Oncoviral infection is responsible for 12%-15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contamination and noncausal viruses complicate the process of identifying genuine oncoviruses. Here, we propose a novel strategy to address these challenges by performing virome-wide screening of early-stage clonal viral integrations. To implement this strategy, we developed VIcaller, a novel platform for identifying viral integrations that are derived from any characterized viruses and shared by a large proportion of tumor cells using whole-genome sequencing (WGS) data. The sensitivity and precision were confirmed with simulated and benchmark cancer data sets. By applying this platform to cancer WGS data sets with proven or speculated viral etiology, we newly identified or confirmed clonal integrations of hepatitis B virus (HBV), human papillomavirus (HPV), Epstein-Barr virus (EBV), and BK Virus (BKV), suggesting the involvement of these viruses in early stages of tumorigenesis in affected tumors, such as HBV in TERT and KM...Continue Reading
Molecular bases for the development of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC)
MLL-GAS7 transforms multipotent hematopoietic progenitors and induces mixed lineage leukemias in mice
Epstein-Barr virus is integrated between REL and BCL-11A in American Burkitt lymphoma cell line (NAB-2)
African great apes are naturally infected with polyomaviruses closely related to Merkel cell polyomavirus
CaPSID: a bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data
Simultaneous characterization of somatic events and HPV-18 integration in a metastatic cervical carcinoma patient using DNA and RNA sequencing
A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
High-throughput RNA sequencing-based virome analysis of 50 lymphoma cell lines from the Cancer Cell Line Encyclopedia project
Microbial contamination in next generation sequencing: implications for sequence-based analysis of clinical samples
Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism
HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human papillomavirus 18
VERSE: a novel approach to detect virus integration in host genomes through reference genome customization
Virus-Clip: a fast and memory-efficient viral integration site detection tool at single-base resolution with annotation capability
Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data
Comprehensive mapping of the human papillomavirus (HPV) DNA integration sites in cervical carcinomas by HPV capture technology
Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers
VIpower: Simulation-based tool for estimating power of viral integration detection via high-throughput sequencing
Mechanisms underlying the activation of TERT transcription and telomerase activity in human cancer: old actors and new players
Human papillomavirus infection and cervical dysplasia in HIV-positive women: potential role of the vaginal microbiota.
Human papillomavirus prevalence and integration status in tissue samples of bladder cancer in Chinese population
Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data.
B-cell lymphomas include lymphomas that affect B cells. This subtype of cancer accounts for over 80% of non-Hodgkin lymphomas in the US. Here is the latest research.
BK Virus Infection
BK virus infection is a significant complication of modern immunosuppression used in kidney transplantation. Discover the latest research on BK virus infection here.
Blood And Marrow Transplantation
The use of hematopoietic stem cell transplantation or blood and marrow transplantation (bmt) is on the increase worldwide. BMT is used to replace damaged or destroyed bone marrow with healthy bone marrow stem cells. Here is the latest research on bone and marrow transplantation.