Method for predicting neoantigen production of fusion gene

A fusion of genes, a new technology, applied in biochemical equipment and methods, genomics, bioinformatics, etc., can solve the problems of traditional algorithms that cannot be detected or spliced ​​correctly, to improve sensitivity and accuracy, improve accuracy, improve The effect of sensitivity

Active Publication Date: 2019-10-11
HANGZHOU NEOANTIGEN THERAPEUTICS CO LTD
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Problems solved by technology

For such cases, traditional algorithms are often unable to detect or correctly stitch

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  • Method for predicting neoantigen production of fusion gene
  • Method for predicting neoantigen production of fusion gene
  • Method for predicting neoantigen production of fusion gene

Examples

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Embodiment 1

[0137] according to Figure 1 The shown workflow uses both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) to verify positive samples for the three fusion gene events (DCC-DYM, MED13-BRIP1, and MAP2K4-SPOCK1) for high-throughput The raw data obtained by sequencing are used as the input data of the method of the present invention to predict the fusion gene neoantigen. The specific steps and detection parameters are set as follows:

[0138]Sequencing raw data quality control, remove adapter sequence contamination bases greater than 5bp. For paired-end sequencing, if one end is contaminated by adapters, the Reads at both ends are removed. Remove low-quality Reads. Bases with a quality value Q≤19 in Reads account for more than 50% of the total bases. For paired-end sequencing, if one end is low-quality Reads, both ends of the Reads will be removed. Reads with an N ratio greater than 5% are removed. For paired-end sequencing, if one end contains an N rat...

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Abstract

The invention discloses a method for predicting the neoantigen production of a fusion gene. The method comprises the following steps: performing quality control on original data obtained by sequencing; comparing the quality-controlled data to a reference genome, and marking a repetitive sequence; predicting HLA first-class and second-class types by using software; predicting fusion gene events byusing software; annotating, scoring, sequencing and screening the predicted fusion gene events; extracting and translating the upstream and downstream nucleotide sequences of the screened fusion genebreakpoints to obtain new polypeptides; carrying out MHC affinity prediction on the new polypeptides, carrying out affinity prediction by using a plurality of pieces of HLA typing affinity predictionsoftware, and screening out the polypeptides with relatively strong affinity from a prediction result; screening and designing the new polypeptides according to the epitope binding capacity and polypeptide characteristics of the new polypeptides of the fusion gene. According to the invention, the method can greatly improve the sensitivity and specificity of detecting the target gene fusion neoantigen while the detection speed is optimized.

Description

technical field [0001] The invention relates to the technical field of gene detection, in particular to a method for predicting neoantigens produced by fusion genes using bioinformatics methods. Background technique [0002] The treatment of malignant tumors faces many difficulties, and new therapeutic strategies are urgently needed. In recent years, tumor immunotherapy has received more and more attention and made breakthroughs. Tumor immunotherapy refers to the use of the body's own immune system to eliminate tumor cells, including antibody therapy, cell therapy, and tumor vaccines. [0003] The occurrence of tumors is often accompanied by fusion gene breakpoints of multiple genes. Neoantigens refer to epitope-specific antigens produced by tumor cell mutations, which are only expressed on tumor cells and will not lead to immune tolerance of the body. Many studies have shown that immunotherapy targeting neoantigens has achieved good clinical results in some cancer patient...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/00G16B30/00C12Q1/6886
CPCC12Q1/6886G16B20/00G16B30/00
Inventor 罗凯莫凡林志伟
Owner HANGZHOU NEOANTIGEN THERAPEUTICS CO LTD
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