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Method and device for HLA genotyping, storage medium and processor

A genotyping and genotyping technology, applied in the fields of instruments, sequence analysis, bioinformatics, etc., can solve the problem of high false positives in HLA genotyping, achieve the effect of reducing false positive results and solving high false positives

Pending Publication Date: 2019-07-19
ZHENYUE BIOTECHNOLOGY JIANGSU CO LTD
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

For example, the false positive of HLA genotyping is relatively high, therefore, the existing HLA genotyping methods still need to be improved

Method used

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  • Method and device for HLA genotyping, storage medium and processor
  • Method and device for HLA genotyping, storage medium and processor
  • Method and device for HLA genotyping, storage medium and processor

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0121] DNA extraction and HLA gene capture were performed on FFPE samples of tumor tissues from 4 patients, and HLA genotyping was performed based on this method. The specific test method is as follows:

[0122] 1. Sequencing library construction

[0123] 1) Based on the NGS sequencing method, the library construction steps of tissue samples (FFPE) and blood leukocyte samples (BC) are as follows:

[0124] 1.1 Sample interruption:

[0125] 1.1.1 Cut the polytetrafluoroethylene thread to a length of about 1cm with medical scissors sterilized by ultraviolet light, and ensure that the length of the breaking rod is uniform. Place it in a clean container and sterilize it by ultraviolet light for 3-4 hours. After the sterilization is completed, put the 1cm polytetrafluoroethylene line into the 96-well plate with sterilized tweezers. Put 2 break rods in each well, and then sterilize the 96-well plate by ultraviolet for 3-4 hours.

[0126] 1.1.2 Take 300ng FFPE / bc DNA samples accor...

Embodiment 2

[0235] DNA extraction and HLA gene capture were performed on FFPE samples and BC (blood leukocyte) samples of tumor tissues of 89 patients, and HLA genotyping was performed based on this method, and finally the consistency of HLA genotyping results between the two groups of samples was compared. Concrete test method is with embodiment 1.

[0236] test results:

[0237] The HLA gene typing and matching of tumor tissue FFPE samples and BC (blood leukocyte) samples of 89 patients were performed respectively, and the consistency between the two groups of results was 100%, achieving high sensitivity, accuracy and accuracy pair.

[0238] From the results of the above examples, it can be seen that the HLA genotyping method of the present application constructs an HLA genotyping database containing HLA pseudogene sequences very similar to the HLA gene sequence, and adds DNA sequences other than the coding region DNA sequence. The DNA sequence of the intron region can reduce the fals...

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Abstract

The invention discloses a method and device for HLA genotyping, a storage medium and a processor. The method for HLA genotyping includes the steps: constructing an HLA genotype database, wherein the HLA genotype database comprises a DNA sequence of pseudogenes associated with HLA-A genes; comparing the sequencing data of the sample to be tested with the HLA genotype database, and retaining the genotype satisfying the predetermined condition as a comparison result; and selecting the genotype with the highest comparison value in the comparison result as the result of HLA genotyping of the sampleto be tested. For the method for HLA genotyping, adding an HLA pseudogene sequence very similar to the HLA gene sequence in the HLA genotyping database helps to reduce the false positive results of typing, thus solving the technical problem of high false positive HLA genotyping in the prior art.

Description

technical field [0001] This application relates to the field of gene sequencing data analysis, in particular, to a method, device, storage medium and processor for HLA genotyping. Background technique [0002] HLA (Human Leukocyte Antigen) is a highly polymorphic complex composed of a series of closely linked gene loci. It is a gene cluster encoding the human major histocompatibility complex (MHC). HLA is located at the 6th on the short arm of the chromosome. This system is the most complex polymorphic system known to the human body. [0003] HLA is a highly polymorphic alloantigen, and its chemical essence is a kind of glycoprotein, which is composed of an α heavy chain (glycosylated) and a β light chain non-covalently combined. The amino terminal of the peptide chain is outward (accounting for about 3 / 4 of the whole molecule), the carboxyl terminal penetrates into the cytoplasm, and the middle hydrophobic part is in the cell membrane. According to their distribution and...

Claims

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Application Information

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IPC IPC(8): G16B30/00
Inventor 郭现超宋小凤赵义陈维之杜波何骥
Owner ZHENYUE BIOTECHNOLOGY JIANGSU CO LTD
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