Viruses cause approximately 30 % of all human cancers. New viruses are discovered weekly, as are novel, putative associations between viruses and cancers. Next Generation Sequencing (NGS) has evolved as a new tool to find viruses in cancer and to support virus-cancer associations. Importantly, NGS-based approaches can be applied to clinical samples without the need for intermediate culture of the agent, and the approach is agnostic with regard to the target sequence. This allows for the discovery of entirely novel, as well as novel but evolutionary related viral agents. Since viral genomes are so much smaller than the human genome, they offer unique opportunities and challenges in NGS. Here, we outline some of these challenges and potential bioinformatics solutions using Kaposi Sarcoma-associated herpesvirus (KSHV) as an example. We provide an abbreviated overview about viral cancers as well as NextGen sequencing platforms. This is followed by a summary of open source computing tools as they apply to the bioinformatics analysis of viral contributions to cancer, as well as a virus-specific case study mapping open chromatin regions in KSHV.
VIRONOMICS: The study of viral genomics in human cancer and disease / Dittmer, D. P.; Yang, D.; Sanders, M.; Xiong, J.; Texier, J.; Bigi, R.. - (2015), pp. 345-366. [10.1007/978-3-319-15811-2_20].
VIRONOMICS: The study of viral genomics in human cancer and disease
Yang, D.;Bigi, R.
2015
Abstract
Viruses cause approximately 30 % of all human cancers. New viruses are discovered weekly, as are novel, putative associations between viruses and cancers. Next Generation Sequencing (NGS) has evolved as a new tool to find viruses in cancer and to support virus-cancer associations. Importantly, NGS-based approaches can be applied to clinical samples without the need for intermediate culture of the agent, and the approach is agnostic with regard to the target sequence. This allows for the discovery of entirely novel, as well as novel but evolutionary related viral agents. Since viral genomes are so much smaller than the human genome, they offer unique opportunities and challenges in NGS. Here, we outline some of these challenges and potential bioinformatics solutions using Kaposi Sarcoma-associated herpesvirus (KSHV) as an example. We provide an abbreviated overview about viral cancers as well as NextGen sequencing platforms. This is followed by a summary of open source computing tools as they apply to the bioinformatics analysis of viral contributions to cancer, as well as a virus-specific case study mapping open chromatin regions in KSHV.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
