS, fully considers the influence of common gene mutation of MDS, corrects the age, and combines the influence of EVI1 expression level, so that the evaluation of the disease before treatment of MDS patients at the initial diagnosis is relatively comprehensive and specific, the positive guidance is provided for the treatment after the patients, the patients which are originally in the same relatively low-risk component group of IPSS and actually contain bad prognosis mutation (such as TP53, NRAS and the like) are distinguished, and more positive chemotherapy or transplantation is recommended compared with the original treatment scheme, thereby the patients obtain relatively good prognosis. In addition, the evaluation method of the invention can predict event-free survival at the same time.
The invention designs the system aiming at the new integral model, so that a user can obtain corresponding integral groups only by inputting corresponding detection values and calculated values, thereby saving time and labor.
Drawings
FIG. 1 is a graph of the effect of individual factors on overall survival time of MDS in an experimental group, wherein a is age, b is EVI1 expression level, c is IPSS-R integral grouping, d is IPSS integral grouping, e is the effect of gene mutation on overall survival, and OS is overall survival time;
FIG. 2 is a graph of overall survival time for risk stratification obtained by the method of the present invention for an experimental group and a validated group, where a is the outcome of the experimental group, b is the outcome of the validated group, and OS is the overall survival time.
Detailed Description
The invention is further described in connection with the following embodiments in order to make the technical means, the creation features, the achievement of the purpose and the effect of the invention easy to understand.
Embodiments of the present invention will be described in detail below with reference to examples, but it will be understood by those skilled in the art that the following examples are only for illustrating the present invention and should not be construed as limiting the scope of the present invention. The specific conditions are not noted in the examples and are carried out according to conventional conditions or conditions recommended by the manufacturer. The reagents or apparatus used are commercially available without the manufacturer's knowledge.
The method comprises the steps of collecting 491 cases of complete adult information patients of 51 common genetic mutations in MDS through RT-PCR detection during initial diagnosis in 2920 MDS patients from 2010 to 2018 in the first 12 months of Suda attached, and randomly dividing the patients into 2 groups of patients by SPSS software (random number 2000000), wherein the patients are in an experimental group 337, a verification group 154 and a periodic follow-up treatment scheme and survival condition of the patients.
First, the general clinical characteristics, cytogenetics and molecular genetics of two groups of patients are compared with each other, the results are shown in table 1, and the two groups of data are not significantly different from each other, which means that the two groups of patients are homogeneous before the model is built, and no significant difference factors cause deviation of judgment of the results.
TABLE 1
Note that: MDS: myelodysplastic syndrome; WHO: world health organization; MDS-SLD: MDS accompanies single line dysplasia; MDS-RS: MDS accompanies cyclic iron granulocytes; MDS-MLD: MDS accompanies multiple dysplasia; MDS-EB1: MDS is accompanied by primordial cell excess-1; MDS-EB2: MDS primordial cell excess-2; MDS-U: MDS-unclassified; IPSS: an international prognosis scoring system for myelodysplastic syndrome; IPSS-R: revising an international prognosis scoring system for myelodysplastic syndrome; no: number of pieces; percent: percent.
In the preliminary analysis of the single factors with significance for MDS prognosis in an experimental model group, the significant single factors (age, IPSS-R prognosis layering, IPSS prognosis layering, DNMT3A, IDH1/IDH2, SRSF2, NRAS/NRAS, SF3B1, GATA2 and TP53 gene mutation) are brought into a COX regression model, a mode of less influencing the prognosis is entered and continuously removed, finally, independent influence factors on MDS prognosis by the combination of age, IPSS prognosis layering, EVI1 expression quantity, NRAS, SF3B1 and TP53 gene mutation are finally obtained, and specific results are shown in a figure 1, wherein a in figure 1 is age, B in figure 1 is EVI1 expression quantity, c in figure 1 is IPSS-R prognosis layering, d in figure 1 is IPSS prognosis layering, e in figure 1 is influence of gene mutation on overall survival, and OS is overall survival time.
The values of the factors are combined with the magnitude of the influence of the factors on prognosis, the specific values are shown in a table 2, and the values of the factors are calculated integrally according to the values of the table 2 by using the formula of Age multiplied by 0.8+IPSS multiplied by 0.6+EVI1 multiplied by 0.2+TP53 multiplied by 1+NRAS multiplied by 0.7+SF3B1 multiplied by 0.9.
TABLE 2
Patients were divided into three groups using curve fitting and determination of the about log index that best judged for sensitivity and specificity of the outcome: the integral calculation result is <1.20, which is a low-risk group; the integral calculation result is a medium-risk group between 1.20 and 3.0; the integral calculation result is more than or equal to 3.00 and is a high-risk group.
Grouping the experimental groups according to the method, wherein the experimental results are shown in a in fig. 2, the median survival time is 113 months for the low-risk groups, 18 months for the medium-risk groups and 10 months for the high-risk groups; patients in the low-risk group are recommended to observe and wait, small-dose demethylating dose treatment can be also performed, and patients in the middle-and high-risk groups are recommended to be actively subjected to chemotherapy or transplantation. The consistency of this model for prognosis assessment (consistency index (C-index): 0.741) is higher than that of IPSS-R stratification (C-index: 0.649), IPSS stratification (C-index: 0.653).
The integration formula obtained for this time was then validated in a validation set of 154 MDS patients, see b in fig. 2, demonstrating that the model was executable and repeatable.
The above calculation is performed by a computer system.
The applicant states that the detailed method of the present invention is illustrated by the above examples, but the present invention is not limited to the detailed method described above, i.e. it does not mean that the present invention must be practiced in dependence upon the detailed method described above. It should be apparent to those skilled in the art that any modification of the present invention, equivalent substitution of raw materials for the product of the present invention, addition of auxiliary components, selection of specific modes, etc., falls within the scope of the present invention and the scope of disclosure.
Claims (6)
1. A method for assessing myelodysplastic syndrome, characterized by: the method comprises the following steps:
(1) Collecting age data, collecting data required by an IPSS evaluation system, collecting EVI1 expression quantity data, and detecting whether NRAS, SF3B1 and TP53 genes are mutated or not;
(2) Age data collected in step (1) is less than 60 years old, age=0, and age=0.6 when Age data collected in step (1) is more than or equal to 60 years old;
(3) Performing integral grouping according to the data required by the IPSS evaluation system acquired in the step (1) and the IPSS evaluation system, wherein when the integral grouping is low-risk, the IPSS=0; ipss=0.6 when the integral packet is medium risk-1; ipss=1.2 when the integral packet is medium risk-2; ipss=1.8 when the integral packet is high-risk;
(4) When the expression level of EVI1 collected in the step (1) is less than 300 copies/10000 abl copies, evi1=0; when the EVI1 expression amount acquired in the step (1) is more than or equal to 300 copies/10000 abl copies, EVI1=0.2;
(5) When the TP53 gene detected in step (1) is not mutated, TP 53=0; when the TP53 gene detected in step (1) is mutated, TP 53=1;
(6) Nras=0 when no mutation occurs in the NRAS gene detected in step (1); nras=0.7 when the NRAS gene detected in step (1) is mutated;
(7) When the SF3B1 gene detected in step (1) is not mutated, sf3b1=0; when the SF3B1 gene detected in step (1) is mutated, sf3b1=0.9;
(8) Substituting the Age value obtained in the step (2), the IPSS value obtained in the step (3), the EVI1 value obtained in the step (4), the TP53 value obtained in the step (5), the NRAS value obtained in the step (6) and the SF3B1 value obtained in the step (7) into the following formulas to calculate, wherein the formulas are: age×0.8+ipss×0.6+evi1×0.2+tp53×1+nras×0.7+sf3b1×0.9;
(9) Grouping according to the result of the formula calculation in the step (8), wherein the calculation result <1.20 is a low-risk group; and the calculation result is not less than 1.20, the calculation result is not less than 3 and is a medium-risk group, and the calculation result is not less than 3 and is a high-risk group.
2. The method for evaluating myelodysplastic syndrome according to claim 1, wherein: recommending a treatment scheme according to the group obtained by the assessment method, and recommending to observe and wait or administer a small-dose demethylating dose treatment when the group is a low-risk group; when the groupings are medium-risk or high-risk, aggressive chemotherapy or transplantation is recommended.
3. The method for evaluating myelodysplastic syndrome according to claim 1, wherein: the EVI1 expression amount data in the step (1) is detected by RT-PCR.
4. An assessment system for reporting risk of myelodysplastic syndrome, characterized by: the evaluation system includes:
(a) At least one memory unit configured to receive a data input comprising age from a subject, IPSS assessing system packet data, EVI1 expression levels, NRAS, SF3B1, and TP53 genes are mutated;
(b) A computer processor operably coupled to the memory unit, wherein the computer processor is programmed to (i) assign Age to 0 when the input Age data is <60 years old and to assign Age to 0.6 when the input Age data is greater than or equal to 60 years old;
(ii) assigning 0 to the IPSS when the incoming IPSS evaluation system packet is low risk; when the input IPSS evaluation system group is medium-risk-1, assigning 0.6 to the IPSS; when the input IPSS evaluation system group is medium-risk-2, assigning 1.2 to the IPSS; when the input IPSS evaluation system packet is high-risk, assigning 1.8 to the IPSS;
(iii) assigning an EVI1 value of 0 when the input EVI1 expression level is <300 copies/10000 abl copies; when the input EVI1 expression quantity is more than or equal to 300 copies/10000 abl copies, the EVI1 is assigned to be 0.2;
(iv) assigning a value of 0 to TP53 when no mutation occurs in the inputted TP53 gene; when the input TP53 gene is mutated, assigning 1 to TP 53;
(v) assigning a value of 0 to NRAS when no mutation of the input NRAS gene has occurred; when the input NRAS gene is mutated, assigning 0.7 for NRAS;
(vi) assigning a value of 0 to SF3B1 when no mutation occurs in the input SF3B1 gene; when the input SF3B1 gene is mutated, assigning 0.9 to SF3B 1;
(vii) substituting the values assigned by Age, IPSS, EVI, TP53, NRAS and SF3B1 into the formula AgeX0.8+IPSS X0.6+EVI1×0.2+TP53×1+NRAS×0.7+SF3B1×0.9 to calculate to obtain a calculation result;
and (viii) generating an output, wherein when the calculation result is <1.20, the output is a low risk group; when the calculated result is less than or equal to 1.20 and is less than or equal to 3, outputting the calculated result as a medium-risk group; when the calculated result is more than or equal to 3, outputting the calculated result as a high-risk group.
5. The evaluation system according to claim 4, wherein: the outputting further comprises recommending a treatment regimen based on the outputted groupings, wherein observing and waiting or administering a small dose of demethylated dose treatment is recommended when the groupings are low risk groups; when the groupings are medium-risk or high-risk, aggressive chemotherapy or transplantation is recommended.
6. The evaluation system according to claim 4 or 5, characterized in that: the assessment system also includes a module for delivering the output to a user interface for display.
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| WO2003094086A2 (en) * | 2002-05-02 | 2003-11-13 | Biotech Research Ventures Pte Limited | Analysis of gene expression data for multi-class prediction |
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| WO2003094086A2 (en) * | 2002-05-02 | 2003-11-13 | Biotech Research Ventures Pte Limited | Analysis of gene expression data for multi-class prediction |
| CN110232974A (en) * | 2019-04-22 | 2019-09-13 | 福建医科大学附属第一医院 | A kind of novel Huppert's disease integrated risk methods of marking |
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