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Method and equipment for neoantigen epitope prediction

An antigen epitope and prediction model technology, applied in biochemical equipment and methods, biological testing, anti-tumor drugs, etc., can solve the problem of antigen selection that needs to be further deepened, and achieve good quality sequencing results, convenient operation, and high sequencing throughput Effect

Active Publication Date: 2016-04-27
BGI SHENZHEN CO LTD
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Problems solved by technology

[0004] However, the current research on antigen selection still needs to be in-depth

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  • Method and equipment for neoantigen epitope prediction
  • Method and equipment for neoantigen epitope prediction
  • Method and equipment for neoantigen epitope prediction

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Embodiment 1

[0120] Illumina HiSeq2000 was used to perform exome sequencing on transplanted tumors and peripheral blood of C57 mouse liver cancer. The tumor group sequencing data is 6.12GB, and the peripheral blood sequencing data is 6.79GB. In the first step, the short sequence alignment software BWA was used to compare the tumor group sequencing data and peripheral blood sequencing data to the mouse reference genome sequence mm9. Step 2: Use the single nucleotide polymorphism (SNP) detection software SOAPsnp to compare the results of tumor sequencing data and peripheral blood sequencing data to detect SNP, and then use the peripheral blood sample as a control to screen out the tumor data. List of somatic single nucleotide non-synonymous mutation sites. In the third step, according to the list of single nucleotide non-synonymous mutation sites, a characteristic mutant peptide with a length of 10 is extracted, and the specificity means that the peptide does not exist in the database (Ense...

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Abstract

The invention provides a method and equipment for neoantigen epitope prediction. The method for neoantigen epitope prediction includes (1), building a candidate epitope library; (2), building a prediction model based on a historical database, and (3) taking at least one subset of the candidate epitope library as an input variable of the prediction model to predict neoantigen epitope. The candidate epitope library is composed of differential expression peptides which are peptides with difference between samples having predetermined state and samples having no predetermined state. The historical database is composed of known epitopes related with the predetermined state. By the method for neoantigen epitope prediction, antigen mutation information can be determined according to gene level and protein level really, neoantigen epitopes capable of being bound with MHC are acquired effectively rapidly, and binding capacity of neoantigen epitopes and NHC can be predicted precisely. Besides, the method is easy and convenient and capable of saving manpower and material resources greatly.

Description

technical field [0001] The present invention relates to the field of biotechnology, in particular, to neoantigen epitopes and methods and applications for predicting them, more specifically, to methods and equipment for predicting neoantigen epitopes, and to determining the probability of differentially expressed peptides having the properties of epitopes Method and equipment, antigenic epitopes and their use in the preparation of medicines. Background technique [0002] Tumors have the following ten characteristics: self-sufficient growth signals; insensitivity to anti-growth signals; avoidance of immune destruction; tumor-promoting inflammation; abnormal cellular energy; Tissue invasion and metastasis; resistance to cell death. Tumor is the most common genetic disease. All tumors originate from abnormalities in DNA sequences. Therefore, although different tumors have different causes and symptoms, they can all be explained by gene mutations. In recent years, the rapid de...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68C12M1/34G01N33/68G06F19/22C07K7/06A61K38/08A61P35/00
Inventor 林鸿刚刘耿叶晓飞侯勇朱师达吴逵李光磊
Owner BGI SHENZHEN CO LTD
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