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Determining method for evaluation gene groups for gastric cancer prognosis prediction

A technology for determining methods and genes, applied in the direction of biochemical equipment and methods, microbial determination/inspection, etc., can solve problems such as difficult application, no significant relationship, lack of evidence of genetic biological mechanism, etc., to reduce mutation frequency. limit, reduce the limit of robustness, evaluate the effect of high accuracy

Pending Publication Date: 2019-09-13
SHANGHAI ORIGIMED CO LTD
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Problems solved by technology

However, the prognosis of the RhoA mutation was analyzed through survival analysis, and the prognosis was established with the mutation of the RhoA gene alone for survival analysis, and it was found that there was no significant relationship
Therefore, only the RhoA gene can be used to correlate the prognosis of gastric cancer, which cannot meet the needs of predicting the prognosis of gastric cancer. It is necessary to find new predictive indicators that are highly correlated with the prognosis of gastric cancer
[0004] In addition, for the relationship between genes and prognosis in gastric cancer, the current technical solutions mainly fall into two categories: the first category is to correlate the outcome of the prognosis with the mutation of a single gene. However, this indicator is limited by the frequency of mutations in the population, such as The mutation frequency of the RhoA gene is 6.3%, and the size of the collected samples will limit the robustness of the survival analysis results; the second category is to correlate the prognosis with the mutation status of certain gene combinations, and the molecular markers from the combination of multiple genes can reach higher mutation frequency
However, the genes usually selected are synthesized from gene sets with high mutation frequencies found in tumors, lacking reliable evidence of biological mechanisms between genes, and it is difficult to reliably apply them in clinical practice

Method used

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  • Determining method for evaluation gene groups for gastric cancer prognosis prediction
  • Determining method for evaluation gene groups for gastric cancer prognosis prediction
  • Determining method for evaluation gene groups for gastric cancer prognosis prediction

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0048] figure 2 It is a flowchart of steps of the determination method involved in Embodiment 1 of the present invention.

[0049] This embodiment is to specifically illustrate the determination method of the evaluation gene group used for the prediction of the prognosis of gastric cancer, such as figure 2 As shown, the determination method specifically includes the following steps:

[0050] Step S1, determine the set of candidate target genes, specifically:

[0051] All the genes included in the RhoA protein activity regulation pathway are used as an alternative target gene set, specifically, the alternative target gene set in this embodiment is the regulatory gene of the RhoA protein activity regulation pathway verified by the experimental data in the NCI database, In this embodiment, a total of 48 regulatory genes were selected as the set of candidate target genes through the literature progress tracking and verification.

[0052] Step S2, determine the pending evaluat...

Embodiment 2

[0097] This example is to clarify the possible biological mechanism of the prognosis of the evaluation gene group (RhoA_S) determined in Example 1. For this reason, we perform functional enrichment on all genes that meet the predetermined mutation conditions in the RhoA_S of the good prognosis sample, and the results show The pathways mainly enriched for mutations in samples with good prognosis are shown in Table 3.

[0098]

[0099]

[0100] The results in Table 3 show the pathways with significantly enriched mutations in samples with good prognosis: the function number is the pathway number; the function description refers to the function corresponding to the pathway, or the function it plays; the number of pathway genes is the total number of genes in the corresponding pathway. number; the number of genes that meet the predetermined mutation conditions refers to the number of times that the genes that meet the predetermined condition mutations appear in the pathway in ...

Embodiment 3

[0110] This example is to confirm that the evaluation gene group obtained by the determination method in Example 1 can indeed be used as a clinical basis for prognosis prediction of gastric cancer.

[0111] In this example, we collected clinical samples of 61 cases of diffuse gastric cancer and 50 cases of intestinal type gastric cancer from Chinese patients. These samples are mainly concentrated in clinical stage II to III samples. The overall survival period of the disease, death and other clinical information such as gender, age, EBV, HER2 amplification and other information were collected (see Table 5).

[0112]

[0113]

[0114]

[0115]

[0116]

[0117]

[0118] DNA from these 111 clinical samples of gastric cancer was extracted, whole exome sequencing (results of exome sequencing) was performed on these samples, and then the sequencing results were processed.

[0119] Wherein, in the processing of the sequencing results in this embodiment, adapters a...

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Abstract

The present invention provides a determining method for evaluation gene groups for gastric cancer prognosis prediction. The determining method is characterized in that a RhoA protein activity regulation and control pathway for regulating and controlling RhoA protein activity comprises the evaluation gene groups comprising a plurality of genes obtained by gene screening. The determining method specifically comprises the following steps: step 1, genes included in a RhoA gene regulation and control pathway are used as a candidate target gene set; step 2, gene groups to be evaluated are determinedaccording to a predetermined determination rule based on expression data of each gene in the candidate target gene set of each gastric cancer sample for screening and expression data of the RhoA gene; and step 3, cox survival analysis of all good prognosis samples with good prognosis of gastric cancers and all poor prognosis samples with poor prognosis of the gastric cancers obtained by each gastric cancer verification sample are determined based on gastric cancer verification sample groups comprising a plurality of the gastric cancer verification samples and according to a predetermined limiting method, and whether the gene groups to be evaluated are the evaluation gene groups capable of being used for evaluating the gastric cancer prognosis is determined.

Description

technical field [0001] The invention belongs to the field of biology, and in particular relates to a method for determining an evaluation gene group for prognosis prediction of gastric cancer. Background technique [0002] The prognosis prediction of gastric cancer is of great significance for evaluating and guiding the setting of clinical treatment plan and the research of new therapeutic targets. [0003] In gastric cancer, through the mutation analysis of the whole exome genome, it was found that the mutation rate of RhoA gene in the gastric cancer population is high, especially in the diffuse subtype of gastric cancer, there is an enrichment of mutations. However, the prognosis of RhoA mutation was analyzed by survival analysis, and the prognosis was established with the mutation of RhoA gene alone for survival analysis, and no significant relationship was found. Therefore, only the RhoA gene can be used to correlate the prognosis of gastric cancer, which cannot meet th...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886
CPCC12Q1/6886C12Q2600/118C12Q2600/156
Inventor 施巍炜牟硕王凯柳文进赵松辉
Owner SHANGHAI ORIGIMED CO LTD
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