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Review
. 2016 May 13:7:676.
doi: 10.3389/fmicb.2016.00676. eCollection 2016.

Strategies for Human Tumor Virus Discoveries: From Microscopic Observation to Digital Transcriptome Subtraction

Ezra D Mirvish  1 , Masahiro Shuda  2
Affiliations
Review

Strategies for Human Tumor Virus Discoveries: From Microscopic Observation to Digital Transcriptome Subtraction

Ezra D Mirvish et al. Front Microbiol. .

Abstract

Over 20% of human cancers worldwide are associated with infectious agents, including viruses, bacteria, and parasites. Various methods have been used to identify human tumor viruses, including electron microscopic observations of viral particles, immunologic screening, cDNA library screening, nucleic acid hybridization, consensus PCR, viral DNA array chip, and representational difference analysis. With the Human Genome Project, a large amount of genetic information from humans and other organisms has accumulated over the last decade. Utilizing the available genetic databases, Feng et al. (2007) developed digital transcriptome subtraction (DTS), an in silico method to sequentially subtract human sequences from tissue or cellular transcriptome, and discovered Merkel cell polyomavirus (MCV) from Merkel cell carcinoma. Here, we review the background and methods underlying the human tumor virus discoveries and explain how DTS was developed and used for the discovery of MCV.

Keywords: Merkel cell polyomavirus; digital transcriptome subtraction; history; methods; tumor virus discoveries.

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Figures

FIGURE 1
FIGURE 1
Digital transcriptome subtraction (DTS). L-SAGE libraries were constructed from BCBL1, a KSHV positive cell line and squamous cell conjunctival carcinoma (SCCC), and short cDNA tags were sequenced for whole transcriptome analysis. High throughput sequencing (HTS) was performed on cDNA libraries from human Merkel cell carcinoma (MCC).
See this image and copyright information in PMC

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