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A microbial marker for colorectal cancer and its application

A technology of colorectal cancer and microorganisms, applied in the field of microorganisms, can solve the problems of high experimental process and operation costs, imprecise annotations, and poor versatility, and achieve high sensitivity, reduce morbidity, and improve the effect of disease treatment

Active Publication Date: 2020-01-24
SHANGHAI BIOTECAN PHARMA +1
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] CN108064273A discloses a biomarker used to predict diseases related to microorganisms, but the combination of biomarkers in this invention is random, and the prediction of the disease requires metagenomic sequencing to analyze the abundance of reads, which is only limited to specific Fragments, high data requirements, high experimental process and operation costs, are not conducive to the application of technology
Imprecise annotations make the markers in most patents suitable for 16S sequencing, and are not very versatile in metagenomics or other methods for quantifying the abundance of fungi

Method used

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  • A microbial marker for colorectal cancer and its application
  • A microbial marker for colorectal cancer and its application
  • A microbial marker for colorectal cancer and its application

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0052] The selection of embodiment 1 model algorithm

[0053] The present invention selects Xgboost as the basis of the optimal model through the screening and matching of a large amount of information, and the specific method is as follows:

[0054] (1) Download the metagenomic sequencing data of the intestinal flora of colorectal cancer and control healthy people from the European Bioinformatics Institute (EBI);

[0055] (2) Match the abundance data of different intestinal bacteria according to the metagenomic data. In order to find markers as much as possible, and considering the matching between the metagenomic database and the 16S database, and considering the reasons that qPCR cannot measure the species with particularly small content, this match reached the genus level, and there were a total of 206 genus-level bacteria;

[0056] (3) Use machine learning to select model algorithms. Supervised learning is to generate a function through the corresponding relationship be...

Embodiment 2

[0062] The bacterium of embodiment 2 specific species is selected

[0063] (1) The Xgboost model obtains the Feature-importance score of variable features (see Figure 4 ), according to the ranking of the score, gradually increase the number of bacterial variables to obtain the variables required for the optimal ROC-AUC (see image 3 ), the results show that the ROC-AUC value is the largest when inputting the bacterial abundance of 11 specific species of characteristic variables;

[0064] (2) Test the model, split the data into a training set and a test set, input the bacterial abundance of 11 specific species of the sample, input the Xgboost model, and optimize the parameters of the model according to GridsearchCV, train with the training set, and test with the test set ;

[0065] (3) Storage model for colorectal cancer risk prediction of subsequent measurement data.

[0066] Depend on image 3 It can be seen that the number and combination of input variables will produce...

Embodiment 3

[0067] Embodiment 3 clinical verification

[0068] (1) Detection of the relative abundance of intestinal microbial markers: 16S sequencing was performed on the stool bacteria of 4 cases of intestinal cancer and 32 cases of healthy people, and the abundance of 11 specific species of bacteria was found, and the test data was input into the model;

[0069] (2) Risk value output: The algorithm model after learning and training is input into the test data obtained in the experiment, and the probability between 0 (control) and 1 (colorectal cancer) is obtained, and finally the probability value of 1 (disease) is confirmed as Risk value, those who are less than 0.5 are judged as healthy people, but those whose risk value is between 0.4 and 0.5 are recommended to adjust certain intestinal bacteria to reduce the risk of subsequent colon cancer, and those who are more than 0.5 are judged as high-risk groups of colorectal cancer , it is recommended to undergo colonoscopy to confirm the d...

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Abstract

The invention provides a microbial marker of colorectal cancer and application of the marker. The microbial marker comprises Faecalibacterium, Streptococcus and Fusobacterium. The microbial marker ofcolorectal cancer has high precision of predicting the risk of colorectal cancer and high sensitivity, only the abundance of the microbial marker of colorectal cancer needs to be obtained, a risk early warning is given out through model calculation, and the possibility of getting colorectal cancer is evaluated. The microbial marker can be used for preventing colorectal cancer, warning a subject and giving the subject a prompt about whether it is necessary to further conduct diagnosis confirmation or not, and is also conductive for individuals to improve the intestinal microbial environment byadjusting diet or medical treatment, so that the risk of getting colorectal cancer is reduced for the individuals.

Description

technical field [0001] The invention belongs to the field of microorganisms, and relates to a colorectal cancer microbial marker and application thereof. Background technique [0002] Colorectal cancer is a common malignant tumor. Due to changes in people's living environment and living habits, the incidence of colorectal cancer has been increasing in recent years. The tumor may occur in any part of the colon or rectum, and can spread to other tissues and organs through lymphatic, blood circulation and direct spread. There are no obvious symptoms in the early stage of bowel cancer, and when the problem is discovered, it is basically in the advanced stage, and the cure rate is only 5%-40%. Early screening can effectively reduce the incidence and mortality of colorectal cancer. Doctors recommend that people over the age of 40 should be screened once a year; people under the age of 40 should also be screened every 3-5 years. [0003] The current screening methods for colorec...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886C12Q1/689C12Q1/14C12Q1/04C12R1/01C12R1/46
Inventor 王丽君李无霜高军晖龚建兵袁卫兰杨广超林灵张英霞
Owner SHANGHAI BIOTECAN PHARMA
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