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Ranking system for immunogenic cancer-specific epitopes

An antigen-determining and immunological technology, applied in the direction of cancer antigen components, specific peptides, immunoglobulins, etc., can solve problems such as impact prediction and consideration of specific cancer antigens

Pending Publication Date: 2020-02-14
ACT GENOMICS IP CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Also, each patient or sample has specific properties that affect the prediction, and these sample-specific properties are not considered by current cancer antigen (neoantigen) ranking methods

Method used

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  • Ranking system for immunogenic cancer-specific epitopes
  • Ranking system for immunogenic cancer-specific epitopes
  • Ranking system for immunogenic cancer-specific epitopes

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0061] Example 1: Using the binding affinity (binding affinity) and binding stability (binding stability) between the peptide chain and the major histocompatibility complex type I (MHC class I) to predict the type of the major histocompatibility complex for the peptide chain A situation presented.

[0062] For a peptide chain to be an antibody, the peptide chain needs to be presented on the cell surface by the major histocompatibility complex and then recognized by immune cells. The above process includes: the peptide chain is presented to CD4+ T cells by the major histocompatibility complex type II (MHC class II) in the antigen-presenting cell, and the peptide chain is presented to the CD4+ T cell by the major histocompatibility complex type I in the antigen-presenting cell. Presentation to CD8+ T cells and peptide chains are presented to CD8+ T cells by major histocompatibility complex type-1 in tumor cells. In this example, we construct a model with selected features to pr...

Embodiment 2

[0064] Example 2: Using the binding affinity between the peptide chain and the major histocompatibility complex type I and the expression level of the gene to which the peptide chain belongs to predict the situation that the peptide chain is presented by the major histocompatibility complex type I.

[0065] In addition to the peptide's ability to bind to major histocompatibility complex type 1, the degree to which the peptide is represented is also important for whether the peptide is represented. In this example, we constructed a model based on the expression of the gene to which the peptide chain belongs and the binding affinity between the peptide chain and the major histocompatibility complex type 1 to predict that the peptide chain is bound by the major histocompatibility complex type A situation presented.

[0066] We calculated the binding affinity between the peptide chain and major histocompatibility complex type 1 in the manner disclosed in Example 1, and calculated ...

Embodiment 3

[0067] Example 3: Using the binding affinity between the peptide chain and the major histocompatibility complex type 1 and the expression of the protein to which the peptide chain belongs to predict the situation that the peptide chain is presented by the major histocompatibility complex type 1.

[0068] In addition to the binding capacity of the peptide chain to MHC type 1, the amount of the peptide chain represented also affects the amount of the peptide chain represented by the MHC. In this example, we used the binding affinity between the peptide chain and major histocompatibility complex type 1 and the performance of the peptide chain as the selected features to construct a method for predicting that the peptide chain is major histocompatibility A model of sexual complex type-presentation situations.

[0069]We constructed a model to predict peptides based on two properties (peptide binding affinity and peptide expression, respectively) that affect the binding capacity an...

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Abstract

This disclosure relates to systems and methods that identify, predict, and rank immunogenic T-cell epitopes. In particular, this disclosure identifies epitopes that arose from disease-associated mutations, wherein the epitopes are predicted to elicit immune response from T cells. Specifically, this disclosure simultaneously considers peptide-level information, including MHC Class I and II presentation, helper and cytotoxic T cell response and sample-level information, including mutation clonality and MHC allele dosage. In some embodiment, the systems and methods are used for personalized treatment of cancers.

Description

technical field [0001] The present invention relates to immunogenic epitopes, especially a system and method for judging, predicting and ranking immunogenic cancer-specific epitopes. Background technique [0002] Eliciting an immune response against tumor cells with tumor-specific antigens provides an opportunity to fight cancer. These antigens are identified as the link between tumor genomics and the clinical utility of immunotherapy. In general, genes with cancer-causing mutations produce mutated peptides. These peptides bind to major histocompatibility complex (MHC) types I and II and are presented on the surface of tumor cells as antigens. In the immune system, especially cytotoxic T cells and helper T cells will recognize these antigens as foreign substances and trigger an immune response. Many of these antigens are specific to tumors and have never been recognized by the immune system. Therefore, they are suitable targets for immunotherapy because the treatment can...

Claims

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Application Information

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IPC IPC(8): A61K31/7052A61K31/7105A61K39/00A61K39/02A61K48/00C07H21/02
CPCA61K39/0011G16B20/00G16B40/20A61K38/00C07K16/2833C07K2317/92C07K14/70539
Inventor 杨沛佳郑人豪陈映嘉陈淑贞陈华键
Owner ACT GENOMICS IP CO LTD
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