title: IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis.
abstract: The advance of next generation sequencing (NGS) techniques provides an unprecedented opportunity to probe the enormous diversity of the immune repertoire by deep sequencing T-cell receptors (TCRs) and B-cell receptors (BCRs). However, an efficient and accurate analytical tool is still on demand to process the huge amount of data. We have developed a high-resolution analytical pipeline, Immune Monitor ("IMonitor") to tackle this task. This method utilizes realignment to identify V(D)J genes and alleles after common local alignment. We compare IMonitor with other published tools by simulated and public rearranged sequences, and it demonstrates its superior performance in most aspects. Together with this, a methodology is developed to correct the PCR and sequencing errors and to minimize the PCR bias among various rearranged sequences with different V and J gene families. IMonitor provides general adaptation for sequences from all receptor chains of different species and outputs useful statistics and visualizations. In the final part of this article, we demonstrate its application on minimal residual disease detection in patients with B-cell acute lymphoblastic leukemia. In summary, this package would be of widespread usage for immune repertoire analysis.
authors: BGI-Shenzhen, Shenzhen 518083, China Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China.
authors: Wei
authors: W
authors: Zhang
authors: BGI-Shenzhen, Shenzhen 518083, China Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China.
authors: Yuanping
authors: Y
authors: Du
authors: BGI-Shenzhen, Shenzhen 518083, China Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, Shenzhen 518083, China.
authors: Zheng
authors: Z
authors: Su
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Changxi
authors: C
authors: Wang
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Xiaojing
authors: X
authors: Zeng
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Ruifang
authors: R
authors: Zhang
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Xueyu
authors: X
authors: Hong
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Chao
authors: C
authors: Nie
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Jinghua
authors: J
authors: Wu
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Hongzhi
authors: H
authors: Cao
authors: BGI-Shenzhen, Shenzhen 518083, China.
authors: Xun
authors: X
authors: Xu
authors: BGI-Shenzhen, Shenzhen 518083, China Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark liuxiao@genomics.cn.
authors: Xiao
authors: X
authors: Liu
mesh_terms: D000483:Alleles; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics* / Q000276:immunology / Q000473:pathology; D011947:Receptors, Antigen, B-Cell / Q000235:genetics* / Q000276:immunology; D011948:Receptors, Antigen, T-Cell / Q000235:genetics* / Q000276:immunology; D050441:VDJ Exons / Q000235:genetics / Q000276:immunology
chemical_list: D011947:Receptors, Antigen, B-Cell; D011948:Receptors, Antigen, T-Cell
keywords: TCR/BCR; bioinformatics; immune repertoire; next generation sequencing