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MIBC typing and prognosis prediction model construction method based on microbial abundance

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

Active Publication Date: 2022-03-18
上海仁东医学检验所有限公司 +1
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  • Claims
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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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  • MIBC typing and prognosis prediction model construction method based on microbial abundance
  • MIBC typing and prognosis prediction model construction method based on microbial abundance
  • MIBC typing and prognosis prediction model construction method based on microbial abundance

Examples

Experimental program
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Embodiment 1

[0054] 1. Collection of MIBC and clinical data

[0055] The gene expression profile data and clinical information data of MIBC patients were obtained from the Cancer Genome Atlas (TCGA) database (website: https: / / portal.gdc.cancer.gov) (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 samples of T1 stage and repeated sequencing samples of the same patient, the number of samples included in the actual analysis was 406 cases.

[0057] 2. TCGA microbial testing process

[0058] 1. Identification of 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 were filtered according to whether the mass fraction was greater than 0.8. After filtering, 5503 viruses and 54471 bacteria / archaea remained, i...

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Abstract

The invention discloses a MIBC (muscular invasive bladder cancer) typing method. According to the MIBC typing method, MIBC is subjected to molecular typing according to tissue microorganism abundance spectrum characteristics of MIBC patients. The invention further discloses an MIBC prognosis prediction model based on the typing method and a construction method of the MIBC prognosis prediction model. According to the MIBC prognosis prediction method, MIBC transcriptome RNA-seq data in a TCGA database are utilized, microbial data of MIBC patients are obtained through analysis, then NMF clustering is carried out with a microbial abundance spectrum as a feature, molecular typing of the MIBC microbial level is established, accordingly, correlation between microorganisms and MIBC is deeply analyzed from the tumor tissue microbial level, an MIBC prognosis prediction model is established, and the MIBC prognosis prediction method is applied to the MIBC prognosis prediction of the MIBC patients. The model is helpful for accurately predicting the survival rate of MIBC patients in 1-5 years.

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), more specifically, to a method for typing muscle-invasive bladder cancer based on microbial abundance profiles and A method for constructing a prognostic prediction model. Background technique [0002] Bladder cancer is one of the most common malignant tumors of the urinary system. Globally, there are approximately 540,000 new cases of bladder cancer and 188,000 deaths. According to forecast data in my country in 2016, there were 80,500 new cases of bladder cancer, including 62,100 males and 18,400 females; 32,900 deaths, including 25,100 males (the 11th male malignant tumor) and 7,800 females. [0003] Bladder cancer generally originates in the epithelium (urothelium) that covers the inner surface of the bladder. According to the 2004 WHO classification of tumors of the urinary tra...

Claims

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Application Information

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Patent Type & Authority Applications(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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