title: An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology.
abstract: Next-generation sequencing (NGS) technologies that have advanced rapidly in the past few years possess the potential to classify diseases, decipher the molecular code of related cell processes, identify targets for decision-making on targeted therapy or prevention strategies, and predict clinical treatment response. Thus, NGS is on its way to revolutionize oncology. With the help of NGS, we can draw a finer map for the genetic basis of diseases and can improve our understanding of diagnostic and prognostic applications and therapeutic methods. Despite these advantages and its potential, NGS is facing several critical challenges, including reduction of sequencing cost, enhancement of sequencing quality, improvement of technical simplicity and reliability, and development of semiautomated and integrated analysis workflow. In order to address these challenges, we conducted a literature research and summarized a four-stage NGS workflow for providing a systematic review on NGS-based analysis, explaining the strength and weakness of diverse NGS-based software tools, and elucidating its potential connection to individualized medicine. By presenting this four-stage NGS workflow, we try to provide a minimal structural layout required for NGS data storage and reproducibility.
authors.affiliation: Institute for Medical Informatics, Biometry and Epidemiology, Ludwig Maximilian University of Munich, Munich, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.affiliation: Institute for Medical Informatics, Biometry and Epidemiology, Ludwig Maximilian University of Munich, Munich, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.; German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Aarif Mohamed Nazeer
authors.initials: AM
authors.lastname: Batcha
authors.affiliation: Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany.; Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Grüning
authors.affiliation: Institute for Medical Informatics, Biometry and Epidemiology, Ludwig Maximilian University of Munich, Munich, Germany.; German Cancer Consortium (DKTK), Heidelberg, Germany.
authors.forename: Ulrich R
authors.initials: UR
authors.lastname: Mansmann
keywords: mutation annotation; pathway analysis; sequence alignment; single-nucleotide polymorphism; template preparation