HLA typing method and equipment based on Sanger sequencing

Abstract

The invention relates to an HLA typing method and equipment based on Sanger sequencing. The HLA typing method comprises the following steps: acquiring sequencing data of a gene to be identified; according to the sequencing data of the to-be-identified gene, based on a pre-trained base identification model, obtaining a correct base signal of each site of the to-be-identified gene; and interpreting a nucleic acid sequence of the to-be-identified gene, comparing the nucleic acid sequence with a reference sequence to obtain a difference site, and comparing by adopting bit operation based on a pre-arranged allele type and the difference site to obtain an HLA typing result. Because the base recognition model is trained by taking sequencing data of abnormal bases as sample data, the base recognition model obtained by training can recognize abnormal bases such as low-quality heterozygous bases and pollution signals in Sanger sequencing data, and an allele typing result is quickly obtained by using bit operation; and the problems of low speed and low accuracy of manual recognition are solved.

Description

technical field [0001] The present application relates to the field of biological information technology, in particular to a method and equipment for HLA typing based on Sanger sequencing. Background technique [0002] HLA (human leukocyte antigen, human leukocyte antigen) is the expression product of the human major histocompatibility complex (MHC), which is the most complex polymorphic system known to the human body. An important field of study in disciplines such as biochemistry. HLA typing has important value in medical immunology. Currently, HLA typing methods mainly include serological typing and DNA typing. The HLA-SBT algorithm in the DNA typing method is currently recognized as the gold standard. It detects highly polymorphic exons of HLA-related genes (type I A, B, C genes are exon2, 3, 4, type II DQB1 , DRB1 gene exon2, 3) for Sanger sequencing (cooperating with GSSP Sanger sequencing if necessary) to achieve the purpose of high-level typing. [0003] Sanger s...

AI Technical Summary

Problems solved by technology

In the sequencing result data, there are often some overlapping peaks, which may be caused by poor sequencing quality or heterozygous original template.

[0004] The HLA-SBT typing algorithm is based on the base polymorphism of the HLA gene, so the algorithm is highly dependent on the accuracy of the input sequence, but there are low-quality, heterozygous bases, and contamination signals in the Sanger sequencing data

At present, for the uncertain base results of Sanger sequencing results, it mainly relies on manual interpretation. The existing software only gives the allelic type of the sample based on the manually determined bases, and does not directly obtain the results. People with different work experience Interpretation may have different results, and for large-scale sequencing, manual interpretation will consume a lot of time, and accuracy and timeliness are crucial for patients

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