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hla genotype-snp linkage database, its construction method, and hla typing method

A typing method and database technology, applied in the field of genomics and bioinformatics, can solve problems such as expensive, difficult to apply to large-scale HLA high-resolution typing projects, and electropherogram recognition ability are greatly affected

Active Publication Date: 2015-10-07
北京六合华大基因科技有限公司
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AI Technical Summary

Problems solved by technology

The advantage of the Sanger-based sequencing method is that the accuracy is relatively high, but the disadvantage is that the sequencing throughput is small, time-consuming, and expensive, and the quality of the imported sequencing profile during software typing has an impact on the peak profile recognition ability of the typing software. Very large, when the software recognizes an error, the typing personnel are required to find and correct the error in time
Software typing has not achieved automation, which reduces typing efficiency and is difficult to apply to large-scale HLA high-resolution typing projects

Method used

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  • hla genotype-snp linkage database, its construction method, and hla typing method
  • hla genotype-snp linkage database, its construction method, and hla typing method
  • hla genotype-snp linkage database, its construction method, and hla typing method

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Embodiment 1

[0062] Example 1: HLA typing of 94 samples

[0063] 1. Purpose of the experiment:

[0064] Exon 2, 3, 4 of HLA-A / B / C, exon 2 of HLA-DRB1, exon 2, 3 of HLA-DQB1 obtained from 94 samples obtained from 94 people using SOLEXA sequencing technology Sequencing was performed separately, and HLA typing was performed on HLA-A / B / C / DRB1 / DQB1 through the sequence information of these exons.

[0065] 2. Experimental method:

[0066] (1) Construction of HLA genotype-SNP linkage database structure

[0067] According to the method of the present invention, the HLA genotype-SNP linkage (relationship) database structure is constructed, wherein the reference sequence used is SEQ ID NO: 1-5, and the existing database is the EBI database (EBI: http: / / www.ebi. ac.uk / imgt / hla / ).

[0068] (2) Find out the SNP site

[0069]Here, BWA comparison software and samtools software are used as examples to illustrate. These sequences were compared with specific reference sequences by BWA alignment soft...

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Abstract

The invention belongs to the fields of genomics and bioinformatics, relates to an HLA genotype-SNP linkage database, a construction method thereof, and a HLA typing method. Specifically, the construction method of the HLA genotype-SNP linkage database comprises the following steps: a) selecting one or more HLA loca sequences as a reference sequence; b) comparing the known type HLA genes in a conventional HLA database with the reference sequence to find out a difference site of the reference sequence i.e. a SNP site, and to obtain an SNP linkage relationship relative to the reference sequence for constructing the HLA genotype-SNP linkage database. The present invention also relates to a method for determining SNP linkage relationship of HLA gene, and an HLA typing device. The method of the present invention achieves low-cost, high-throughput, high-accuracy and high-resolution typing for HLA.

Description

technical field [0001] The invention belongs to the fields of genomics and biological information. The invention relates to an HLA genotype-SNP linkage database, a construction method thereof, a method for determining the SNP linkage relationship of HLA genes, an HLA typing method, and an HLA typing device. technical background [0002] Human leukocyte antigen, namely HLA (human leukocyte antigen, HLA), is one of the most polymorphic gene systems found so far. It is closely related to the rejection of allogeneic organ transplantation. Studies have shown that, in organ transplantation, the higher the degree of HLA matching between the donor and the recipient, the higher the success rate of transplantation (U. Shankarkumar. The Human Leukocyte Antigen (HLA) System. Int J Hum Genet, 4(2) :91-103(2004)). [0003] The HLA gene is located on the short arm of chromosome 6 and is about 4000Kb long. HLA has dozens of loci (loci), and each locus has dozens of alleles, which are co...

Claims

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Application Information

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IPC IPC(8): C12Q1/68
CPCC12Q1/6881C12Q2600/156
Inventor 曹红志张伟王煜
Owner 北京六合华大基因科技有限公司
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