Method and device for detecting tumor neoantigen polypeptide

An antigen peptide, nascent technology, applied in bioinformatics, instrumentation, genomics, etc., can solve the problems of incomplete and inaccurate tumor neoantigen detection results, and achieve the effect of improving guiding significance and comprehensive sources.

Active Publication Date: 2020-01-17
北京橡鑫生物科技有限公司 +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0004] The main purpose of the present invention is to provide a method and device for detecting tumor neoantigen polyp

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  • Method and device for detecting tumor neoantigen polypeptide
  • Method and device for detecting tumor neoantigen polypeptide
  • Method and device for detecting tumor neoantigen polypeptide

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Embodiment 1

[0040] In a preferred embodiment of the present application, a method for detecting tumor neoantigen polypeptides is provided, figure 1 It is a flowchart of a method for detecting tumor neoantigen polypeptides according to an embodiment of the present invention. Such as figure 1 As shown, the method includes:

[0041] Step S101, obtaining somatic mutations and germline mutations of the tumor tissue;

[0042] Step S102, using the sequencing data of the tumor control blood cell sample to perform HLA typing to obtain the HLA typing result;

[0043] Step S103, using HLA typing results to predict neoantigen polypeptides for somatic mutations and germline mutations to obtain candidate neoantigen polypeptides;

[0044] Step S104, scoring and sorting the candidate neoantigen polypeptides, and the one with the highest score is the neoantigen polypeptide.

[0045] In the above method, the neoantigen polypeptide prediction is performed by obtaining the sum of mutations including soma...

Embodiment 2

[0068] Objective: To detect neoplastic antigens in tumor patients (sample ID 180504502TT1).

[0069] step:

[0070] 1. Use the software optitype (v2.1.0) and the sequencing fastq file of the tumor patient's blood cell sample to perform HLA typing, and obtain the typing results (see Table 1).

[0071] 2. Use the Mutect2 module of GATK (v4.0.5.1) to pair the tumor tissue and blood cells of tumor patients to detect somatic mutations, obtain the somatic mutation vcf file, and select mutations that pass the filtering criteria for subsequent use.

[0072] 3. Use the HaplotypeCaller module of GATK (v4.0.5.1) to detect germline mutations in the blood cells of tumor patients, obtain germline mutation vcf files, and select mutations that pass the filtering criteria for subsequent use.

[0073] 4. Merge the somatic mutation file with the Germline mutation file using the CombineVariants module of GATK (v4.0.5.1).

[0074] 5. Use vep (v94.5) to annotate the merged file to obtain the gene...

Embodiment 3

[0085] In this embodiment, a device for detecting tumor neoantigen polypeptides is also provided, such as image 3 As shown, the device includes: an acquisition module 10, an HLA typing module 20, a candidate neoantigen prediction module 30 and a neoantigen prediction module 40, and the acquisition module 10 is used to acquire somatic mutations and germline mutations of tumor tissues; The type module 20 is used to perform HLA typing using the sequencing data of tumor control blood cell samples to obtain HLA typing results; the candidate neoantigen prediction module 30 is used to use the HLA typing results to perform neoantigen classification for somatic mutations and germline mutations. Polypeptide prediction to obtain candidate neoantigen polypeptides; the neoantigen prediction module 40 is used to score and sort candidate neoantigen polypeptides, and record the highest score as neoantigen polypeptides.

[0086] The device predicts neoantigen polypeptides by obtaining the sum...

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Abstract

The invention provides a method and a device for detecting tumor neoantigen polypeptide. The method comprises the following steps of: acquiring somatic mutation and embryonic system mutation of tumortissues; carrying out HLA (Human Leukocyte Antigen) typing by utilizing sequencing data of a tumor control blood cell sample to obtain an HLA typing result; carrying out neoantigen polypeptide prediction on the somatic mutation and the embryonic system mutation by utilizing the HLA typing result to obtain candidate neoantigen polypeptides; and scoring and sequencing the candidate neoantigen polypeptides, wherein the neoantigen polypeptide with the highest score is the neoantigen polypeptide. New antigen polypeptide prediction is carried out by obtaining the sum of mutations comprising two sources, the sources of the mutations are more comprehensive, and the prediction result is relatively more accurate. The predicted candidate neoantigen polypeptides are scored and sorted, and the subsequent neoantigen polypeptide with the highest score is used as the neoantigen polypeptide, so that the more accurate neoantigen polypeptide can be conveniently obtained, and the guiding significance of subsequent immunotherapy medication is further improved.

Description

technical field [0001] The invention relates to the field of gene sequencing data analysis, in particular to a method and device for detecting tumor neoantigen polypeptides. Background technique [0002] In recent years, tumor immunotherapy has continued to heat up, new clinical trials have continuously obtained good results, and the effective remission rate and cure rate have both increased significantly. Accurate and rapid tumor neoantigen detection is the most basic and important work. [0003] At present, the detection method for tumor neoantigens is mainly based on the whole exome data of tumor and normal tissues, using GATK to detect somatic cell variation, and using NetMHCpan to predict the binding ability of MHC-I on the detection results. This method is incomplete, and the detected tumor neoantigens have no order of pros and cons, which brings great troubles to subsequent immunotherapy trials. Contents of the invention [0004] The main purpose of the present inv...

Claims

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Application Information

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IPC IPC(8): G16B20/50G16B30/10
CPCG16B20/50G16B30/10
Inventor 周涛陈利斌郭璟楼峰曹善柏
Owner 北京橡鑫生物科技有限公司
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