title: Structural variation discovery in the cancer genome using next generation sequencing: computational solutions and perspectives.
abstract: Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome.
authors: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors: Biao
authors: B
authors: Liu
authors: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors: Jeffrey M
authors: JM
authors: Conroy
authors: Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors: Carl D
authors: CD
authors: Morrison
authors: Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors: Adekunle O
authors: AO
authors: Odunsi
authors: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, USA.
authors: Maochun
authors: M
authors: Qin
authors: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, USA.
authors: Lei
authors: L
authors: Wei
authors: Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors: Donald L
authors: DL
authors: Trump
authors: Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA.
authors: Candace S
authors: CS
authors: Johnson
authors: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, USA.
authors: Song
authors: S
authors: Liu
authors: Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, USA.
authors: Jianmin
authors: J
authors: Wang
mesh_terms: D056914:Genomic Structural Variation; D023281:Genomics / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: cancer genome analysis; next generation sequencing; somatic mutation; structural variation