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Colorectal adenoma biomarker, kit and screening method of biomarker

A technology of biomarkers and screening methods, applied in the screening of kits and biomarkers, in the field of colorectal adenoma biomarkers, to achieve high specificity, high accuracy, and good screening efficiency and accuracy.

Pending Publication Date: 2022-04-19
TONGJI UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Most studies on early screening of colorectal tumors based on intestinal flora use the abundance of intestinal microorganisms, for example, the construction of diagnostic models based on bacterial abundance, but these methods have certain limitations

Method used

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  • Colorectal adenoma biomarker, kit and screening method of biomarker
  • Colorectal adenoma biomarker, kit and screening method of biomarker
  • Colorectal adenoma biomarker, kit and screening method of biomarker

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0057] Example 1 Screening of markers for early screening of colorectal adenoma based on microbial SNVs and construction of early screening models

[0058] 1.1. Data collection

[0059] From the National Center for Biotechnology Information SRA database (URL: https: / / www.ncbi.nlm.nih.gov / sra) and the European Bioinformatics Institute ENA database (URL: https: / / www.ebi.ac.uk / ena) Obtain the fecal microbial metagenomic sequencing data and clinical information data of colorectal adenoma patients and healthy control samples (clinical information mainly includes: disease status, age, gender and BMI).

[0060] The cohorts included in this embodiment are: Japanese JAP cohort (DRA006684, DRA008156), Austrian AUS cohort (ERP008729), French FRA cohort (ERP005534) and Italian ITA cohort (SRP136711), and the number of samples included in the actual analysis is 622, including 183 colorectal adenoma samples and 439 healthy control samples.

[0061] 1.2. Data preprocessing

[0062] Quali...

Embodiment 2

[0086] Example 2 Different cohort cross-validation and leave-one-out method validation

[0087] Experimental materials: Cross-validation and leave-one-out validation were performed using cohorts from different countries in public data to test the robustness and versatility of microbial biomarkers.

[0088]experimental method:

[0089] 2.1. 5-fold cross-validation within different cohorts

[0090] For cohorts from different countries, based on our identified optimal strain SNV combinations (E.coli_58110, F.prausnitzii_57453, F.prausnitzii_61481, P.distasonis_56985, F.prausnitzii_62201, B.longum_57796, B.adolescentis_56815, A.hadrus_55206 .uniformis_57318, B.vulgatus_57955, 10 strains), and internal 5-fold cross-validation for each queue, that is, each queue is randomly divided into 5 folds, and each fold is used as a test set in turn, and the remaining 4 folds are used as a training set Perform model building to obtain an average AUC with a 50% discount.

[0091] 2.2. Cross-...

Embodiment 3

[0096] Example 3 specificity verification

[0097] Experimental materials: Collect the microbiological sequencing data of intestinal diseases other than colorectal adenoma in the database for specific verification, including colorectal cancer (cohort ERP008729, ERP005534, DRA006684, DRA008156, SRP136711, the number of disease samples is 386, healthy controls The number of samples is 439), Crohn's disease (cohort PRJNA400072, the number of disease samples is 68, the number of healthy control samples is 34) and ulcerative colitis (cohort PRJNA400072, the number of disease samples is 53, the number of healthy control samples is 34).

[0098] Experimental method: For the sequencing data of different diseases, based on the optimal strain SNV combination we confirmed, we constructed a model for each disease, and obtained the result of 10-fold cross-validation, that is, each disease data was randomly divided into 10 folds internally. One fold is used as a test set in turn, and the re...

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Abstract

The invention discloses a colorectal adenoma biomarker, a kit and a screening method of the biomarker. The colorectal adenoma biomarker comprises the following components: an internal organ Odorbacter splanchnicus62174, Bacteroides cellulolyticus 58046, Alistipes shahii62199 and the like, and is characterized in that the internal organ Odorbacter splanchnicus62174, the internal organ Bacteroides cellulolyticus 58046, the internal organ Alistipes shahii62199, the internal organ Alistipes shahii62199, the internal organ Alistipes shahii62199 and the internal organ Alistipes shahii62199 and the internal organ Alistipes shahii62199 and the internal organ Alistipes The tumor biomarker screening method comprises the following steps: S1, acquiring microorganism sequencing data and clinical information data of a disease control group and a normal control group, and preprocessing; s2, screening the preprocessed microbial sequencing data, and annotating SNV levels of strains with enough sequencing depth and coverage to obtain information such as SNV mutation frequency of each strain; s3, performing difference analysis on the microbial SNV data of the disease patient and the healthy control group to obtain SNV sites with significant difference in different strains; s4, screening the differential SNV loci, and determining an optimal SNV biomarker; in conclusion, the biomarker and the screening method provided by the invention can be used for better early diagnosis and treatment of cancers, and have important significance and clinical application value.

Description

technical field [0001] The invention relates to the technical field of medicine, in particular to a colorectal adenoma biomarker, a kit and a screening method for the biomarker. Background technique [0002] In recent years, the morbidity and mortality of cancer in the world have been increasing year by year. Early screening and early intervention of tumors can effectively reduce the morbidity and mortality. [0003] Take colorectal cancer as an example. Worldwide, about 10% of newly diagnosed cancers are colorectal cancer, which has brought huge health and economic burdens to the global society. Colorectal adenoma is the most important precancerous lesion of colorectal cancer. Early screening and intervention of colorectal adenoma can significantly reduce the incidence of colorectal cancer and improve the five-year survival rate of patients. clinical significance. Currently, the main methods for screening colorectal tumors include imaging examinations, endoscopy, and immu...

Claims

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Application Information

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IPC IPC(8): C12Q1/689G16B15/30
CPCC12Q1/689G16B15/30C12Q2600/156Y02A50/30
Inventor 朱瑞新高文星
Owner TONGJI UNIV
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