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Method, device and storage medium for predicting tumor neoantigen

A new tumor technology, applied in the field of biological information, can solve problems affecting the accuracy of neoantigen prediction

Active Publication Date: 2021-07-30
XUKANG MEDICAL SCI & TECH (SUZHOU) CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The design flaws of traditional methods directly affect the accuracy of neoantigen prediction

Method used

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  • Method, device and storage medium for predicting tumor neoantigen
  • Method, device and storage medium for predicting tumor neoantigen
  • Method, device and storage medium for predicting tumor neoantigen

Examples

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Embodiment 1

[0092] This embodiment starts with the mutation file of a sample of non-small cell lung cancer. The specific mutation information is shown in Table 1, and Topiary, pVACtools and the method of the present invention are compared to predict nascent polypeptides with a length of 8-11 amino acids.

[0093] This embodiment can be an implementation example of the verification scheme of the present invention, and proves the advantages of the present invention compared with the two current mainstream tools. image 3 The comparison process and results between the neoantigen prediction method of the present invention and two mainstream open source tools are illustrated. Since the three tools use the same method for the affinity of peptides and HLA molecules, we only focus on the differences in the generation of nascent peptides among the three tools.

[0094] Table 1 Information on 58 somatic mutation sites in patients with non-small cell lung cancer

[0095]

[0096]

[0097] In ...

Embodiment 2

[0103] Example 2 is a specific application scenario of the method provided by the present invention in tumor immunotherapy, to illustrate the application value of the present invention in tumor immunotherapy, and its advantages compared with the currently approved tumor mutation load. High tumor mutational burden indicates that there are more tumor somatic mutations, which means that more tumor neoantigens can be produced, so that the tumor cells are more likely to be recognized by immune cells, which is why tumor mutational burden is used as a biomarker The biological rationale for assessing the effects of immunotherapy. Example 2 verifies the effectiveness of the tumor neoantigen load calculated by the present invention as a biomarker for immunotherapy.

[0104] Table 3 lists the overall survival data of 13 hepatocellular carcinoma patients undergoing immunotherapy, the tumor mutation load detected by whole exome sequencing, and the sample neoantigen load calculated by the p...

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Abstract

The invention relates to a method for predicting tumor neoantigens, comprising steps: (1) performing somatic mutation and gene fusion detection according to tumor-germline control samples; (2) generating fusion mutant peptides and corresponding wild-type peptides for each pair of fusion genes (3) Generate mutant peptides and corresponding wild peptides based on each somatic mutation; (4) Construct a tumor sample-specific personal genome and generate mutant peptides containing multiple mutations; (5) Identify single mutations and multiple mutations Authenticity; (6) Remove mutant peptides that are completely consistent with other positions of the wild-type protein; (7) Perform HLA molecular typing detection to predict the affinity of nascent peptides and HLA molecules, and use nascent peptides with high affinity as candidate tumor neoantigens . The invention also provides the corresponding device and computer storage medium. By adopting the method, device and storage medium of the present invention, it is possible to effectively evaluate tumor treatment response biomarkers, and provide accurate candidate peptides for the design of tumor vaccines.

Description

technical field [0001] The present invention relates to the field of biological information, in particular to the discovery of biomarkers for tumor immunotherapy, specifically a method for predicting tumor neoantigens formed by somatic cell mutation and gene fusion and its application. Background technique [0002] tumor neoantigen [0003] Tumor neoantigens refer to "non-self" neonatal protein polypeptides that are recognized by human antigen-presenting cells and do not exist in the human body. The "non-self" neonatal polypeptides are mainly apoptotic mutant proteins formed by tumor cell mutations. Specifically, in terms of the biological process of neoantigen presentation, it is divided into five steps: 1. Antigen-presenting cells (APCs) can endocytose tumor cells and cleave proteins (including mutant proteins) in tumor cells into short Peptides; 2. The transport protein (TAP, endosome) in APC cells transports these peptides to the endoplasmic reticulum; 3. HLA class I mo...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/50G16B50/00
Inventor 叶浩李祥永戴珩
Owner XUKANG MEDICAL SCI & TECH (SUZHOU) CO LTD
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