Pindel-TD: a tandem duplication detector based on a pattern growth approach

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

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

Authors 5

1. Xiaofei Yang

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

   Affiliation as printed

   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

   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, 71009, China

   School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 70049, 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, China

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

   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, China

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

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 71009, 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, China

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

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 71009, 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 · First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

   Affiliation as printed

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

   Faculty of Science, Leiden University, Leiden 2311EZ, 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, 71009, 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