Microbial marker of colorectal cancer and application of marker

A technology for 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: 2019-06-28
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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  • Microbial marker of colorectal cancer and application of marker
  • Microbial marker of colorectal cancer and application of marker
  • Microbial marker of colorectal cancer and application of marker

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0052] Example 1 Selection of Model Algorithms

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

[0054] (1) Download metagenomic sequencing data of gut microbiota of colorectal cancer and control healthy individuals from the European Bioinformatics Institute (EBI);

[0055] (2) The abundance data of different intestinal bacteria were matched according to the metagenomic data. In order to search for markers as much as possible, considering the matching between the metagenomic database and the 16S database, and considering that qPCR cannot measure species with particularly small contents, this match reached the genus level, and there were 206 bacteria at the genus level;

[0056] (3) Use machine learning to select model algorithms. Supervised learning is to generate a function through the corresponding relationship between a part of the input da...

Embodiment 2

[0062] Example 2 Bacterial selection of specific species

[0063] (1) The Xgboost model obtains the feature-importance score of the variable feature (see Figure 4 ), according to the ranking of the scores, 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 the bacterial abundance of 11 specific species of the characteristic variable is input;

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

[0065] (3) The storage model is used 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 produc...

Embodiment 3

[0067] Example 3 Clinical validation

[0068] (1) Detection of relative abundance of intestinal microbial markers: 16S bacteria in the stools of 4 cases of intestinal cancer and 32 healthy people were sequenced to find the abundance of 11 specific species of bacteria, and input the test data into the model;

[0069] (2) Risk value output: The algorithm model after learning and training is input into the test data obtained from the experiment, and the probability between 0 (control) and 1 (suffering from colorectal cancer) is obtained, and finally the probability value of 1 (sickness) is confirmed as If the risk value is less than 0.5, it is determined as a healthy person, but if the risk value is between 0.4 and 0.5, it is recommended to carry out certain intestinal bacteria adjustment to reduce the risk of subsequent colorectal cancer. , It is recommended to carry out colonoscopy to confirm the diagnosis. For people without colon cancer, it is recommended to adjust the intest...

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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 microorganism 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 rising 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. Colon cancer has no obvious symptoms in the early stage. 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 bowel cancer incidence and mortality. 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 colorectal cancer include: ligna...

Claims

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Application Information

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Patent Type & Authority Applications(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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