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SNP site combination for colorectal cancer onset risk prediction, onset risk prediction model and system

A colorectal cancer and risk prediction technology, applied in the field of biomedicine, can solve the problems of unclear screening effect and no genetic prediction model for the incidence of colorectal cancer in the general population.

Pending Publication Date: 2022-04-12
SUN YAT SEN UNIV CANCER CENT
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0006] In China, there is no feasible genetic prediction model for the risk of colorectal cancer in the general population, and its screening role in the population is still unclear

Method used

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  • SNP site combination for colorectal cancer onset risk prediction, onset risk prediction model and system
  • SNP site combination for colorectal cancer onset risk prediction, onset risk prediction model and system
  • SNP site combination for colorectal cancer onset risk prediction, onset risk prediction model and system

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0051] Example 1 SNP site combination and model construction related to colorectal cancer risk prediction model

[0052] Based on the 75 key susceptibility gene mutation sites found in international colorectal cancer GWAs studies (Table 1), the large-scale sample size of Chinese colorectal cancer population and healthy control population (3049 cases of colorectal cancer population cohort in southern China) Cancer patients and 2557 healthy control individuals) were based on the association analysis, using the LASSO statistical method to perform fitting analysis on 75 SNPs, using 10-fold cross-validation to train the model, and randomly selecting the test data set each time.

[0053] Table 1. The prediction model invented by the present invention is based on 75 SNPs derived from GWAs

[0054]

[0055]

[0056]

[0057] The present invention fits models containing different numbers of SNPs in the analysis process, and finally obtains an optimized colorectal cancer risk p...

Embodiment 2

[0064] Example 2 Colorectal Cancer Risk Prediction Kit

[0065] A kit for predicting the risk of colorectal cancer, comprising: PCR amplification primers and single-base extension primers for detecting 19 SNP sites in the human genome (the 19 SNP sites shown in Table 2).

[0066] The preparation of the specific kit is as follows:

[0067] 1. Design and synthesize PCR-specific recognition primers and extension primers of the SNP site, as shown in Table 3

[0068] Table 3 PCR amplification primers (Primer Allele_FAM, Primer Allele_HEX) and co-extension primers (Primer_Common) for specific recognition of biallelic genes at 19 SNP sites to be tested

[0069]

[0070]

[0071]

[0072] 2. Construction of the kit

[0073] Other components of the kit, including: Taq enzyme, dNTP mixture, diluent, buffer, etc., see the detection method below for details.

[0074] 3. The detection method, the process is as follows:

[0075] (1) DNA sample extraction

[0076] Genomic DNA w...

Embodiment 3

[0088] Embodiment 3 The internal verification of the forecasting performance of the forecasting model constructed by the present invention

[0089] The prediction performance of the model constructed by the present invention has been confirmed in an independent verification cohort from southern China. The verification cohort is 3017 cases of colorectal cancer patients and 2488 cases of healthy control individuals. The AUC of the prediction risk of colorectal cancer is 0.59 ( image 3 ), showing that the model has good internal validity.

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Abstract

The invention provides a colorectal cancer onset risk prediction model and system. On the basis of research on colorectal cancer susceptibility gene screening results of Chinese people, the colorectal cancer onset risk prediction system and the kit comprising 19 SNP locus typing information are constructed, the risk degree of colorectal cancer suffering from a subject can be predicted and prompted, the performance is stable in colorectal cancer onset risk prediction of different people, and the kit has the advantages of being high in specificity, high in sensitivity and the like. The kit is good in repeatability, high in reliability and convenient in detection technology, provides the possibility of evaluating the onset risk level for common risk people, does not need age limitation and sex difference consideration, can carry out large-scale population general survey, screens high-risk groups of colorectal cancer onset, realizes colorectal cancer risk prediction and early warning, improves the early diagnosis rate, and is suitable for popularization and application. The method can be used as the first step of individualized early screening and prevention strategies of the colorectal cancer in China, is beneficial for identifying high-risk individuals of the colorectal cancer, and has the prospect of being recommended as one of auxiliary means of common screening items of the colorectal cancer.

Description

technical field [0001] The invention belongs to the technical field of biomedicine. More specifically, it relates to a combination of SNP sites for colorectal cancer risk prediction, colorectal cancer risk prediction model and system. Background technique [0002] The global incidence of colorectal cancer ranks third among malignant tumors, and its mortality rate ranks second. With the development of social economy and the adjustment of dietary structure, China has become a high incidence area of ​​bowel cancer in the world. Colorectal cancer is characterized by obvious genetic heterogeneity, phenotypic complexity, and racial differences. Genetic factors can fundamentally promote the occurrence of colorectal cancer. Hereditary colorectal cancer accounts for about 5% of the total colorectal cancer, and this part of colorectal cancer is mainly caused by rare germline mutations in APC and DNA mismatch repair genes (MSH2, MSH6, MLH1, PMS2). The remaining hereditary risk of c...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16H50/30G16B20/40G16B20/30G06Q10/06C12Q1/6886
Inventor 徐瑞华何彩云陈乐宗
Owner SUN YAT SEN UNIV CANCER CENT
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