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Construction method of mibc typing and prognosis prediction model based on microbial abundance

A classification method and prediction model technology, applied in the field of urinary system tumors, can solve the problem that factors have not been included, and achieve the effect of accurate prognosis prediction

Active Publication Date: 2022-06-21
上海仁东医学检验所有限公司 +1
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AI Technical Summary

Problems solved by technology

[0012] Although there is an EU consensus on MIBC as of 2020, the existing molecular typing of MIBC is mainly based on the expression clustering analysis of RNA transcriptome data, and there are still many dimensional factors that have not been included in the typing of MIBC considerations, e.g. micro-organisms

Method used

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  • Construction method of mibc typing and prognosis prediction model based on microbial abundance
  • Construction method of mibc typing and prognosis prediction model based on microbial abundance
  • Construction method of mibc typing and prognosis prediction model based on microbial abundance

Examples

Experimental program
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Effect test

Embodiment 1

[0054] 1. Collection of MIBC and clinical data

[0055] Gene expression profiling data and clinical information data (clinical information mainly includes: age, disease stage, DSS and OS).

[0056] The MIBC cohort included in this example is: TCGA-BLCA cohort (n=410), excluding T1 stage samples and samples from the same patient that were repeatedly sequenced, and the actual number of samples included in the analysis was 406 cases.

[0057] 2. TCGA microbial detection process

[0058] 1. Identify microbial data

[0059] A total of 71,782 microbial genomes were downloaded using the RepoPhlan (https: / / bitbucket.org / nsegata / repophlan) database, of which 5,503 were viruses and 66,279 were bacteria / archaea. Bacteria or archaea are filtered according to whether the mass fraction is greater than 0.8. After filtering, 5503 viruses and 54471 bacteria / archaea remained, ie a total of 59974 microbial genomes, for subsequent analysis.

[0060] Sequencing reads that were not aligned to ...

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Abstract

The invention discloses a method for typing muscle invasive bladder cancer (MIBC). The method performs molecular typing of MIBC according to the characteristics of tissue microbial abundance spectrum of MIBC patients. The invention also discloses an MIBC prognosis prediction model based on the typing method and a construction method thereof. The present invention utilizes the muscle invasive bladder cancer transcriptome RNA-seq data in the TCGA database to analyze and obtain the microbial data of MIBC patients, and then performs NMF clustering based on the microbial abundance spectrum to establish molecular typing at the microbial level of MIBC. Thus, the correlation between microorganisms and MIBC was deeply analyzed from the level of tumor tissue microorganisms, and a MIBC prognosis prediction model was established, which is helpful to accurately predict the 1‑5-year survival rate of MIBC patients.

Description

technical field [0001] The present invention relates to the field of urinary system tumors, in particular to the field of muscle-invasive bladder cancer (Muscle-invasive bladder cancer, MIBC), and more particularly, to a method for typing muscle-invasive bladder cancer based on microbial abundance spectrum and the Methods of constructing prognostic prediction models. Background technique [0002] Bladder cancer is one of the most common malignant tumors of the urinary system. Globally, there are about 540,000 new cases of bladder cancer and 188,000 deaths. In 2016, the predicted data in my country showed that there were 80,500 new bladder cancer cases, including 62,100 males and 18,400 females; 32,900 died, including 25,100 males (11th in male malignant tumors) and 7,800 females. [0003] Bladder cancer typically arises from the epithelium (urothelium) that covers the inner surface of the bladder. According to the 2004 WHO classification of tumors of the urinary tract sys...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B15/30G16B20/00G16B30/00G16B40/00
CPCG16B15/30G16B20/00G16B30/00G16B40/00
Inventor 金鸽薛银鸽林为丽徐小红赵婷婷
Owner 上海仁东医学检验所有限公司
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