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Tumour virology in the era of high-throughput genomics

Journal article
Authors Ka-Wei Tang
Erik Larsson
Published in Philosophical Transactions of the Royal Society B-Biological Sciences
Volume 372
Issue 1732
ISSN 0962-8436
Publication year 2017
Published at Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology
Institute of Biomedicine, Department of Infectious Medicine
Language en
Links dx.doi.org/10.1098/rstb.2016.0265
Keywords tumour virus, next-generation sequencing, virus integration, human cytomegalovirus-infection, human-papillomavirus, integration, sites, seronegative hepatitis, endometrial cancer, virus integration, chinese patients, breast-cancer, dna virus, rna-seq, oo ql, 1989, science, v244, p359, ang y, 1994, science, v266, p1865
Subject categories Biological Sciences

Abstract

With the advent of massively parallel sequencing, oncogenic viruses in tumours can now be detected in an unbiased and comprehensive manner. Additionally, new viruses or strains can be discovered based on sequence similarity with known viruses. Using this approach, the causative agent for Merkel cell carcinoma was identified. Subsequent studies using data from large collections of tumours have confirmed models built during decades of hypothesis-driven and low-throughput research, and a more detailed and comprehensive description of virus-tumour associations have emerged. Notably, large cohorts and high sequencing depth, in combination with newly developed bioinformatical techniques, have made it possible to rule out several suggested virus-tumour associations with a high degree of confidence. In this review we discuss possibilities, limitations and insights gained from using massively parallel sequencing to characterize tumours with viral content, with emphasis on detection of viral sequences and genomic integration events.

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