Tumor neoantigen prediction platform and application thereof in neoantigen vaccine development system

A platform and new technology, applied in the fields of molecular biology and bioinformatics, can solve problems such as low accuracy, and achieve the effect of improving prediction accuracy, screening and R&D efficiency

Active Publication Date: 2019-11-22
深圳市新合生物医疗科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] In order to overcome the shortcomings of the above-mentioned low accuracy of the public prediction algorithm, in order to improve the screening and development efficiency of tumor neoantigen vaccines

Method used

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  • Tumor neoantigen prediction platform and application thereof in neoantigen vaccine development system
  • Tumor neoantigen prediction platform and application thereof in neoantigen vaccine development system
  • Tumor neoantigen prediction platform and application thereof in neoantigen vaccine development system

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0031] Example 1: Construction of HLA subtype 721.221 cell line

[0032] 1. Using HLA locus-specific primers to copy HLA gene fragments from HLA homozygous human B lymphocyte cell lines

[0033] (1) Using the RNeasy kit to obtain HLA homozygous human B lymphocytes (cultured in RPMI cell culture medium, containing 10% fetal bovine serum, 1% penicillin / streptomycin mixed solution / glutamine and 1mM sodium pyruvate ) to extract total RNA;

[0034] (2) Add Oligo dT primers, dNTP mixture, dithiothreitol and MMLV reverse transcriptase to the extracted total RNA to produce cDNA;

[0035] (3) Add 2 μl cDNA to PCR buffer, 200 μM dNTP mixture, 0.3 μM HLA locus-specific primers and 0.5 μl Taq polymerase to carry out PCR reaction;

[0036] The operating procedures of the thermal cycler are shown in Table 1 below:

[0037] Table 1 Operation procedure of thermal cycler

[0038]

[0039] The sequences of HLA locus-specific primers are shown in Table 2 below:

[0040] Table 2 HLA locus...

Embodiment 2

[0063] Example 2: Using high-sensitivity protein mass spectrometry to analyze the binding protein groups of 55 HLA subtype MHC-negative 721.221 cell lines with a high proportion of the Chinese population and construct an HLA-binding polypeptide database

[0064] The present invention uses the HLA subtype gene frequency database (http: / / www.allelefrequencies.net) to screen out a total of 55 HLA-A and HLA-B subtypes with a high proportion in the Chinese population, covering a total of 98.47% of HLA-A subtypes and 89.39% of HLA-B subtypes in the Chinese population. The 55 HLA subtypes include 24 HLA-A subtypes and 31 HLA-B subtypes, the specific numbers are as follows: HLA-A*01:01, HLA-A*02:01, HLA-A*02:02 , HLA-A*02:03, HLA-A*02:04, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, HLA-A*03:01, HLA -A*11:01, HLA-A*11:02, HLA-A*23:01, HLA-A*24:02, HLA-A*24:03, HLA-A*26:01, HLA-A *29:02, HLA-A*30:01, HLA-A*31:01, HLA-A*32:01, HLA-A*33:01, HLA-A*33:03, HLA-A*66 :01, HLA-A*68:01, HLA-A*68:0...

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Abstract

The invention belongs to the fields of molecular biology and bioinformatics, and particularly relates to a tumor neoantigen prediction platform and application thereof in a neoantigen vaccine development system. According to a public database, 55 HLA-A and HLA-B subtypes with a high proportion in the Chinese population are selected, then a method for constructing a related HLA subtype cell line isestablished, then a protein mass spectrometry technology of 10<-18> mole / liter is used for analyzing an obtained HLA subtype cell line binding proteome, by performing extra-high-precision mass spectrometry on proteinograms provided by single cell surfaces, a high-frequency HLA binding peptide database of Chinese population is constructed, and then the prediction platform containing the HLA binding peptide database is used for optimizing a tumor neoantigen prediction algorithm, thereby significantly improving the prediction accuracy of tumor neoantigens, and application of the prediction platform in the tumor neoantigen vaccine development system is conductive to improving the screening and research and development efficiency of vaccines.

Description

technical field [0001] The invention belongs to the fields of molecular biology and bioinformatics, and in particular relates to a tumor neoantigen prediction platform and its application in a neoantigen vaccine development system. Specifically, the tumor neoantigen prediction platform of the present invention includes an HLA-binding polypeptide database, which is constructed by using high-sensitivity protein mass spectrometry technology to analyze 55 HLA-binding protein groups with a high proportion of the Chinese population. The invention prediction platform can optimize the tumor neoantigen prediction algorithm, significantly improve the prediction accuracy of tumor neoantigens, and use it in the tumor neoantigen vaccine development system to help improve the efficiency of vaccine screening and research and development. Background technique [0002] Tumor neoantigen (Neoantigen) refers to the specific polypeptide produced by tumor cells due to gene mutation, which is pres...

Claims

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Application Information

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IPC IPC(8): G16B50/00G16B30/10G16B25/20G16B25/10C12N15/867C12N5/10C12R1/91
CPCG16B25/10G16B25/20G16B50/00G16B30/10C12N15/86C07K14/70539C12N2740/10043A61K39/00G16B40/10C07K16/2833G01N33/56977G01N2333/70539G01N33/57484G01N33/6878Y02A90/10H01J49/26
Inventor 潘有东宋麒万季黄润元肖安刘刚文颖
Owner 深圳市新合生物医疗科技有限公司
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