title: Computational characterisation of cancer molecular profiles derived using next generation sequencing.
abstract: Our current understanding of cancer genetics is grounded on the principle that cancer arises from a clone that has accumulated the requisite somatically acquired genetic aberrations, leading to the malignant transformation. It also results in aberrent of gene and protein expression. Next generation sequencing (NGS) or deep sequencing platforms are being used to create large catalogues of changes in copy numbers, mutations, structural variations, gene fusions, gene expression, and other types of information for cancer patients. However, inferring different types of biological changes from raw reads generated using the sequencing experiments is algorithmically and computationally challenging. In this article, we outline common steps for the quality control and processing of NGS data. We highlight the importance of accurate and application-specific alignment of these reads and the methodological steps and challenges in obtaining different types of information. We comment on the importance of integrating these data and building infrastructure to analyse it. We also provide exhaustive lists of available software to obtain information and point the readers to articles comparing software for deeper insight in specialised areas. We hope that the article will guide readers in choosing the right tools for analysing oncogenomic datasets.
authors.affiliation: Laboratory of Gene Therapy, Department of Cancer Immunology, The Greater Poland Cancer Centre, Poznan, Poland ; Department of Cancer Immunology and Diagnostics, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland ; These authors contributed equally to this paper.
authors.forename: Urszula
authors.initials: U
authors.lastname: Oleksiewicz
authors.affiliation: Laboratory of Gene Therapy, Department of Cancer Immunology, The Greater Poland Cancer Centre, Poznan, Poland ; Department of Cancer Immunology and Diagnostics, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland ; Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw ; These authors contributed equally to this paper.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Tomczak
authors.affiliation: Poznan University of Economics, Poznań, Poland ; These authors contributed equally to this paper.
authors.forename: Jakub
authors.initials: J
authors.lastname: Woropaj
authors.affiliation: Transition Technologies S.A., Warsaw, Poland.
authors.forename: Monika
authors.initials: M
authors.lastname: Markowska
authors.affiliation: Transition Technologies S.A., Warsaw, Poland.
authors.forename: Piotr
authors.initials: P
authors.lastname: Stępniak
authors.affiliation: Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Parantu K
authors.initials: PK
authors.lastname: Shah
keywords: next generation sequencing