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Immune repertoire biological information analysis process based on molecular markers

A technology of immune repertoire and molecular markers, which is applied in the field of biological information analysis process of immune repertoire, can solve the problems that the biological information analysis of immune repertoire cannot be used well, and achieve the goal of wide application, promotion of development and improvement of accuracy Effect

Active Publication Date: 2018-11-13
广州华银医学检验中心有限公司
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

This invention is only designed for the specific bioinformatics analysis process of DNA mutation detection, and cannot be well used for the bioinformatics analysis of immune repertoire

Method used

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  • Immune repertoire biological information analysis process based on molecular markers
  • Immune repertoire biological information analysis process based on molecular markers
  • Immune repertoire biological information analysis process based on molecular markers

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0039] Construction and screening of test sequences before embodiment 1 UMI self-correction

[0040](1) Construct the test sequence required for paired-end sequencing: take the single-chain immunoglobulin M gene with the same structure and divide it into two equal parts, and add primers to the 3' end of each immunoglobulin M gene in one part And the UMI sequence with the structure UAAAGUCCAGUGCAAU, add primers and the UMI sequence with the structure UAAAGUCCAGUGCAAU to the 5' end of each immunoglobulin M gene in the other copy, one of which has a single-chain immunoglobulin with primers and UMI at the 3' end The M gene and a single-chain immunoglobulin M gene with a primer and UMI at the 5' end are called a pair of test sequences; take the single-chain immunoglobulin A gene with the same structure and divide it into two equal parts, and in one part Add primers and a UMI sequence with the structure UGGCAUAAGCUAGCAU to the 3' end of each Immunoglobulin A gene, and add primers an...

Embodiment 2

[0047] Example 2 UMI self-correction and immune gene number statistics

[0048] (4) Use the following steps to perform UMI self-correction on the test sequence obtained in step (3):

[0049] ① Tree building: use different UMIs as different nodes, connect UMI nodes with a Hamming distance of 1, and build multiple directed acyclic trees;

[0050] ② Assignment: assign values ​​to the nodes of the directed acyclic tree built in step ①, and the assigned value is the number of types of immune gene sequences marked by the UMI;

[0051] ③ Tree cutting: When the value assigned to node A (any node) is greater than the value assigned to the connected node B (any node) × 2+1, cut off the edge between node A and node B; otherwise, keep An edge between node A and node B;

[0052] ④Cluster formation: Perform the operation described in step ③ on each node on the tree built in step ①, and finally divide the tree built in step ① into multiple new trees, each new tree is a cluster, and the clu...

Embodiment 3

[0054] Example 3 Correction and assembly of immune gene sequences within the cluster

[0055] (6) Correction of immune gene sequences in each cluster: the immune gene sequences in the same cluster are compared with each other using the multi-sequence comparison software muscle. If the proportion of consistent bases at a certain position is greater than 0.6, then the site is the consensus base, otherwise it is replaced by N, and the sequence of the immune gene in each cluster is obtained;

[0056] (7) Immune gene sequence assembly: Assemble the immune genes on each cluster. For full-length sequencing, splice according to the overlapping regions of the ends. For non-full-length sequences, use the method of comparing the reference sequences in the imgt database for splicing , when there is a deletion in the gene sequence, fill in the missing part according to the reference sequence in the imgt database.

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Abstract

The invention discloses an immune repertoire biological information analysis process based on molecular markers. In the process, single-chain immune globulin genes with the same sequence are selected,and primers and UMI sequences with the same structure are added to 3' ends or 5' ends of the selected single-chain immune globulin genes; after addition is completed, PCR amplification is performed on the immune genes to obtain a test sequence, and the test sequence is filtered; after filtering, the UMI sequence carried by the immune genes is corrected by establishing a directed acyclic tree, then the immune genes marked by the corrected UMI sequence are corrected, and the corrected immune genes are assembled; and finally the assembled immune genes are subjected to statistical analysis and reporting. According to the process, through correction of UMI and correction of the immune genes, the influences of amplification errors and sequencing errors on immune gene sequencing are effectivelyremoved, and the accuracy of sequencing data is improved.

Description

technical field [0001] The invention belongs to the field of molecular biological information analysis and processing systems, and in particular relates to a molecular marker-based immune repertoire biological information analysis process. Background technique [0002] High-throughput sequencing technology (High-throughput sequencing, HTS), also known as deep sequencing technology, is a revolutionary change to traditional Sanger sequencing (called generation sequencing technology), which can analyze hundreds of thousands to millions of nucleic acids at a time. Molecular sequencing enables detailed and comprehensive analysis of a species' transcriptome and genome. The development of high-throughput sequencing technology has greatly promoted the development of precision medicine, and many clinical applications of high-throughput sequencing have been implemented, such as non-invasive prenatal genetic testing (NIPT). [0003] The immune repertoire is the sum of all functionally...

Claims

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Application Information

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IPC IPC(8): G06F19/20G06F19/18G06F19/22
Inventor 李芬香李雪飞王勇斯董少玲王晓丹
Owner 广州华银医学检验中心有限公司
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