Cancer Genomics - Cancer PHGKB -

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Epstein-Barr virus strain variation and cancer. Kanda Teru et al. Cancer science 2019 Jan
Genetic variations in human papillomavirus and cervical cancer outcomes. Rader Janet S et al. International journal of cancer 2018 Dec
ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses. Tokuyama Maria et al. Proceedings of the National Academy of Sciences of the United States of America 2018 Nov
Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome. Hannigan Geoffrey D et al. mBio 2018 Nov (6)
Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer. Shah Manasi S et al. PloS one 2018 (11) e0207002
Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers. Hale Vanessa L et al. Genome medicine 2018 Oct (1) 78
Methylation of High-Risk Human Papillomavirus Genomes are Associated with Cervical Precancer in HIV-positive Women. Gradíssimo Ana et al. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2018 Sep
Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer. Mangifesta Marta et al. Scientific reports 2018 Sep (1) 13974
Genome-wide microRNA analysis of HPV-positive self-samples yields novel triage markers for early detection of cervical cancer. Snoek Barbara C et al. International journal of cancer 2018 Sep
Bile Acids, the Microbiome, Immunity, and Liver Tumors. Schramm Christoph et al. The New England journal of medicine 2018 08 (9) 888-890
Effect of Screening With Primary Cervical HPV Testing vs Cytology Testing on High-grade Cervical Intraepithelial Neoplasia at 48 Months: The HPV FOCAL Randomized Clinical Trial. Ogilvie Gina Suzanne et al. JAMA 2018 Jul (1) 43-52
Molecular Aspects of Varicella-Zoster Virus Latency. Depledge Daniel P et al. Viruses 2018 Jun (7)
E. coli and colorectal cancer: a complex relationship that deserves a critical mindset. Wassenaar Trudy M et al. Critical reviews in microbiology 2018 Jun 1-14
Correcting for batch effects in case-control microbiome studies. Gibbons Sean M et al. PLoS computational biology 2018 Apr (4) e1006102
Tumour virology in the era of high-throughput genomics. Tang Ka-Wei et al. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2017 Oct (1732)
Deep sequencing of HBV pre-S region reveals high heterogeneity of HBV genotypes and associations of word pattern frequencies with HCC. Bai Xin et al. PLoS genetics 2018 Feb (2) e1007206
Human Papillomavirus DNA methylation as a biomarker for cervical precancer: Consistency across 12 genotypes and potential impact on management of HPV-positive women. Clarke Megan A et al. Clinical cancer research : an official journal of the American Association for Cancer Research 2018 Feb
The clinical and phylogenetic investigation for a nosocomial outbreak of respiratory syncytial virus infection in an adult hemato-oncology unit. Nabeya Daijiro et al. Journal of medical virology 2017 Aug (8) 1364-1372
Searching for human oncoviruses: histories, challenges, and opportunities. Cao Jian et al. Journal of cellular biochemistry 2018 Jan
Association of genetic variants in the interleukin-18 gene promoter with risk of hepatocellular carcinoma and metastasis in patients with hepatitis c virus infection. Bakr Noha M et al. IUBMB life 2018 Jan
Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study. Fan Xiaozhou et al. Gut 2018 Jan (1) 120-127
Association of Oral Microbiome With Risk for Incident Head and Neck Squamous Cell Cancer. Hayes Richard B et al. JAMA oncology 2018 Jan
Deep Sequencing Shows Low Level Oncogenic Hepatitis B Virus Variants Persisting Post-Liver Transplant Despite Potent Anti-HBV Prophylaxis. Lau Keith Ck et al. Journal of viral hepatitis 2018 Jan
Putative biomarkers for cervical cancer: SNVs, methylation and expression profiles. Cardoso Maria de Fátima Senra et al. Mutation research 2017 Jul 161-173
Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection. Weiss Eric R et al. Journal of virology 2018 Jan (2)
Analysis of Epstein-Barr Virus Genomes and Expression Profiles in Gastric Adenocarcinoma. Borozan Ivan et al. Journal of virology 2018 Jan (2)
Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? Papanicolas Lito E et al. Trends in microbiology 2017 Nov
Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Bullman Susan et al. Science (New York, N.Y.) 2017 Nov
Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use. Parsons Bryony N et al. PLoS pathogens 2017 Nov (11) e1006653
Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Routy Bertrand et al. Science (New York, N.Y.) 2017 Nov
Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota. Ferreira Rui M et al. Gut 2017 Nov
Genome-wide association and HLA region fine-mapping studies identify susceptibility loci for multiple common infections. Tian Chao et al. Nature communications 2017 Sep (1) 599
Viruses in cancers among the immunosuppressed. Arroyo Mühr Laila Sara et al. International journal of cancer 2017 Dec (12) 2498-2504
Genome-wide analysis of Epstein-Barr virus identifies variants and genes associated with gastric carcinoma and population structure. Yao Youyuan et al. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2017 Oct (10) 1010428317714195
The future of DNA sequencing. Green Eric D et al. Nature 2017 Oct (7675) 179-181
The gastric microbiome, its interaction with Helicobacter pylori, and its potential role in the progression to stomach cancer. Noto Jennifer M et al. PLoS pathogens 2017 Oct (10) e1006573
Intestinal microbiota is altered in patients with colon cancer and modified by probiotic intervention. Hibberd Ashley A et al. BMJ open gastroenterology 2017 (1) e000145
Diagnosis of Fatal Human Case of St. Louis Encephalitis Virus Infection by Metagenomic Sequencing, California, 2016. Chiu Charles Y et al. Emerging infectious diseases 2017 Oct (10) 1964-1968
Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments. Noto Jennifer M et al. Gut 2017 Sep
HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis. Mirabello Lisa et al. Cell 2017 Sep (6) 1164-1174.e6
The role of the microbiome in cancer development and therapy. Bhatt Aadra P et al. CA: a cancer journal for clinicians 2017 Jul (4) 326-344
Defining the genetic susceptibility to cervical neoplasia-A genome-wide association study. Leo Paul J et al. PLoS genetics 2017 Aug (8) e1006866
Plasma Epstein-Barr Virus DNA for Screening. Ambinder Richard F et al. The New England journal of medicine 2017 Aug (6) 584-585
Analysis of Plasma Epstein-Barr Virus DNA to Screen for Nasopharyngeal Cancer. Chan K C Allen et al. The New England journal of medicine 2017 Aug (6) 513-522
Genome-wide analysis of eighteen Epstein-Barr viruses isolated from primary nasopharyngeal carcinoma biopsies. Tu Chaofeng et al. Journal of virology 2017 Jun
Limited diagnostic value of a multiplexed gastrointestinal pathogen panel for the detection of adenovirus infection in an oncology patient population. McMillen Tracy et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 Jul 37-41
Protecting Privacy in Large Datasets-First We Assess the Risk; Then We Fuzzy the Data. Ursin Giske et al. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2017 Jul
Hepatitis B virus core antigen mutations predict post-operative prognosis of patients with primary hepatocellular carcinoma. Jia Jian'an et al. The Journal of general virology 2017 Jun (6) 1399-1409
Streptococcus gallolyticus subsp. gallolyticus promotes colorectal tumor development. Kumar Ritesh et al. PLoS pathogens 2017 Jul (7) e1006440
Exposure to bacterial products lipopolysaccharide and flagellin and hepatocellular carcinoma: a nested case-control study. Fedirko Veronika et al. BMC medicine 2017 Apr (1) 72
In vivo analysis of the viable microbiota and Helicobacter pylori transcriptome in gastric infection and early stages of carcinogenesis. Thorell Kaisa et al. Infection and immunity 2017 Jul
Precision Medicine Requires Precision Laboratories. Rajeevan Mangalathu S et al. The Journal of molecular diagnostics : JMD 2017 Mar (2) 226-229
Impact of viral and host DNA methylations on HPV16-related cervical cancer pathogenesis. Sen Shrinka et al. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2017 May (5) 1010428317699799
Polymorphism of TLR5 rs5744174 is associated with disease progression in Chinese patients with chronic HBV infection. Cao Lina et al. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica 2017 May
The role of next generation sequencing in infection prevention in human parainfluenza virus 3 infections in immunocompromised patients. Kothari Atul et al. Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology 2017 May 53-55
Anticancer effects of the microbiome and its products. Zitvogel Laurence et al. Nature reviews. Microbiology 2017 May
Complete genome sequencing and clinical analysis of intrahepatic hepatitis B virus cccDNA from HCC. Jiao Fengping et al. Microbial pathogenesis 2017 May
Study protocol on the role of intestinal microbiota in colorectal cancer treatment: a pathway to personalized medicine 2.0. Aarnoutse R et al. International journal of colorectal disease 2017 Apr
The ovarian cancer oncobiome. Banerjee Sagarika et al. Oncotarget 2017 Mar
Nucleic acid detection with CRISPR-Cas13a/C2c2. Gootenberg Jonathan S et al. Science (New York, N.Y.) 2017 Apr
Molecular tests potentially improving HPV screening and genotyping for cervical cancer prevention. Gradíssimo Ana et al. Expert review of molecular diagnostics 2017 Feb 1-13
Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. Thorell Kaisa et al. PLoS genetics 2017 Feb (2) e1006546
Suspected encephalitis with Candida tropicalis and Fusarium detected by unbiased RNA sequencing. Christopeit M et al. Annals of hematology 2016 Oct (11) 1919-21
Genome-wide Association Study Identifies TLL1 Variant Associated With Development of Hepatocellular Carcinoma After Eradication of Hepatitis C Virus Infection. Matsuura Kentaro et al. Gastroenterology 2017 Feb
From Culture to High-Throughput Sequencing and Beyond: A Layperson's Guide to the "Omics" and Diagnostic Potential of the Microbiome. O'Toole Paul W et al. Gastroenterology clinics of North America 2017 Mar (1) 9-17
Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data. Robinson Kelly M et al. Microbiome 2017 Jan (1) 9
Alteration of Human Papillomavirus Type 16 Genetic and Epigenetic Profiles in Cervical Cancer Patients Is Indicative of Poor Disease Prognosis: A Cohort Analysis. Dutta Sankhadeep et al. International journal of gynecological cancer : official journal of the International Gynecological Cancer Society 2016 May (4) 750-7
Characterisation of microbial communities within aggressive prostate cancer tissues. Yow Melissa A et al. Infectious agents and cancer 2017 4
Collateral damage: insights into bacterial mechanisms that predispose host cells to cancer Gagniere A, et al. Nat Rev Microbiol, Jan 3, 2017.
Multiple HPV infections in female sex workers in Western Kenya: implications for prophylactic vaccines within this sub population. Menon Sonia et al. Infectious agents and cancer 2017 2
Examining the potential use and long-term stability of guaiac faecal occult blood test cards for microbial DNA 16S rRNA sequencing. Taylor Morag et al. Journal of clinical pathology 2016 Dec
HPV Genotyping of Modified General Primer-Amplicons Is More Analytically Sensitive and Specific by Sequencing than by Hybridization. Meisal Roger et al. PloS one 2017 (1) e0169074
The gut microbiota in conventional and serrated precursors of colorectal cancer. Peters Brandilyn A et al. Microbiome 2016 Dec (1) 69
A polyclonal outbreak of bloodstream infections by Enterococcus faecium in patients with hematologic malignancies. Alatorre-Fernández Pamela et al. American journal of infection control 2016 Nov
HPV16 variants distribution in invasive cancers of the cervix, vulva, vagina, penis, and anus. Nicolás-Párraga Sara et al. Cancer medicine 2016 Sep
Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia. Bogdanovic G et al. British journal of cancer 2016 Aug
Variability of high risk HPV genotypes among HIV infected women in Mwanza, Tanzania- the need for evaluation of current vaccine effectiveness in developing countries. Mujuni Fridolin et al. Infectious agents and cancer 2016 49
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights. Pasolli Edoardo et al. PLoS computational biology 2016 Jul (7) e1004977
Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features. Yu Guoqin et al. Genome biology 2016 (1) 163
Human Papillomavirus Genotyping Testing Practice in 2014: Results of a College of American Pathologists National Survey. Zhao Chengquan et al. Archives of pathology & laboratory medicine 2016 Aug
Human Cytomegalovirus DNA Quantification and Gene Expression in Gliomas of Different Grades. Stangherlin Lucas Matheus et al. PloS one 2016 (7) e0159604
Metagenome-wide association studies: fine-mining the microbiome. Wang Jun et al. Nature reviews. Microbiology 2016 Aug (8) 508-22
A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association. Strong Michael J et al. Acta neuropathologica communications 2016 (1) 71
The microbiota of breast tissue and its association with tumours. Urbaniak Camilla et al. Applied and environmental microbiology 2016 Jun
Virus and Host Testing to Manage Chronic Hepatitis B. Wong Grace Lai-Hung et al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 2016 Jun S298-305
Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Gu W et al. Genome biology 2016 41
Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection. Montassier Emmanuel et al. Genome medicine 2016 (1) 49
HPV16 Sublineage Associations With Histology-Specific Cancer Risk Using HPV Whole-Genome Sequences in 3200 Women. Mirabello Lisa et al. Journal of the National Cancer Institute 2016 Sep (9)
Clonal deleted latent membrane protein 1 variants of Epstein-Barr virus are predominant in European extranodal NK/T lymphomas and disappear during successful treatment. Halabi Mohamad Adnan et al. International journal of cancer 2016 Apr
HPV genotype distribution and anomalous association of HPV33 to cervical neoplastic lesions in San Luis Potosí, Mexico. DelaRosa-Martínez Raúl et al. Infectious agents and cancer 2016 16
Modeling the integration of bacterial rRNA fragments into the human cancer genome. Sieber Karsten B et al. BMC bioinformatics 2016 (1) 134
RAD51 G135C genetic polymorphism and their potential role in gastric cancer induced by Helicobacter pylori infection in Bhutan. Trang T T H et al. Epidemiology and infection 2016 Jan (2) 234-40
Incidence of Hepatocellular Carcinoma According to Hepatitis B Virus Genotype in Alaska Native People. Ching Lance K et al. Liver international : official journal of the International Association for the Study of the Liver 2016 Mar
Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia. Gyarmati P et al. Scientific reports 23532
Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Flemer Burkhardt et al. Gut 2016 Mar
Helicobacter pylori CagL Hypervariable Motif: a Global Analysis of Geographical Diversity and Association with Gastric Cancer. Gorrell Rebecca J et al. The Journal of infectious diseases 2016 Feb
A Toolbox for Herpesvirus miRNA Research: Construction of a Complete Set of KSHV miRNA Deletion Mutants. Jain Vaibhav et al. Viruses 2016 (2)
Human Papillomavirus Laboratory Testing: the Changing Paradigm. Burd Eileen M et al. Clinical microbiology reviews 2016 Apr (2) 291-319
Single-cell genome sequencing: current state of the science. Gawad Charles et al. Nature reviews. Genetics 2016 Jan
The role of HPV RNA transcription, immune response-related gene expression and disruptive TP53 mutations in diagnostic and prognostic profiling of head and neck cancer. Wichmann Gunnar et al. International journal of cancer. Journal international du cancer 2015 Dec (12) 2846-57