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HLA genotyping method and device and storage medium

A genotyping method and genotyping technology, applied in the field of bioinformatics, can solve the problem of unknown accuracy of HLA typing, and achieve the effect of reducing the low accuracy rate and improving the accuracy rate

Inactive Publication Date: 2021-09-03
深圳裕泰抗原科技有限公司
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0009] However, there are still many challenges in HLA typing based on next-generation sequencing data, such as the polymorphism of HLA sequences, the limitation of the detection length of next-generation sequencing data, and the unknown accuracy of HLA typing in cancer patients.

Method used

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  • HLA genotyping method and device and storage medium
  • HLA genotyping method and device and storage medium

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Embodiment 1

[0091] In this embodiment, two genotyping tools, OptiType and Polysolver, are used to obtain the HLA prediction typing of the tumor sample and the tissue sample of the subject respectively, and type a certain allele of the HLA-A locus of the first subject The integration is performed to obtain the final HLA typing of a certain allele at the HLA-A site of the first subject to be tested.

[0092] The specific steps of the HLA genotyping method of this embodiment are as follows:

[0093] 1) HLA prediction typing acquisition steps:

[0094] Obtain the sequencing data of the tumor sample of the first subject to be tested and the sequencing data of the control sample, and use the OptiType genotyping tool to determine that the HLA-A prediction type of the tumor sample of the first subject to be tested is HLA-A*02:13, and the comparison The HLA-A prediction type of the sample is HLA-A*02:01, and the Polysolver genotyping tool is used to determine that the HLA-A prediction type of the...

Embodiment 2

[0105] In this embodiment, two genotyping tools, OptiType and Polysolver, are used to obtain the HLA prediction typing of the tumor sample and tissue sample of the second test subject respectively, and a certain allele of the HLA-C locus of the second test subject The typing is integrated to obtain the final HLA typing of a certain allele of the HLA-C locus of the second test subject.

[0106] The specific steps of the HLA genotyping method of this embodiment are as follows:

[0107] 1) HLA prediction typing acquisition steps:

[0108] Obtain the sequencing data of the tumor sample of the second subject to be tested and the sequencing data of the control sample, and use the OptiType genotyping tool to determine that the HLA-C prediction type of the tumor sample of the second subject to be tested is HLA-C*07:01, and the comparison The predicted HLA-C typing of the sample was HLA-C*07:01, and the Polysolver genotyping tool was used to determine that the predicted HLA-C typing o...

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Abstract

The invention discloses an HLA genetic typing method and a device and a storage medium. The method comprises an HLA prediction typing acquisition step, an HLA typing marking step and an HLA typing integration step. According to the HLA genotyping method, the weight scores of the HLA prediction types obtained by different genotyping tools are marked, and the HLA prediction types obtained by the different genotyping tools are integrated according to the weight scores, so that the detection advantages of each genotyping tool can be fully utilized; and the problems of low accuracy of some genetic typing tools and the like caused by factors such as sequencing depth are reduced, so that the accuracy of HLA typing is improved.

Description

technical field [0001] The present application relates to the technical field of bioinformatics, in particular to an HLA genotyping method, device and storage medium. Background technique [0002] The human leukocyte antigen (HLA) complex is located within the 3.6Mbp stretch of the short arm of chromosome 6 (6q21.31), which can encode human major histocompatibility complex (MHC) proteins. HLA is mainly divided into two categories: HLA-I genes encode MHC class I proteins, which exist in all cells except red blood cells, and focus on recognizing antigens produced in cells due to virus infection, gene mutation, etc., and transporting antigens to the cell surface. When toxic T cells come into contact with an antigen-producing cell, they recognize the antigen and clear the cell; HLA class II genes encode MHC class 2 proteins that are present in antigen-presenting cells and recognize intracellular and extracellular Antigen, eventually via CD 4+ Helper T cells stimulate B cells ...

Claims

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Application Information

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IPC IPC(8): G16B20/20G16B20/30
CPCG16B20/20G16B20/30
Inventor 易坚陈前兴王佳茜陈龙昀苏小凡
Owner 深圳裕泰抗原科技有限公司
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