Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach

Genomics Proteomics & Bioinformatics, vol. 22

Abstract

Tandem duplication (TD) is a major type of structural variations (SVs) that plays an important role in novel gene formation and human diseases. However, TDs are often missed or incorrectly classified as insertions by most modern SV detection methods due to the lack of specialized operation on TD-related mutational signals. Herein, we developed a TD detection module for the Pindel tool, referred to as Pindel-TD, based on a TD-specific pattern growth approach. Pindel-TD is capable of detecting TDs with a wide size range at single nucleotide resolution. Using simulated and real read data from HG002, we demonstrated that Pindel-TD outperforms other leading methods in terms of precision, recall, F1-score, and robustness. Furthermore, by applying Pindel-TD to data generated from the K562 cancer cell line, we identified a TD located at the seventh exon of SAGE1, providing an explanation for its high expression. Pindel-TD is available for non-commercial use at https://github.com/xjtu-omics/pindel.

Authors 5

1. Xiaofei Yang

   Xi'an Jiaotong University · First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   Center for Mathematical Medical, the First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

   Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   Center for Mathematical Medical, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

   School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

2. Gaoyang Zheng

   First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   Center for Mathematical Medical, the First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

   Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

   Center for Mathematical Medical, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China

3. Peng Jia

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

4. Songbo Wang

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

5. Kai Ye corresponding Aachen Faculty of Science, Leiden University

   Leiden University · Xi'an Jiaotong University · First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   Center for Mathematical Medical, the First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

   Faculty of Science, Leiden University , Leiden 2311 EZ,

   Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   School of Life Science and Technology, Xi’an Jiaotong University , Xi’an 710049,

   Center for Mathematical Medical, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China

   Faculty of Science, Leiden University, Leiden, 2311 EZ, Netherland

   Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China

   School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China