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Construction method of tumor immune microenvironment prediction model based on RNAseq

A tumor microenvironment and prediction model technology, which is applied in the field of tumor immune microenvironment prediction model construction, can solve the problems of insufficient pertinence in the prediction of the curative effect of immunotherapy, and the accuracy of prediction results is not high, achieving stable results, reasonable division, The results are accurate

Pending Publication Date: 2019-06-14
杭州西合森医学检验实验室有限公司
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Problems solved by technology

Moreover, the accuracy of the prediction results of several current methods is not high, and the division of its own cell types is not pertinent enough to predict the efficacy of immunotherapy

Method used

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  • Construction method of tumor immune microenvironment prediction model based on RNAseq
  • Construction method of tumor immune microenvironment prediction model based on RNAseq
  • Construction method of tumor immune microenvironment prediction model based on RNAseq

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Embodiment 1

[0047] The construction method of the RNAseq-based tumor immune microenvironment prediction model of this embodiment comprises the following steps:

[0048] Step 1: Search the existing literature, integrate 32 tumor microenvironment-related cells, assign each microenvironment cell to a single cell type according to its function and importance, and determine 24 immune microenvironment-related cells.

[0049] Step 2: Search the literature comprehensively and collect all 583 relevant potential marker genes corresponding to 24 tumor microenvironmental cells; use TCGA RNA-seq data to perform cluster analysis on these candidate marker genes; eliminate generally low-expression genes according to the clustering results , to eliminate the relevant genes that have no difference among multiple cell types, and obtain 301 marker genes after screening.

[0050] Step 3: Use kallisto software to calculate the gene expression amount TPM, calculate the average expression amount of the marker ge...

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Abstract

The invention discloses a construction method of a tumor immune microenvironment prediction model based on RNAseq. The method comprises the first step of determining 24 cell types related to the tumormicroenvironment; the second step of selecting 301 marker genes preferably according to the cell types obtained according to the above step; the third step of calculating the gene expression amount TPM using kallisto software, calculating the average expression amount of a corresponding marker gene of each cell type and then taking a log value as the relative abundance of the cell type. Accordingto the construction method, the average expression amount of the corresponding marker gene of each cell type is calculated, that is, the average value of a set of marker genes, and the result is relatively more stable and less affected by the relative error compared with calculation of the single marker gene.

Description

technical field [0001] The invention relates to a method for constructing a prediction model of tumor immune microenvironment based on RNAseq. Background technique [0002] Immunotherapy activates the body's own immune system and relies on its own immune function to kill cancer cells. At present, it has demonstrated strong anti-tumor activity in the treatment of solid tumors such as melanoma, non-small cell lung cancer, kidney cancer and prostate cancer. Although the success of immunotherapy is exciting, countless patients have achieved remarkable results under its intervention. But there are still some patients who do not respond to immunotherapy. With the advancement of technology, people gradually understand the complexity and diversity of the immune environment of the tumor microenvironment and its important impact on immunotherapy. Further analysis and understanding of the tumor immune microenvironment will contribute to the improvement of immunotherapy responsivenes...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6881G16B5/00
Inventor 莫凡
Owner 杭州西合森医学检验实验室有限公司
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