Biomarker combination for molecular typing and/or prognosis prediction of muscle-invasive bladder cancer and application of biomarker combination

A technology of biomarkers and molecular typing, applied in the fields of bioinformatics, microbial determination/examination, biochemical equipment and methods, etc. Low requirements and the effect of meeting the needs of large sample analysis

Pending Publication Date: 2019-05-24
SHANGHAI TENTH PEOPLES HOSPITAL
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  • Claims
  • Application Information

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Problems solved by technology

These molecular typing methods are helpful to understand the disease mechanism, but due to their complexity, clinical implementation is difficult, and there is still an urgent need for simple and effective molecular typing markers and omics analysis methods

Method used

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  • Biomarker combination for molecular typing and/or prognosis prediction of muscle-invasive bladder cancer and application of biomarker combination
  • Biomarker combination for molecular typing and/or prognosis prediction of muscle-invasive bladder cancer and application of biomarker combination
  • Biomarker combination for molecular typing and/or prognosis prediction of muscle-invasive bladder cancer and application of biomarker combination

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Embodiment 1

[0036] This embodiment is a screening method for a combination of biomarkers for molecular typing and / or prognosis prediction of muscle invasive bladder cancer, such as figure 1 As shown, the screening process of the biomarker combination gene set is as follows:

[0037] Download the clinical data of muscle-invasive bladder cancer cases (405 cases) and the corresponding tumor tissue RNA-Seq transcriptome data from the TCGA (The Cancer Genome Atlas) database (https: / / portal.gdc.cancer.gov), select The downloaded data type is the FPKM (fragments per kilobase of transcript per million fragments mapped) value standardized by the Upper Quartile method.

[0038] In the RNA-Seq data, genes with a median expression value of 0 were removed, and then the correlation of each gene with overall survival (OS) was analyzed. For each gene, according to whether it is greater than or less than the median expression value, patients are divided into high-expression group and low-expression group...

Embodiment 2

[0051] In this embodiment, the human expression profile chip data of 71 cases of muscle-invasive bladder cancer are taken as an example, and the data set and non-negative matrix factorization analysis method described in the present invention are used to predict the survival and prognosis of bladder cancer. The details are as follows:

[0052] The transcriptome data and patient overall survival data of tumor specimens were downloaded from the GEO database (accession number GSE48277), the data type was human expression profiling chip data, and the specimen type was fresh frozen tissue.

[0053] From the transcriptome data, the expression values ​​of FGF10, TP53INP1, DDR2, MYC, CDC73, IGF1, PLA2G1B, SKI, FN1, EGFR, PPARG, PDGFRA, PDGFD, GAS6, PDGFC, FNTB and CCNB1 genes were extracted to establish an expression matrix.

[0054] Import the expression matrix into the NMF software in Matlab, preset the grouping parameter range from 1 to 7 (k=1 to k=7), and run the analysis program; ...

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Abstract

The invention relates to a biomarker combination for molecular typing and / or prognosis prediction of the muscle-invasive bladder cancer, and a screening method and application thereof. The biomarker combination comprises the following genes: FGF10, TP53INP1, DDR2, MYC, CDC73, IGF1, PLA2G1B, SKI, FN1, EGFR, PPARG, PDGFRA, PDGFD, GAS6, PDGFC, FNTB and CCNB1. Through non-negative matrix factorizationclustering analysis based on transcription data of the biomarker combination, the muscle-invasive bladder cancer can be classified to respectively correspond to different expression characteristic spectrums. The classification corresponds to significantly different overall survival statuses, thus being used for survival prognosis assessment. The transcription data analysis method adopted has theadvantages that the number of biomarker combinations is small, the analysis steps are simple, the requirements of large sample analysis are met, the requirements for the calculation ability are low, and the method is applicable to standardized transcription data; the transcription data can be a transcriptomic data sub set or a set of genetic transcription data for individual detection.

Description

technical field [0001] The invention belongs to the technical field of biomedicine, and in particular relates to a combination of biomarkers for molecular typing and / or prognosis prediction of muscle-invasive bladder cancer, a screening method and application thereof. Background technique [0002] Bladder cancer is the most common malignant tumor of the urinary system. According to whether the tumor invades the muscle layer, bladder cancer is divided into non-muscle-invasive bladder cancer (NMIBC) and muscle-invasive bladder cancer (Muscle-invasive bladder cancer, MIBC). Muscle-invasive bladder cancer accounts for about 25% of primary bladder tumors. In addition, 10%-20% of non-muscle-invasive bladder cancers will progress to muscle-invasive bladder cancer. Muscle-invasive bladder cancer has a high degree of malignancy and poor prognosis. The 5-year overall survival rate (overall survival) is less than 50%. If lymph node metastasis or distant metastasis occurs, the prognos...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6886G16B25/10
Inventor 毕德玺蔚青
Owner SHANGHAI TENTH PEOPLES HOSPITAL
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