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Colon cancer prognosis assessment gene set and its construction method

A technology of colon cancer and gene sets, applied in the direction of biochemical equipment and methods, instruments, microbial determination/inspection, etc., can solve the problems of incomplete evaluation, affecting protein content and RNA expression, long observation time, etc., and achieve accurate prediction Effect

Active Publication Date: 2022-02-01
SHANGHAI ORIGIMED CO LTD +2
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The disadvantage is that the observation time is long, and all events need to be recorded, that is, the death of all patients
However, the immune response in the body works through protein or RNA. Mutations at the DNA level do not necessarily affect expression, thereby affecting protein content and RNA expression, and the occurrence of the body's immune response involves the generation of various immune cells and immune substances. Participation, single immune-related genes or small numbers of immune cells are incomplete for prognostic assessment

Method used

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  • Colon cancer prognosis assessment gene set and its construction method
  • Colon cancer prognosis assessment gene set and its construction method
  • Colon cancer prognosis assessment gene set and its construction method

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0088] Embodiment 1: Lasso regression method builds a model, obtains the selected characteristic gene set

[0089] data processing

[0090] Colon cancer gene expression data and clinical overall survival time data were obtained from The Cancer Genome Atlas project TCGA. Contains RNA-seq data of 471 TCGA colon cancer samples and survival data of 454 TCGA colon cancer samples. First, the samples were cleaned, and samples with both expression data and survival data were selected, and the survival time was longer than 30 days, and 435 colon cancer samples were obtained, and each sample had expression data of 60,488 genes.

[0091] Preliminary screening of related immune genes

[0092] The intersection genes with 547 immune-related genes in CIBERSORT were selected from 60488 genes, and the genes were screened.

[0093] In all the colon cancer sample data after sample screening, the genes with an average expression value 90% of the samples were removed, and 516 immune-relate...

Embodiment 2

[0117] Example 2: Comparison of the predictive power of selected feature gene sets and random gene sets

[0118]In order to further verify the validity of the evaluation gene set of the selected 9 genes, 9 genes were randomly selected from 516 genes (except the above 9 genes) to form a new "random gene set", and compared with the selected A defined "assessment gene set" was used for comparison.

[0119] With reference to the process described in Example 1, patients are also randomly divided into a training set (80%) and a verification set (20%), and the expression values ​​of 9 random genes and the weight coefficients of each gene on survival are summed. As the survival risk score Risk Score of each sample, the calculation formula of Risk Score is the same as that in Example 1.

[0120] The median value of the risk score calculated by the training set is also used as the boundary, and the patients in the training set and validation set are divided into High group and Low grou...

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Abstract

The invention relates to a colon cancer prognosis evaluation gene set and a construction method thereof. Specifically, the present invention uses a gene set composed of 9 immune-related genes to evaluate the prognosis and survival of colon cancer patients and provide scientific basis for medical decision-making. The invention also relates to a colon cancer prognosis kit, computing equipment, storage medium, and a method for constructing the evaluation gene set.

Description

technical field [0001] The invention relates to a method for evaluating the prognosis and survival of patients with colon cancer by using an immune-related gene set, which can be used as one of the reference conditions for clinical trial enrollment and provide scientific basis for medical decision-making. Background technique [0002] As an incurable disease, tumors have very clear treatment goals. After the tumor is diagnosed, patients can live longer through treatment. Colon cancer is a common malignant tumor of the digestive tract that occurs in the colon, accounting for the third place among gastrointestinal tumors. The incidence rate of the Chinese population is lower than that of Western countries. The rate showed an upward trend year by year. According to the research data on the global cancer status released by the International Agency for Research on Cancer, the morbidity and mortality of colon cancer are relatively high, and some patients with colon cancer have a ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886G16B35/20G16H50/30
CPCC12Q1/6886G16B35/20G16H50/30C12Q2600/118C12Q2600/158
Inventor 王凯车月王丛茂
Owner SHANGHAI ORIGIMED CO LTD
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