Tissue-associated microbial detection in cancer using human sequencing data
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Open Access
REVIEW
Tissue‑associated microbial detection in cancer using human sequencing data Rebecca M. Rodriguez1,3,4†, Vedbar S. Khadka1*† , Mark Menor1, Brenda Y. Hernandez2,3* and Youping Deng1*
From The 20th International Conference on Bioinformatics & Computational Biology (BIOCOMP 2019) Las Vegas, NV, USA. 29 July-01 August 2019 *Correspondence: [email protected]; [email protected]; [email protected] † Rebecca M. Rodriguez and Vedbar S. Khadka contributed equally and should be considered co-first authors 1 Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Mānoa, Honolulu, HI, USA 2 Epidemiology, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA Full list of author information is available at the end of the article
Abstract Cancer is one of the leading causes of morbidity and mortality in the globe. Microbiological infections account for up to 20% of the total global cancer burden. The human microbiota within each organ system is distinct, and their compositional variation and interactions with the human host have been known to attribute detrimental and beneficial effects on tumor progression. With the advent of next generation sequencing (NGS) technologies, data generated from NGS is being used for pathogen detection in cancer. Numerous bioinformatics computational frameworks have been developed to study viral information from host-sequencing data and can be adapted to bacterial studies. This review highlights existing popular computational frameworks that utilize NGS data as input to decipher microbial composition, which output can predict functional compositional differences with clinically relevant applicability in the development of treatment and prevention strategies. Keywords: Cancer microbiome, Computational frameworks, NGS
Introduction Cancer is one of the leading causes of morbidity and mortality in the globe. Annually an estimated 14.1 million are diagnosed, and 8.2 million die from cancers around the world. In the United States alone, 1.7 million cases are diagnosed, and about six hundred thousand die from the disease [1–3]. Cancer is a multifactorial disease with known genetic and environmental etiologies. Microbiological infections account for up to 20% of the total global cancer burden [4, 5]. Viruses are commonly attributed and are responsible for at least 10% of all human cancers [6]. Multiple studies have evaluated viral content and its influence on cancer pathogenesis utilizing advanced technologies and bioinformatics approaches. Meanwhile, recent limited evidence exists proposing relationships between bacterial species and disease either as effector or consequence of tumorigenesis. While much effort has gone into characterizing cavity organs microbiota, that of solid tumors is less © The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium
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