{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T16:58:07Z","timestamp":1782233887615,"version":"3.54.5"},"reference-count":80,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,3,14]],"date-time":"2023-03-14T00:00:00Z","timestamp":1678752000000},"content-version":"vor","delay-in-days":72,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["2475\/19"],"award-info":[{"award-number":["2475\/19"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007028","name":"Leona M and Harry B Helmsley Charitable Trust","doi-asserted-by":"publisher","award":["2012PG-ISL013"],"award-info":[{"award-number":["2012PG-ISL013"]}],"id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004694","name":"Kaohsiung Medical University","doi-asserted-by":"publisher","award":["KMU-TC109B05"],"award-info":[{"award-number":["KMU-TC109B05"]}],"id":[{"id":"10.13039\/501100004694","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004694","name":"Kaohsiung Medical University","doi-asserted-by":"publisher","award":["KMUKI1100002"],"award-info":[{"award-number":["KMUKI1100002"]}],"id":[{"id":"10.13039\/501100004694","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003975","name":"Israel Cancer Association","doi-asserted-by":"publisher","award":["20160120"],"award-info":[{"award-number":["20160120"]}],"id":[{"id":"10.13039\/501100003975","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","cmghjournal.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"published-print":{"date-parts":[[2023]]},"DOI":"10.1016\/j.jcmgh.2023.03.004","type":"journal-article","created":{"date-parts":[[2023,3,23]],"date-time":"2023-03-23T22:15:04Z","timestamp":1679609704000},"page":"63-81","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":14,"title":["High-Resolution Genomic Profiling of Liver Cancer Links Etiology With Mutation and Epigenetic Signatures"],"prefix":"10.1016","volume":"16","author":[{"given":"Shira","family":"Perez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anat","family":"Lavi-Itzkovitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Moriah","family":"Gidoni","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom","family":"Domovitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roba","family":"Dabour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ishant","family":"Khurana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ateret","family":"Davidovich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Tobar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Livoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evgeny","family":"Solomonov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaakov","family":"Maman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Assam","family":"El-Osta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yishan","family":"Tsai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming-Lung","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salomon M.","family":"Stemmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Izhak","family":"Haviv","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gur","family":"Yaari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7831-6847","authenticated-orcid":false,"given":"Meital","family":"Gal-Tanamy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jcmgh.2023.03.004_bib1","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1038\/nature07943","article-title":"The cancer genome","volume":"458","author":"Stratton","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib2","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/nrg3729","article-title":"Mechanisms underlying mutational signatures in human cancers","volume":"15","author":"Helleday","year":"2014","journal-title":"Nat Rev Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib3","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nature08658","article-title":"A\u00a0comprehensive catalogue of somatic mutations from a human cancer genome","volume":"463","author":"Pleasance","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib4","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1038\/nature08768","article-title":"Signatures of mutation and selection in the cancer genome","volume":"463","author":"Bignell","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib5","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1002\/humu.21616","article-title":"The large-scale distribution of somatic mutations in cancer genomes","volume":"33","author":"Hodgkinson","year":"2012","journal-title":"Hum Mutat"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib6","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1038\/nrg3098","article-title":"Variation in the mutation rate across mammalian genomes","volume":"12","author":"Hodgkinson","year":"2011","journal-title":"Nat Rev Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib7","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nrg3890","article-title":"The effects of chromatin organization on variation in mutation rates in the genome","volume":"16","author":"Makova","year":"2015","journal-title":"Nat Rev Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib8","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1038\/nsmb.3474","article-title":"Nuclear topology modulates the mutational landscapes of cancer genomes","volume":"24","author":"Smith","year":"2017","journal-title":"Nat Struct Mol Biol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib9","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1038\/s41588-020-0708-0","article-title":"Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure","volume":"52","author":"Akdemir","year":"2020","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib10","doi-asserted-by":"crossref","first-page":"1363","DOI":"10.1038\/s41467-020-15185-0","article-title":"Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome","volume":"11","author":"Li","year":"2020","journal-title":"Nat Commun"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib11","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1038\/ng.363","article-title":"Human mutation rate associated with DNA replication timing","volume":"41","author":"Stamatoyannopoulos","year":"2009","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib12","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib13","doi-asserted-by":"crossref","first-page":"2109","DOI":"10.1073\/pnas.1416622112","article-title":"Crossovers are associated with mutation and biased gene conversion at recombination hotspots","volume":"112","author":"Arbeithuber","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib14","doi-asserted-by":"crossref","DOI":"10.1126\/science.aau1043","article-title":"Characterizing mutagenic effects of recombination through a sequence-level genetic map","volume":"363","author":"Halldorsson","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib15","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/nature17661","article-title":"Nucleotide excision repair is impaired by binding of transcription factors to DNA","volume":"532","author":"Sabarinathan","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib16","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/nature11273","article-title":"Chromatin organization is a major influence on regional mutation rates in human cancer cells","volume":"488","author":"Schuster-Bockler","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib17","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/nature14221","article-title":"Cell-of-origin chromatin organization shapes the mutational landscape of cancer","volume":"518","author":"Polak","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib18","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.fob.2013.08.007","article-title":"Contribution of histone N-terminal tails to the structure and stability of nucleosomes","volume":"3","author":"Iwasaki","year":"2013","journal-title":"FEBS Open Bio"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib19","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/j.bbagrm.2014.03.001","article-title":"Interpreting the language of histone and DNA modifications","volume":"1839","author":"Rothbart","year":"2014","journal-title":"Biochim Biophys Acta"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib20","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nature13268","article-title":"Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing","volume":"510","author":"Hovestadt","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib21","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1016\/j.celrep.2014.10.031","article-title":"Transcription restores DNA repair to heterochromatin, determining regional mutation rates in cancer genomes","volume":"9","author":"Zheng","year":"2014","journal-title":"Cell Rep"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib22","doi-asserted-by":"crossref","DOI":"10.1016\/j.dnarep.2019.102645","article-title":"Organization of DNA damage, excision repair, and mutagenesis in chromatin: a genomic perspective","volume":"81","author":"Mao","year":"2019","journal-title":"DNA Repair (Amst)"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib23","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1038\/s41467-020-15912-7","article-title":"Mutational signatures are jointly shaped by DNA damage and repair","volume":"11","author":"Volkova","year":"2020","journal-title":"Nat Commun"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib24","doi-asserted-by":"crossref","first-page":"2557","DOI":"10.1053\/j.gastro.2007.04.061","article-title":"Hepatocellular carcinoma: epidemiology and molecular carcinogenesis","volume":"132","author":"El-Serag","year":"2007","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib25","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.canlet.2013.12.024","article-title":"Multiple interactive factors in hepatocarcinogenesis","volume":"346","author":"Ding","year":"2014","journal-title":"Cancer Lett"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib26","doi-asserted-by":"crossref","first-page":"15584","DOI":"10.1073\/pnas.242608099","article-title":"A\u00a0comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades","volume":"99","author":"Tanaka","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib27","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/ng.3252","article-title":"Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets","volume":"47","author":"Schulze","year":"2015","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib28","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/ng.3547","article-title":"Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer","volume":"48","author":"Fujimoto","year":"2016","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib29","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1038\/ng.2291","article-title":"Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators","volume":"44","author":"Fujimoto","year":"2012","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib30","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1038\/ng.2256","article-title":"Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma","volume":"44","author":"Guichard","year":"2012","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib31","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1038\/ng.2391","article-title":"Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma","volume":"44","author":"Huang","year":"2012","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib32","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.canlet.2012.09.027","article-title":"Next generation sequencing reveals genetic landscape of hepatocellular carcinomas","volume":"340","author":"Li","year":"2013","journal-title":"Cancer Lett"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib33","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1016\/j.jhep.2006.05.013","article-title":"The contributions of hepatitis B virus and hepatitis C virus infections to cirrhosis and primary liver cancer worldwide","volume":"45","author":"Perz","year":"2006","journal-title":"J\u00a0Hepatol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib34","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/S2468-1253(16)30181-9","article-title":"Global prevalence and genotype distribution of hepatitis C virus infection in 2015: a modelling study","volume":"2","year":"2017","journal-title":"Lancet Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib35","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1008181","article-title":"Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals","volume":"15","author":"Perez","year":"2019","journal-title":"PLoS Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib36","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1053\/j.gastro.2019.02.038","article-title":"HCV-induced epigenetic changes associated with liver cancer risk persist after sustained virologic response","volume":"156","author":"Hamdane","year":"2019","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib37","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1136\/gutjnl-2019-318918","article-title":"Targeting clinical epigenetic reprogramming for chemoprevention of metabolic and viral hepatocellular carcinoma","volume":"70","author":"Juhling","year":"2021","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib38","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1016\/j.cell.2017.05.046","article-title":"Comprehensive and integrative genomic characterization of hepatocellular carcinoma","volume":"169","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib39","doi-asserted-by":"crossref","first-page":"765","DOI":"10.1038\/ng.2295","article-title":"Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma","volume":"44","author":"Sung","year":"2012","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib40","doi-asserted-by":"crossref","first-page":"e259","DOI":"10.1038\/cddis.2011.136","article-title":"BRAF and PIK3CA genes are somatically mutated in hepatocellular carcinoma among patients from South Italy","volume":"3","author":"Colombino","year":"2012","journal-title":"Cell Death Dis"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib41","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1158\/0008-5472.CAN-07-3049","article-title":"Spontaneous squamous cell carcinoma induced by the somatic inactivation of retinoblastoma and Trp53 tumor suppressors","volume":"68","author":"Martinez-Cruz","year":"2008","journal-title":"Cancer Res"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib42","doi-asserted-by":"crossref","first-page":"7180","DOI":"10.1038\/onc.2008.327","article-title":"Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer","volume":"27","author":"Schaeffer","year":"2008","journal-title":"Oncogene"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib43","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1016\/S0002-9440(10)65461-2","article-title":"A\u00a0high frequency of sequence alterations is due to formalin fixation of archival specimens","volume":"155","author":"Williams","year":"1999","journal-title":"Am J Pathol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib44","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1002\/hep.32111","article-title":"Interferon drives HCV scarring of the epigenome and creates targetable vulnerabilities following viral clearance","volume":"75","author":"Hlady","year":"2022","journal-title":"Hepatology"},{"issue":"Suppl 16","key":"10.1016\/j.jcmgh.2023.03.004_bib45","doi-asserted-by":"crossref","first-page":"S13","DOI":"10.1186\/1471-2105-13-S16-S13","article-title":"Knowledge-based analysis of proteomics data","volume":"13","author":"Bessarabova","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib46","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1053\/j.gastro.2012.01.045","article-title":"Is hepatitis C virus carcinogenic?","volume":"142","author":"Lemon","year":"2012","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib47","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1016\/j.canlet.2013.06.028","article-title":"Mechanisms of HCV-induced liver cancer: what did we learn from in\u00a0vitro and animal studies?","volume":"345","author":"Rusyn","year":"2014","journal-title":"Cancer Lett"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib48","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.semcancer.2014.01.004","article-title":"Virus associated malignancies: the role of viral hepatitis in hepatocellular carcinoma","volume":"26","author":"Shlomai","year":"2014","journal-title":"Semin Cancer Biol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib49","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1101\/gr.148346.112","article-title":"Genome-wide bimolecular fluorescence complementation analysis of SUMO interactome in yeast","volume":"23","author":"Sung","year":"2013","journal-title":"Genome Res"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib50","doi-asserted-by":"crossref","first-page":"12042","DOI":"10.1073\/pnas.1108715108","article-title":"Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data","volume":"108","author":"Tao","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib51","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/ng.804","article-title":"High-resolution characterization of a hepatocellular carcinoma genome","volume":"43","author":"Totoki","year":"2011","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib52","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1586\/egh.09.5","article-title":"Molecular profiling to predict hepatocellular carcinoma outcome","volume":"3","author":"Hoshida","year":"2009","journal-title":"Expert Rev Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib53","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.coviro.2015.09.003","article-title":"How do persistent infections with hepatitis C virus cause liver cancer?","volume":"14","author":"Mitchell","year":"2015","journal-title":"Curr Opin Virol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib54","doi-asserted-by":"crossref","DOI":"10.3389\/fmolb.2022.997659","article-title":"Insights from DOCK2 in cell function and pathophysiology","volume":"9","author":"Ji","year":"2022","journal-title":"Front Mol Biosci"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib55","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1002\/eji.201747157","article-title":"Dock2 in the development of inflammation and cancer","volume":"48","author":"Chen","year":"2018","journal-title":"Eur J Immunol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib56","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2021.714639","article-title":"Development and validation of a gene mutation-associated nomogram for hepatocellular carcinoma patients from four countries","volume":"12","author":"Huang","year":"2021","journal-title":"Front Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib57","article-title":"Association of a novel DOCK2 mutation-related gene signature with immune in hepatocellular carcinoma","volume":"13","author":"Huang","year":"2022","journal-title":"Front Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib58","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1038\/nrc3816","article-title":"Hypermutation in human cancer genomes: footprints and mechanisms","volume":"14","author":"Roberts","year":"2014","journal-title":"Nat Rev Cancer"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib59","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1038\/ng.2702","article-title":"An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers","volume":"45","author":"Roberts","year":"2013","journal-title":"Nat Genet"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib60","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.dnarep.2014.03.028","article-title":"Error-free versus mutagenic processing of genomic uracil--relevance to cancer","volume":"19","author":"Krokan","year":"2014","journal-title":"DNA Repair (Amst)"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib61","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1126\/science.1153201","article-title":"Evidence for editing of human papillomavirus DNA by APOBEC3 in benign and precancerous lesions","volume":"320","author":"Vartanian","year":"2008","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib62","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003361","article-title":"Uracil DNA glycosylase counteracts APOBEC3G-induced hypermutation of hepatitis B viral genomes: excision repair of covalently closed circular DNA","volume":"9","author":"Kitamura","year":"2013","journal-title":"PLoS Pathog"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib63","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/nature12477","article-title":"Signatures of mutational processes in human cancer","volume":"500","author":"Alexandrov","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib64","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1007\/s10735-006-9059-0","article-title":"High expression of APOBEC3G in patients infected with hepatitis C virus","volume":"37","author":"Komohara","year":"2006","journal-title":"J\u00a0Mol Histol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib65","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1096\/fj.02-0752rev","article-title":"Oxidative DNA damage: mechanisms, mutation, and disease","volume":"17","author":"Cooke","year":"2003","journal-title":"FASEB J"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib66","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1007\/s00423-006-0073-1","article-title":"Chronic inflammation and oxidative stress in the genesis and perpetuation of cancer: role of lipid peroxidation, DNA damage, and repair","volume":"391","author":"Bartsch","year":"2006","journal-title":"Langenbecks Arch Surg"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib67","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1002\/hep.23697","article-title":"c-Jun mediates hepatitis C virus hepatocarcinogenesis through signal transducer and activator of transcription 3 and nitric oxide-dependent impairment of oxidative DNA repair","volume":"52","author":"Machida","year":"2010","journal-title":"Hepatology"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib68","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1111\/j.1365-2893.2008.00972.x","article-title":"Comparison of hepatic oxidative DNA damage in patients with chronic hepatitis B and C","volume":"15","author":"Fujita","year":"2008","journal-title":"J\u00a0Viral Hepat"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib69","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in cancer immunotherapy","volume":"348","author":"Schumacher","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib70","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.jhep.2013.02.022","article-title":"A\u00a0clinical trial of CTLA-4 blockade with tremelimumab in patients with hepatocellular carcinoma and chronic hepatitis C","volume":"59","author":"Sangro","year":"2013","journal-title":"J\u00a0Hepatol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib71","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/j.jhep.2016.10.029","article-title":"Tremelimumab in combination with ablation in patients with advanced hepatocellular carcinoma","volume":"66","author":"Duffy","year":"2017","journal-title":"J\u00a0Hepatol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib72","doi-asserted-by":"crossref","first-page":"940","DOI":"10.1016\/S1470-2045(18)30351-6","article-title":"Pembrolizumab in patients with advanced hepatocellular carcinoma previously treated with sorafenib (KEYNOTE-224): a non-randomised, open-label phase 2 trial","volume":"19","author":"Zhu","year":"2018","journal-title":"Lancet Oncol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib73","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1128\/JVI.01890-06","article-title":"Compensatory mutations in E1, p7, NS2, and NS3 enhance yields of cell culture-infectious intergenotypic chimeric hepatitis C virus","volume":"81","author":"Yi","year":"2007","journal-title":"J\u00a0Virol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib74","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1016\/j.jhep.2015.07.024","article-title":"A\u00a0cell culture system for distinguishing hepatitis C viruses with and without liver cancer-related mutations in the viral core gene","volume":"63","author":"El-Shamy","year":"2015","journal-title":"J\u00a0Hepatol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib75","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1002\/hep.26566","article-title":"Human serum leads to differentiation of human hepatoma cells, restoration of very-low-density lipoprotein secretion, and a 1000-fold increase in HCV Japanese fulminant hepatitis type 1 titers","volume":"58","author":"Steenbergen","year":"2013","journal-title":"Hepatology"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib76","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1101\/gr.239244.118","article-title":"Maftools: efficient and comprehensive analysis of somatic variants in cancer","volume":"28","author":"Mayakonda","year":"2018","journal-title":"Genome Res"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib77","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib78","doi-asserted-by":"crossref","first-page":"e170","DOI":"10.1093\/nar\/gkt660","article-title":"Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations","volume":"41","author":"Yaari","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib79","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"10.1016\/j.jcmgh.2023.03.004_bib80","doi-asserted-by":"crossref","first-page":"D493","DOI":"10.1093\/nar\/gkh103","article-title":"The UCSC Table\u00a0Browser data retrieval tool","volume":"32","author":"Karolchik","year":"2004","journal-title":"Nucleic Acids Res"}],"container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X23000413?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X23000413?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T19:28:16Z","timestamp":1778873296000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352345X23000413"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023]]},"references-count":80,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023]]}},"alternative-id":["S2352345X23000413"],"URL":"https:\/\/doi.org\/10.1016\/j.jcmgh.2023.03.004","relation":{},"ISSN":["2352-345X"],"issn-type":[{"value":"2352-345X","type":"print"}],"subject":[],"published":{"date-parts":[[2023]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"High-Resolution Genomic Profiling of Liver Cancer Links Etiology With Mutation and Epigenetic Signatures","name":"articletitle","label":"Article Title"},{"value":"Cellular and Molecular Gastroenterology and Hepatology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jcmgh.2023.03.004","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Published by Elsevier Inc. on behalf of the AGA Institute.","name":"copyright","label":"Copyright"}]}}