Method and device for predicting tumor newly-born antigen and storage medium

A neonatal and tumor technology, applied in the field of bioinformatics, can solve problems affecting the accuracy of neoantigen prediction

Active Publication Date: 2019-04-05
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 and device for predicting tumor newly-born antigen and storage medium
  • Method and device for predicting tumor newly-born antigen and storage medium
  • Method and device for predicting tumor newly-born antigen and storage medium

Examples

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Embodiment 1

[0093] 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 the nascent polypeptide with a length of 8-11 amino acids.

[0094] This embodiment can be an implementation example of the verification scheme of the present invention, proving 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 between the three tools in the generation of nascent peptides.

[0095] Table 1 Information on 58 somatic mutation sites in patients with non-small cell lung cancer

[0096]

[0097]

[0098] I...

Embodiment 2

[0104] 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.

[0105] Table 3 lists the overall survival data of 13 cases of hepatocellular carcinoma patients undergoing immunotherapy, as well as the tumor mutation load detected by whole exome sequencing, and the sample neoantigen load...

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Abstract

The invention relates to a method for predicting a tumor newly-born antigen. The method comprises the steps that 1, according to a tumor-embryonal system contrast sample, somatic mutation and gene fusion detection are conducted; 2, for each pair of fusion genes, fusion mutation peptide and corresponding wild peptide are generated; 3, based on each somatic mutation, mutation peptide and corresponding wild peptide are generated; 4, a specific individual genome of a tumor sample is established, and mutation peptide containing multiple mutations is generated; 5, the true and false of mutation peptide of single-mutation and multi-mutation are judged; 6, mutation peptide completely identical to wild protein in other position sequence is removed; 7, HLA molecular subtyping detection is conducted,the appetency of newly-born peptide and HLA molecules is predicted, and newly-born peptide with high appetency is used as a candidate tumor newly-born antigen. The invention further provides a corresponding device and a computer storage medium. By adopting the method and device and the storage medium, the biomarker assessment can be effectively responded to through tumor treatment, and the precise candidate peptide fragment is provided for design of a tumor vaccine.

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 can be divided into five steps: 1. Antigen-presenting cells (APCs) can endocytose tumor cells and cleave proteins (including mutant proteins) in tumor cells into short 2. The transport protein (TAP, endosome) in APC cells transports these peptides to the endoplasmic reticulum; 3. The HLA class I mole...

Claims

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Application Information

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Patent Type & Authority Applications(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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