Dataset Information

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.

ABSTRACT: BACKGROUND:Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. METHODS:In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. RESULTS:Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. CONCLUSIONS:Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

SUBMITTER: Mollerup S

PROVIDER: S-EPMC6743825 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.

Mollerup Sarah S Asplund Maria M Friis-Nielsen Jens J Kjartansdóttir Kristín Rós KR Fridholm Helena H Hansen Thomas Arn TA Herrera José Alejandro Romero JAR Barnes Christopher James CJ Jensen Randi Holm RH Richter Stine Raith SR Nielsen Ida Broman IB Pietroni Carlotta C Alquezar-Planas David E DE Rey-Iglesia Alba A Olsen Pernille V S PVS Rajpert-De Meyts Ewa E Groth-Pedersen Line L von Buchwald Christian C Jensen David H DH Gniadecki Robert R Høgdall Estrid E Langhoff Jill Levin JL Pete Imre I Vereczkey Ildikó I Baranyai Zsolt Z Dybkaer Karen K Johnsen Hans Erik HE Steiniche Torben T Hokland Peter P Rosenberg Jacob J Baandrup Ulrik U Sicheritz-Pontén Thomas T Willerslev Eske E Brunak Søren S Lund Ole O Mourier Tobias T Vinner Lasse L Izarzugaza Jose M G JMG Nielsen Lars Peter LP Hansen Anders Johannes AJ

The Journal of infectious diseases 20190901 8

<h4>Background</h4>Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data.<h4>Methods</h4>In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 dataset ...[more]

PMID: 31253993

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Project description:Next-generation sequencing (NGS) of bacterial genomes has recently become more accessible and is now available to the routine diagnostic microbiology laboratory. However, questions remain regarding its feasibility, particularly with respect to data analysis in nonspecialist centers. To test the applicability of NGS to outbreak investigations, Ion Torrent sequencing was used to investigate a putative multidrug-resistant Escherichia coli outbreak in the neonatal unit of the Mercy Hospital for Women, Melbourne, Australia. Four suspected outbreak strains and a comparator strain were sequenced. Genome-wide single nucleotide polymorphism (SNP) analysis demonstrated that the four neonatal intensive care unit (NICU) strains were identical and easily differentiated from the comparator strain. Genome sequence data also determined that the NICU strains belonged to multilocus sequence type 131 and carried the bla(CTX-M-15) extended-spectrum beta-lactamase. Comparison of the outbreak strains to all publicly available complete E. coli genome sequences showed that they clustered with neonatal meningitis and uropathogenic isolates. The turnaround time from a positive culture to the completion of sequencing (prior to data analysis) was 5 days, and the cost was approximately $300 per strain (for the reagents only). The main obstacles to a mainstream adoption of NGS technologies in diagnostic microbiology laboratories are currently cost (although this is decreasing), a paucity of user-friendly and clinically focused bioinformatics platforms, and a lack of genomics expertise outside the research environment. Despite these hurdles, NGS technologies provide unparalleled high-resolution genotyping in a short time frame and are likely to be widely implemented in the field of diagnostic microbiology in the next few years, particularly for epidemiological investigations (replacing current typing methods) and the characterization of resistance determinants. Clinical microbiologists need to familiarize themselves with these technologies and their applications.

Dataset Information

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.

Publications

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.

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