文献类型： 会议论文

第一作者： Justyna Mika

作者： Justyna Mika ¹ ; Serge M. Candeias ² ; Christophe Badie ³ ; Joanna Polanska ¹ ;

作者机构： 1.Department of Data Science and Engineering, Silesian University of Technology

2.Laboratoire de Chimie Et Biologie Des Metaux, Universite Grenoble Alpes, CNRS, CEA

3.Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Radiation Chemical & Environmental Hazards, UK Health Security Agency

关键词： TCR detection;Oxford nanopore sequencing;Long reads

会议名称： International Work-Conference on Bioinformatics and Biomedical Engineering

主办单位：

页码： 450-463

摘要： T cells play an essential role in defense of the organism against pathogens and cancer. Efficient protection requires a vast repertoire of immune receptors, which is created by the V(D)J recombination process. There are multiple algorithms designed for the annotation of recombined T cell receptor (TR) sequences from traditional (short-read) RNA-Seq, however, none is adjusted for the long-read data. Here we intend to examine whether existing methods for TR sequences annotation using traditional RNA-Seq can be utilized for long-read sequencing data. ImReP, TRUST4, CATT and MiXCR algorithms were applied to data obtained by nanopore technology (PromethION). Adjustment of parameters was performed. The biggest number of CDR3 sequences was detected by the TRUST4 algorithm (20,599 unique TR sequences out of 73,904,478 total reads), representing 25% of the expected number of sequences. The distribution of annotated V and J genes was the same for MiXCR and TRUST4 algorithms and may be used to analyze the repertoire of V/J gene used in rearranged TR genes. Due to the high sequencing error rate of the analyzed sample (median read quality Q = 6.9), TR clonotype analysis is not suggested, and additional error correction steps are recommended for such analyses.

分类号： Q811.4-53