WO2019206217A1 - 多发性骨髓瘤分子分型及应用 - Google Patents
多发性骨髓瘤分子分型及应用 Download PDFInfo
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- WO2019206217A1 WO2019206217A1 PCT/CN2019/084241 CN2019084241W WO2019206217A1 WO 2019206217 A1 WO2019206217 A1 WO 2019206217A1 CN 2019084241 W CN2019084241 W CN 2019084241W WO 2019206217 A1 WO2019206217 A1 WO 2019206217A1
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Definitions
- the invention belongs to the field of biotechnology, and in particular relates to molecular typing and application of multiple myeloma.
- Multiple Myeloma is a tumor caused by malignant proliferation of plasma cells and is the second most common blood tumor.
- the incidence rate in China is 1-2/100,000.
- Multiple myeloma is a common occurrence in the elderly population older than 60 years old. As the degree of aging in China increases, its incidence has increased year by year, and it has become a serious threat to the health of the elderly.
- a typical feature of multiple myeloma is the presence of a large number of abnormally proliferating plasma cells in the bone marrow. This plasma cell secretes an abnormal immunoglobulin or immunoglobulin fragment, M protein. The concentration of M protein is the diagnosis of multiple bone marrow. An important indicator of tumors.
- prognostic-related gene expression features such as UAMS-70 and UAMS-17, UAMS-80, IFM-15, Millennium-100, EMC-92, gene amplification indices such as GPI-5, MRC-IX-6, and centers
- gene amplification indices such as GPI-5, MRC-IX-6, and centers
- the invention provides an application for obtaining or detecting a substance of 97 gene expression in a patient with multiple myeloma tumors to be tested for preparing a product for predicting the prognosis of a patient with multiple myeloma tumors to be tested.
- the prognosis survival is reflected in the prognosis survival rate, the length of survival or the risk of survival.
- the prognosis survival rate is overall survival or progression free survival.
- the invention also provides the use of a substance for obtaining or detecting 97 gene expression in a patient with multiple myeloma tumors to be tested for preparing at least one functional product having the following a-c:
- Another object of the present invention is to provide a use of a substance for obtaining or detecting 97 gene expression in a patient with multiple myeloma tumors to be tested and a device for operating a multiple myeloma Bayesian classifier.
- the invention provides a product for obtaining or detecting 97 gene expression substances in a patient with multiple myeloma tumors to be tested and a device for operating a multiple myeloma Bayesian classifier in preparing a prognosis for predicting a patient with multiple myeloma tumors to be tested.
- the prognosis survival is reflected in the prognosis survival rate, the length of survival or the risk of survival.
- the present invention also provides an apparatus for obtaining or detecting 97 gene expression substances in a patient with multiple myeloma tumors to be tested and an apparatus for operating a multiple myeloma Bayesian classifier for preparing at least one functional product having the following ac :
- the above 97 genes are as follows: ACBD3, ADAR, ADSS, ALDH2, ANP32E, ANXA2, ATF3, ATP8B2, CACYBP, CAPN2, CCND1, CCT3, CDC42SE1, CERS2, CHSY3, CLIC1, CLMN, COPA, CSNK1G3, DAP3, DENND1B, ENSA , EPRS, EPSTI1, EVL, FAM13A, FAM49A, FLAD1, FRZB, GLRX2, HAX1, HDGF, HLA-A, HLA-B, HLA-C, HLA-F, HLA-G, IL6R, ISG20L2, JTB, KLF2, LAMTOR2 , LDHA, MCL1, MOXD1, MRPL24, MRPL9, MVP, MYL6, NDUFS2, NOP58, NOTCH2NL, NTAN1, PAK1, PI4KB, PIEZO1, PIK3AP1, PIM2, PIP5K1B, PMV
- the above multiple myeloma Bayesian classifier is obtained by a method comprising the following steps:
- the expression data of 97 genes of n multiple myeloma samples were derived from the existing database or the expression data of 97 genes of multiple myeloma samples with more than 100 samples.
- n is greater than or equal to 100
- the expression levels of 97 genes were the expression levels of 97 genes in multiple myeloma cells;
- step 3 Based on the two subtypes of step 2, the expression data of 97 genes of n multiple myeloma samples of step 1), and the prognostic survival data of n multiple myeloma samples, using the naive Bayesian method Constructed to get the Bayesian classifier.
- the above step 3) is to randomly divide the n multiple myeloma samples into a training set and a verification set according to a ratio of a sample size ratio greater than 1:1; and then use the expression data of the 97 genes in the training, and Combining the MCL1-M-High and MCL1-M-Low subtype tags of each sample obtained by the Consensus Clustering clustering algorithm, using the naive Bayesian algorithm in the R language machine learning package klaR package to predict and predict a single patient MCL1-M Multiple myeloma Bayesian classifiers of the -High subtype and the MCL1-M-Low subtype;
- the above-mentioned manner of obtaining the expression data of 97 genes of each multiple myeloma sample is to detect the expression level of 97 genes of the multiple myeloma sample or to obtain the expression of 97 genes of the multiple myeloma sample from the database. the amount.
- a third object of the invention is to provide a product.
- the product provided by the present invention comprises a substance for obtaining or detecting 97 genes in a patient with multiple myeloma tumors to be tested and a device for operating a multiple myeloma Bayesian classifier (the device may be an optical disk or a computer, etc.).
- the product has at least one of the following functions:
- the product has at least one of the following 1)-4):
- the above products also include a carrier for describing the detection method
- the detecting method comprises the following steps: the detecting method comprises the steps of: obtaining 97 patients with multiple myeloma tumors to be tested by using the substance for obtaining or detecting 97 genes in a patient with multiple myeloma tumors to be tested. Gene expression data; further, the expression data of 97 genes of the multiple myeloma tumor patients to be tested are classified by the multiple myeloma Bayesian classifier, belonging to the MCL1-M-High subtype The prognostic prognosis of patients with multiple myeloma tumors is significantly worse than that of patients with multiple myeloma tumors that are MCL1-M-Low subtypes;
- the detecting method comprises the steps of: obtaining, by the obtaining or detecting a substance expressing 97 genes in a patient with multiple myeloma tumors to be tested, obtaining expression data of 97 genes of the multiple myeloma tumor patient to be tested; Further, the expression data of 97 genes of the multiple myeloma tumor patients to be tested are classified by the multiple myeloma Bayesian classifier, and the MCL1-M-High subtype is to be tested for multiple myeloma tumors.
- the patient's treatment with bortezomib or bortezomib is better than the multiple myeloma tumor patients to be tested belonging to the MCL1-M-Low subtype;
- the detecting method comprises the steps of: obtaining, by the obtaining or detecting a substance expressing 97 genes in a patient with multiple myeloma tumors to be tested, obtaining expression data of 97 genes of the multiple myeloma tumor patient to be tested; Further, the expression data of 97 genes of the multiple myeloma tumor patient to be tested are classified by the multiple myeloma Bayesian classifier, if the patient with multiple myeloma tumors to be tested belongs to MCL1-M-High Asia The type is treated with bortezomib or a drug containing bortezomib; if the patient with multiple myeloma to be tested belongs to the MCL1-M-Low subtype, then bortezomib or a drug containing bortezomib is not used.
- the patient with multiple myeloma tumors to be tested is a single patient or a plurality of patients.
- the n multiple myeloma samples were 551 samples.
- the ratio greater than 1:1 is to randomly divide the training set and the verification set according to a ratio of 2:1.
- a fourth object of the present invention is to provide a method of constructing a model for typing a patient with multiple myeloma tumors.
- the method provided by the invention comprises the following steps:
- the expression data of 97 genes of n multiple myeloma samples were derived from the existing database or the expression data of 97 genes of multiple myeloma samples with more than 100 samples.
- n is greater than or equal to 100
- the expression levels of 97 genes were the expression levels of 97 genes in multiple myeloma cells;
- step 3 Based on the two subtypes of step 2), the expression data of 97 genes of n multiple myeloma samples of step 1), and the prognostic survival data of n multiple myeloma samples, using naive Bayes The method constructs the Bayesian classifier, which is the target model.
- 97 gene expressions in patients with multiple myeloma tumors were derived from 97 gene expression in tumor cells of patients with multiple myeloma tumors.
- the above-mentioned method for obtaining or detecting 97 gene expression substances in a patient with multiple myeloma tumors to be tested and/or the device for operating the multiple myeloma Bayesian classifier or the above method is prepared for predicting multiple bone marrow to be tested
- the use of products in the prognosis survival rate of tumor tumor patients is also within the scope of protection of the present invention.
- the above-mentioned method for obtaining or detecting 97 gene expression substances in a patient with multiple myeloma tumors to be tested and/or the device for operating the multiple myeloma Bayesian classifier or the above method is used to prepare a tumor for predicting multiple myeloma
- the use of a patient's prognostic survival product is also within the scope of the invention.
- the above-mentioned method for obtaining or detecting 97 gene expression substances in a patient with multiple myeloma tumors to be tested and/or the device for operating the multiple myeloma Bayesian classifier or the above method is used to prepare a tumor for predicting multiple myeloma
- the use of a patient's prognosis survival risk product is also within the scope of the invention.
- the invention also provides a method for typing a patient with multiple myeloma tumors, comprising the following steps:
- the device is typed to obtain whether the patient with multiple myeloma tumors to be tested belongs to the MCL1-M-High subtype or the MCL1-M-Low subtype.
- the present invention also provides a method for predicting the prognosis of a patient with multiple myeloma tumors, comprising the steps of: detecting or obtaining the expression data of 97 genes of the multiple myeloma tumor patient to be tested;
- the expression data of 97 genes in patients with multiple myeloma tumors were classified by the above-mentioned multiple myeloma Bayesian classifier, and the prognosis of patients with multiple myeloma tumors belonging to MCL1-M-High subtype was significantly worse. Or inferior to patients with multiple myeloma tumors to be tested belonging to the MCL1-M-Low subtype.
- the prognosis is reflected in the prognosis survival rate, the length of survival or the risk of survival;
- the predicted prognosis survival rate of the multiple myeloma tumor patients to be tested belonging to the MCL1-M-High subtype is significantly inferior to that of the multiple myeloma tumor patients to be tested belonging to the MCL1-M-Low subtype as follows: 1)-3 At least one of:
- the invention also provides a medicament for detecting the treatment effect of bortezomib or bortezomib in a patient with multiple myeloma tumors to be tested, comprising the following steps: obtaining the expression of 97 genes of the patient with multiple myeloma tumors to be tested.
- the data of the 97 genes of the multiple myeloma tumor patients to be tested are classified by the multiple myeloma Bayesian classifier, and belong to the MCL1-M-High subtype to be tested for multiple
- the treatment of bortezomib or bortezomib in patients with myeloma tumors is better than that of patients with multiple myeloma tumors belonging to the MCL1-M-Low subtype.
- the invention also provides a drug for guiding bortezomib or bortezomib in a patient with multiple myeloma tumors to be tested, comprising the following steps: obtaining the expression data of 97 genes of the multiple myeloma tumor patients to be tested Further, the expression data of 97 genes of the multiple myeloma tumor patients to be tested are classified by the multiple myeloma Bayesian classifier, and the multiple bone marrow to be tested belonging to the MCL1-M-High subtype is classified. Tumor tumor patients are treated with bortezomib or a drug containing bortezomib.
- the above-mentioned data of the expression of 97 genes of the multiple myeloma tumor patients to be tested can be obtained from the database, or the expression levels of 97 genes in the sample can be directly detected.
- the expression levels of the above genes are all gene expression levels in multiple myeloma tumor cells.
- Figure 1 shows the ROC diagram of the GSE2658 verification centralized Bayesian classifier.
- Figure 2 is a ROC diagram of the Bayesian classifier classification results in the MMRF dataset.
- Figure 3 is a ROC diagram of the Bayesian classifier classification results in the GSE19784 data set.
- Figure 4 shows the overall survival curves of MCL1-M-High and MCL1-M-Low subtypes of multiple myeloma in GSE2658.
- Figure 5 is the overall survival curve of MCL1-M-High and MCL1-M-Low molecular subtypes of multiple myeloma in GSE2658.
- Figure 6 shows the overall survival curves (top panel) and progression-free survival curves (lower panel) of multiple myeloma MCL1-M-High and MCL1-M-Low subtypes in GSE19784.
- Figure 7 shows that the MCL1-M-High and MCL1-M-Low subtypes of GS19784 have different responses to bortezomib treatment.
- Example 1 Screening of molecular diagnostic markers for multiple myeloma and implementation of molecular typing
- the names of 97 genes are as follows: ACBD3, ADAR, ADSS, ALDH2, ANP32E, ANXA2, ATF3, ATP8B2, CACYBP, CAPN2, CCND1, CCT3, CDC42SE1, CERS2, CHSY3, CLIC1, CLMN, COPA, CSNK1G3, DAP3, DENND1B, ENSA , EPRS, EPSTI1, EVL, FAM13A, FAM49A, FLAD1, FRZB, GLRX2, HAX1, HDGF, HLA-A, HLA-B, HLA-C, HLA-F, HLA-G, IL6R, ISG20L2, JTB, KLF2, LAMTOR2 , LDHA, MCL1, MOXD1, MRPL24, MRPL9, MVP, MYL6, NDUFS2, NOP58, NOTCH2NL, NTAN1, PAK1, PI4KB, PIEZO1, PIK3AP1, PIM2, PIP5K1B, PM
- the 551 patients with multiple myeloma were first divided into MCL1-M- using the Consensus Clustering clustering algorithm in an unsupervised clustering manner. High and MCL1-M-Low two subtypes.
- cluster-based classification methods cannot perform molecular typing on individual samples.
- the 551 samples were randomly divided into a training set (369 cases) and a validation set (182 cases) in a 2:1 ratio for establishing and evaluating individualized classifiers. The sampling was carried out in a stratified sampling manner to ensure that the ratios of the MCL1-M-High and MCL1-M-Low subtypes in the training set and the test set were consistent with the original.
- the machine learning package klaR package provided by R language is provided.
- the naive Bayesian algorithm establishes a multiple myeloma Bayesian classifier that predicts individual patient MCL1-M-High subtypes and MCL1-M-Low subtypes.
- the multiple myeloma Bayesian classifier code is as follows:
- the accuracy of the classification was evaluated using 182 samples from the validation set.
- the model is continually iteratively optimized, and the accuracy of the classification is more than 95%.
- the accuracy data of the classifier is shown in Table 1, and the receiver working curve (ROC) is shown in Figure 1.
- the MMRF data set differs from GSE2658 in that the amount of gene expression is obtained by RNA-seq, not the chip.
- the predicted results are shown in Table 2, and the ROC chart is shown in Figure 2.
- GSE19784 is also a data set for the expression of multiple myeloma. Like GSE2618, the U133 2.0 Plus chip is used to measure gene expression. However, the two are tested at different times by different experiments, and the experimental conditions may be different, which results in significant differences in the distribution and noise levels of the data.
- the subtype prediction results of the database are shown in Table 3, and the ROC curve is shown in Fig. 3.
- the 551 samples were classified using the multiple myeloma Bayesian classifier obtained in Example 1, and 249 were obtained.
- MCL1-M-High subtype multiple myeloma and 302 cases of MCL1-M-Low subtype multiple myeloma were obtained.
- Bayesian classifier to classify 97 genes of MCL1 gene group can be used to predict the prognosis of patients to be tested.
- the expression data of 97 gene expression genes of the MCL1 gene group were respectively used in the multiple myeloma Bayesian classifier obtained in Example 1 to sample 534 samples. Divided into MCL1-M-High (231 cases) and MCL1-M-Low two subtypes (303 cases).
- the multiple myeloma Bayesian classifier obtained in Example 1 was used to verify the expression data of the 97 genes of the MCL1 gene group of 304 samples of multiple myeloma patients (pre-treatment detection) in the database GSE19784. 304 samples were divided into MCL1-M-High (107 cases) and MCL1-M-Low subtypes (196 cases).
- Example 3 molecular diagnostic markers and classification of multiple myeloma in predicting whether the patient to be tested can be treated with bortezomib
- the GSE19784 multiple myeloma expression data set was obtained from a phase III drug clinical trial (HOVON-65/GMMG-HD4) with a patient's medication regimen.
- the trial randomized patients to two groups of VAD (155 cases) and PAD (148 cases). The difference between the two was that the PAD program had more bortezomib (trade name: Wanhao).
- the gene expression data of the enrolled patients were collected before treatment.
- the sample was divided into two subtypes, MCL1-M-High and MCL1-M-Low, and then in MCL1-M-High (51 cases of PAD, VAD).
- Survival analysis KM analysis and cox regression analysis was performed in 56 subtypes of MCL1-M-Low (104 cases of PAD and 92 cases of VAD) by drug treatment.
- A is the overall survival rate of the MCL1-M-High group
- B is the overall survival rate of the MCL1-M-Low group
- C is the progression-free survival rate of the MCL1-M-High group
- D is the MCL1.
- the molecular typing of the present invention can guide the clinical use of drugs, and can avoid the use of bortezomib in the MCL1-M-Low group, on the one hand, the economic burden of the patient can be reduced, and on the other hand, the patient can bear less. Side effects caused by medical treatment.
- Example 4 Bayesian classifier for multiple myeloma in predicting patient risk stratification
- Bone marrow samples from 30 newly diagnosed multiple myeloma patients were newly collected.
- CD138-positive multiple myeloma cells were purified from bone marrow using magnetic beads attached to CD138 antibody, and total RNA of multiple myeloma cells was extracted.
- the expression of the above 97 multiple myeloma typing genes was detected by hybridization with these RNA samples using the Aung Ng PrimeView chip.
- the inventors explored whether the gene co-expression network surrounding the key signaling pathways conserved during the development of germinal center (GC) plasma cells is Can help to elucidate the pathogenesis of MM and apply to the molecular typing of MM.
- the inventors focused on finding a genetic network that controls the dysregulation of B cells into plasma cells in multiple myeloma because it may play a key role in the formation of multiple myeloma.
- MCL1-M a gene module co-expressed with MCL1 gene
- MCL-M-High subtype MCL-M-High subtype
- MCL. -M-Low subtype MCL-M-Low subtype
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Abstract
Description
Claims (17)
- 获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质在制备预测待测多发性骨髓瘤肿瘤患者预后情况的产品中的应用;所述97个基因为如下:ACBD3、ADAR、ADSS、ALDH2、ANP32E、ANXA2、ATF3、ATP8B2、CACYBP、CAPN2、CCND1、CCT3、CDC42SE1、CERS2、CHSY3、CLIC1、CLMN、COPA、CSNK1G3、DAP3、DENND1B、ENSA、EPRS、EPSTI1、EVL、FAM13A、FAM49A、FLAD1、FRZB、GLRX2、HAX1、HDGF、HLA-A、HLA-B、HLA-C、HLA-F、HLA-G、IL6R、ISG20L2、JTB、KLF2、LAMTOR2、LDHA、MCL1、MOXD1、MRPL24、MRPL9、MVP、MYL6、NDUFS2、NOP58、NOTCH2NL、NTAN1、PAK1、PI4KB、PIEZO1、PIK3AP1、PIM2、PIP5K1B、PMVK、POGZ、PPIA、PRCC、PRKCA、PRRC2C、PSMB4、PSMD4、RAB29、RCBTB2、SCAMP3、SCAPER、SDHC、SEL1L3、SELPLG、SHC1、SIDT1、SSR2、STAP1、TAP1、TIMM17A、TLR10、TMCO1、TOR1AIP2、TOR3A、TP53INP1、TPM3、TRANK1、TROVE2、UAP1、UBE2Q1、UBQLN4、UHMK1、VPS45、YY1AP1、ZC3H11A、ZFP36、ZNF593。
- 根据权利要求1所述的应用,其特征在于:所述预后生存情况体现在预后生存率大小、生存期长短或存活风险程度。
- 获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质在制备具有如下a-c中至少一种功能产品中的应用:a、检测待测多发性骨髓瘤肿瘤患者用硼替佐米或含有硼替佐米的药物治疗效果;b、检测待测多发性骨髓瘤肿瘤患者对硼替佐米或含有硼替佐米的药物的敏感度;c、指导待测多发性骨髓瘤肿瘤患者硼替佐米或含有硼替佐米的药物用药;所述97个基因为如下:ACBD3、ADAR、ADSS、ALDH2、ANP32E、ANXA2、ATF3、ATP8B2、CACYBP、CAPN2、CCND1、CCT3、CDC42SE1、CERS2、CHSY3、CLIC1、CLMN、COPA、CSNK1G3、DAP3、DENND1B、ENSA、EPRS、EPSTI1、EVL、FAM13A、FAM49A、FLAD1、FRZB、GLRX2、HAX1、HDGF、HLA-A、HLA-B、HLA-C、HLA-F、HLA-G、IL6R、ISG20L2、JTB、KLF2、LAMTOR2、LDHA、MCL1、 MOXD1、MRPL24、MRPL9、MVP、MYL6、NDUFS2、NOP58、NOTCH2NL、NTAN1、PAK1、PI4KB、PIEZO1、PIK3AP1、PIM2、PIP5K1B、PMVK、POGZ、PPIA、PRCC、PRKCA、PRRC2C、PSMB4、PSMD4、RAB29、RCBTB2、SCAMP3、SCAPER、SDHC、SEL1L3、SELPLG、SHC1、SIDT1、SSR2、STAP1、TAP1、TIMM17A、TLR10、TMCO1、TOR1AIP2、TOR3A、TP53INP1、TPM3、TRANK1、TROVE2、UAP1、UBE2Q1、UBQLN4、UHMK1、VPS45、YY1AP1、ZC3H11A、ZFP36、ZNF593。
- 获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备在制备预测待测多发性骨髓瘤肿瘤患者预后情况的产品中的应用;所述97个基因为如下:ACBD3、ADAR、ADSS、ALDH2、ANP32E、ANXA2、ATF3、ATP8B2、CACYBP、CAPN2、CCND1、CCT3、CDC42SE1、CERS2、CHSY3、CLIC1、CLMN、COPA、CSNK1G3、DAP3、DENND1B、ENSA、EPRS、EPSTI1、EVL、FAM13A、FAM49A、FLAD1、FRZB、GLRX2、HAX1、HDGF、HLA-A、HLA-B、HLA-C、HLA-F、HLA-G、IL6R、ISG20L2、JTB、KLF2、LAMTOR2、LDHA、MCL1、MOXD1、MRPL24、MRPL9、MVP、MYL6、NDUFS2、NOP58、NOTCH2NL、NTAN1、PAK1、PI4KB、PIEZO1、PIK3AP1、PIM2、PIP5K1B、PMVK、POGZ、PPIA、PRCC、PRKCA、PRRC2C、PSMB4、PSMD4、RAB29、RCBTB2、SCAMP3、SCAPER、SDHC、SEL1L3、SELPLG、SHC1、SIDT1、SSR2、STAP1、TAP1、TIMM17A、TLR10、TMCO1、TOR1AIP2、TOR3A、TP53INP1、TPM3、TRANK1、TROVE2、UAP1、UBE2Q1、UBQLN4、UHMK1、VPS45、YY1AP1、ZC3H11A、ZFP36、ZNF593;所述多发性骨髓瘤贝叶斯分类器按照包括如下步骤的方法获得:1)获得n个多发性骨髓瘤样本的97个基因的表达量数据;2)将所述n个多发性骨髓瘤样本的97个基因的表达量数据用Consensus Clustering聚类算法分为MCL1-M-High和MCL1-M-Low两个亚型;3)基于步骤2的两个亚型、步骤1)的n个多发性骨髓瘤样本的97个基因的表达量数据、n个多发性骨髓瘤样本的预后生存期数据,用朴素贝叶斯方法构建得到贝叶斯分类器。
- 根据权利要求4所述的应用,其特征在于:所述预后生存情况体现在预后生存率大小、生存期长短或存活风险程 度。
- 获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备在制备具有如下a-c中至少一种功能产品中的应用:a、检测待测多发性骨髓瘤肿瘤患者用硼替佐米或含有硼替佐米的药物治疗效果;b、检测待测多发性骨髓瘤肿瘤患者对硼替佐米或含有硼替佐米的药物的敏感度;c、指导待测多发性骨髓瘤肿瘤患者硼替佐米或含有硼替佐米的药物用药;所述97个基因为如下:ACBD3、ADAR、ADSS、ALDH2、ANP32E、ANXA2、ATF3、ATP8B2、CACYBP、CAPN2、CCND1、CCT3、CDC42SE1、CERS2、CHSY3、CLIC1、CLMN、COPA、CSNK1G3、DAP3、DENND1B、ENSA、EPRS、EPSTI1、EVL、FAM13A、FAM49A、FLAD1、FRZB、GLRX2、HAX1、HDGF、HLA-A、HLA-B、HLA-C、HLA-F、HLA-G、IL6R、ISG20L2、JTB、KLF2、LAMTOR2、LDHA、MCL1、MOXD1、MRPL24、MRPL9、MVP、MYL6、NDUFS2、NOP58、NOTCH2NL、NTAN1、PAK1、PI4KB、PIEZO1、PIK3AP1、PIM2、PIP5K1B、PMVK、POGZ、PPIA、PRCC、PRKCA、PRRC2C、PSMB4、PSMD4、RAB29、RCBTB2、SCAMP3、SCAPER、SDHC、SEL1L3、SELPLG、SHC1、SIDT1、SSR2、STAP1、TAP1、TIMM17A、TLR10、TMCO1、TOR1AIP2、TOR3A、TP53INP1、TPM3、TRANK1、TROVE2、UAP1、UBE2Q1、UBQLN4、UHMK1、VPS45、YY1AP1、ZC3H11A、ZFP36、ZNF593;所述多发性骨髓瘤贝叶斯分类器按照包括如下步骤的方法获得:1)获得n个多发性骨髓瘤样本的97个基因的表达量数据;2)将所述n个多发性骨髓瘤样本的97个基因的表达量数据用Consensus Clustering聚类算法分为MCL1-M-High和MCL1-M-Low两个亚型;3)基于步骤2的两个亚型、步骤1)的n个多发性骨髓瘤样本的97个基因的表达量数据、n个多发性骨髓瘤样本的预后生存期数据,用朴素贝叶斯方法构建得到贝叶斯分类器。
- 一种产品,包括获得或检测待测多发性骨髓瘤肿瘤患者中97个基 因表达的物质和运行多发性骨髓瘤贝叶斯分类器的设备。
- 根据权利要求7所述的产品,其特征在于:所述产品具有如下1)-4)中至少一种功能:1)预测待测多发性骨髓瘤肿瘤患者预后情况;2)检测待测多发性骨髓瘤肿瘤患者对硼替佐米或含有硼替佐米的药物敏感情况;3)检测待测多发性骨髓瘤肿瘤患者用硼替佐米或含有硼替佐米的药物治疗效果;4)指导待测多发性骨髓瘤肿瘤患者硼替佐米或含有硼替佐米的药物用药。
- 根据权利要求7或8所述的产品,其特征在于:所述产品还包括记载检测方法的载体;所述检测方法包括如下步骤:用所述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质得到所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类,属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预测预后情况显著差于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者;或,所述检测方法包括如下步骤:用所述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质得到所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类,属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者硼替佐米或含有硼替佐米的药物治疗效果好于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者;或,所述检测方法包括如下步骤:用所述获得或检测待测多发性骨髓瘤肿瘤患者中97个基因表达的物质得到所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类,若待测多发性骨髓瘤肿瘤患者属于MCL1-M-High亚型,则用硼替佐米或含有硼替佐米的药物治疗;若待测多发性骨髓瘤肿瘤患者属于MCL1-M-Low亚型,则不用 硼替佐米或含有硼替佐米的药物治疗。
- 根据权利要求7-9中任一所述的产品,其特征在于:所述待测多发性骨髓瘤肿瘤患者为单个患者或多个患者。
- 构建对多发性骨髓瘤肿瘤患者进行分型的模型的方法,包括如下步骤:1)获得n个多发性骨髓瘤样本的97个基因的表达量数据;2)将所述n个多发性骨髓瘤样本的97个基因的表达量数据用Consensus Clustering聚类算法分为MCL1-M-High和MCL1-M-Low两个亚型;3)基于步骤2)的两个亚型、步骤1)的n个多发性骨髓瘤样本的97个基因的表达量数据、n个多发性骨髓瘤样本的预后生存期数据,用朴素贝叶斯方法构建得到贝叶斯分类器,即为目的模型。
- 由权利要求11所述方法制备的素贝叶斯分类器。
- 权利要求12的素贝叶斯分类器在制备如下1)-4)至少一种或制备1)-4)至少一种产品中的应用:1)预测待测多发性骨髓瘤肿瘤患者预后情况;2)检测待测多发性骨髓瘤肿瘤患者对硼替佐米或含有硼替佐米的药物敏感情况;3)检测待测多发性骨髓瘤肿瘤患者用硼替佐米或含有硼替佐米的药物治疗效果;4)指导待测多发性骨髓瘤肿瘤患者硼替佐米或含有硼替佐米的药物用药。
- 一种预测待测多发性骨髓瘤肿瘤患者预后情况方法,包括如下步骤:获得所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类;属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预测预后情况显著劣于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者。
- 根据权利要求14所述的方法,其特征在于:所述预后情况体现在预后生存率大小、生存期长短或存活风险程度;所述属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预测预后生存率显著劣于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者体现为如下1)-3)中至少一种:1)属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预测预后生存率显著低于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者;2)属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者预后生存期显著低于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者;3)属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者存活风险程度显著低于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者。
- 一种检测待测多发性骨髓瘤肿瘤患者用硼替佐米或含有硼替佐米的药物治疗效果,包括如下步骤:获得所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类,属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者硼替佐米或含有硼替佐米的药物治疗效果好于属于MCL1-M-Low亚型的待测多发性骨髓瘤肿瘤患者。
- 一种指导待测多发性骨髓瘤肿瘤患者硼替佐米或含有硼替佐米的药物用药,包括如下步骤:获得所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据;再将所述待测多发性骨髓瘤肿瘤患者97个基因的表达量数据用所述多发性骨髓瘤贝叶斯分类器进行分类,对属于MCL1-M-High亚型的待测多发性骨髓瘤肿瘤患者采用硼替佐米或含有硼替佐米的药物治疗。
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Title |
---|
CHEN, YOUYING ET AL.: "Classification of Colon Cancer Data Based on Bayesian Classifier", JOURNAL OF GUANGXI NORMAL UNIVERSITY ( NATURAL SCIENCE EDITION, vol. 29, no. 3, 30 September 2011 (2011-09-30), pages 187 - 191 * |
KUIPER, R. ET AL.: "A Gene Expression Signature for High-Risk Multiple Myeloma", LEUKEMIA, vol. 26, no. 11, 30 November 2012 (2012-11-30), pages 2406 - 2413, XP055118310, DOI: 10.1038/leu.2012.127 * |
LIU, QIONG ET AL.: "A Microarray Analysis of Bortezomib-Resistant Gene Expression in Multiple Myeloma", JOURNAL OF SHANDONG UNIVERSITY (HEALTH SCIENCE, vol. 53, no. 6, 30 June 2015 (2015-06-30), pages 33 - 38 * |
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