{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T23:22:36Z","timestamp":1791588156018,"version":"4.3.4"},"reference-count":51,"publisher":"Elsevier BV","issue":"5","license":[{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,8,12]],"date-time":"2024-08-12T00:00:00Z","timestamp":1723420800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Genomics"],"published-print":{"date-parts":[[2024,9]]},"DOI":"10.1016\/j.ygeno.2024.110916","type":"journal-article","created":{"date-parts":[[2024,8,13]],"date-time":"2024-08-13T16:17:33Z","timestamp":1723565853000},"page":"110916","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"title":["Identification of whole-genome mutations and structural variations of bile cell-free DNA in cholangiocarcinoma"],"prefix":"10.1016","volume":"116","author":[{"given":"Lei","family":"Yin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anqi","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teng","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoya","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lixue","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baoning","family":"Nian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sheng","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhikuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiaonan","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyu","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longjiu","family":"Cui","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanxin","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Kuang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dadong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongjie","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ygeno.2024.110916_bb0005","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1038\/s41575-020-0310-z","article-title":"Cholangiocarcinoma 2020: the next horizon in mechanisms and management","volume":"17","author":"Banales","year":"2020","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0010","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.jhep.2019.03.013","article-title":"Global trends in mortality from intrahepatic and extrahepatic cholangiocarcinoma","volume":"71","author":"Bertuccio","year":"2019","journal-title":"J. Hepatol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0015","doi-asserted-by":"crossref","first-page":"1021","DOI":"10.1053\/j.gastro.2011.12.005","article-title":"Genomic and genetic characterization of cholangiocarcinoma identifies therapeutic targets for tyrosine kinase inhibitors","volume":"142","author":"Andersen","year":"2012","journal-title":"Gastroenterology"},{"key":"10.1016\/j.ygeno.2024.110916_bb0020","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1016\/j.ejso.2019.04.002","article-title":"Increased multimodality treatment options has improved survival for Hepatocellular carcinoma but poor survival for biliary tract cancers remains unchanged","volume":"45","author":"Alabraba","year":"2019","journal-title":"Eur. J. Surg. Oncol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0025","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nrclinonc.2017.157","article-title":"Cholangiocarcinoma \u2013 evolving concepts and therapeutic strategies","volume":"15","author":"Rizvi","year":"2018","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0030","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1038\/nrclinonc.2013.110","article-title":"Liquid biopsy: monitoring cancer-genetics in the blood","volume":"10","author":"Crowley","year":"2013","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0035","doi-asserted-by":"crossref","DOI":"10.1016\/j.esmoop.2021.100275","article-title":"Cell-free DNA from bile outperformed plasma as a potential alternative to tissue biopsy in biliary tract cancer","volume":"6","author":"Gou","year":"2021","journal-title":"ESMO Open"},{"key":"10.1016\/j.ygeno.2024.110916_bb0040","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/ng.3375","article-title":"Genomic spectra of biliary tract cancer","volume":"47","author":"Nakamura","year":"2015","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ygeno.2024.110916_bb0045","first-page":"549","article-title":"Bile cellfree DNA as a novel and powerful liquid biopsy for detecting somatic variants in biliary tract cancer","volume":"42","author":"Shen","year":"2019","journal-title":"Oncol. Rep."},{"key":"10.1016\/j.ygeno.2024.110916_bb0050","article-title":"Non-invasive detection of biliary tract cancer by low-coverage whole genome sequencing from plasma cell-free DNA: a prospective cohort study","volume":"14","author":"Wang","year":"2020","journal-title":"Transl. Oncol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0055","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1158\/2159-8290.CD-17-0368","article-title":"Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma","volume":"7","author":"Jusakul","year":"2017","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ygeno.2024.110916_bb0060","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1016\/j.jhep.2018.01.009","article-title":"Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations","volume":"68","author":"Wardell","year":"2018","journal-title":"J. Hepatol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0065","article-title":"Comprehensive evaluation and application of a novel method to isolate cell-free DNA derived from bile of biliary tract Cancer patients","volume":"12","author":"Shen","year":"2022","journal-title":"Front. Oncol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0070","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2024.110916_bb0075","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"Genome project data processing, the sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2024.110916_bb0080","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/s41592-018-0051-x","article-title":"Strelka2: fast and accurate calling of germline and somatic variants","volume":"15","author":"Kim","year":"2018","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ygeno.2024.110916_bb0085","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"Chen","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ygeno.2024.110916_bb0090","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ygeno.2024.110916_bb0095","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"C. Genomes Project","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2024.110916_bb0100","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2024.110916_bb0105","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/nature11690","article-title":"Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants","volume":"493","author":"Fu","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2024.110916_bb0110","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","article-title":"The mutational constraint spectrum quantified from variation in 141,456 humans","volume":"581","author":"Karczewski","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2024.110916_bb0115","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1016\/j.cell.2012.04.024","article-title":"Mutational processes molding the genomes of 21 breast cancers","volume":"149","author":"Nik-Zainal","year":"2012","journal-title":"Cell"},{"key":"10.1016\/j.ygeno.2024.110916_bb0120","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s13059-016-0893-4","article-title":"DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution","volume":"17","author":"Rosenthal","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0125","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1004873","article-title":"CNVkit: genome-wide copy number detection and visualization from targeted DNA sequencing","volume":"12","author":"Talevich","year":"2016","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0130","doi-asserted-by":"crossref","first-page":"R41","DOI":"10.1186\/gb-2011-12-4-r41","article-title":"GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers","volume":"12","author":"Mermel","year":"2011","journal-title":"Genome Biol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0135","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"10.1016\/j.ygeno.2024.110916_bb0140","doi-asserted-by":"crossref","first-page":"1474","DOI":"10.1038\/ng.2806","article-title":"Exome sequencing identifies distinct mutational patterns in liver fluke-related and non-infection-related bile duct cancers","volume":"45","author":"Chan-On","year":"2013","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ygeno.2024.110916_bb0145","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2018.03.076","article-title":"Genomic and molecular landscape of DNA damage repair deficiency across the cancer genome atlas","volume":"23","author":"Knijnenburg","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.ygeno.2024.110916_bb0150","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2018.03.035","article-title":"Oncogenic signaling pathways in the cancer genome atlas","volume":"173","author":"Sanchez-Vega","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.ygeno.2024.110916_bb0155","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1007\/s00535-019-01563-z","article-title":"YAP and the Hippo pathway in cholangiocarcinoma","volume":"54","author":"Sugihara","year":"2019","journal-title":"J. Gastroenterol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0160","doi-asserted-by":"crossref","first-page":"1627","DOI":"10.1002\/hep.27687","article-title":"IL-33 facilitates oncogene-induced cholangiocarcinoma in mice by an interleukin-6-sensitive mechanism","volume":"61","author":"Yamada","year":"2015","journal-title":"Hepatology"},{"key":"10.1016\/j.ygeno.2024.110916_bb0165","doi-asserted-by":"crossref","first-page":"8031","DOI":"10.1074\/jbc.M115.698472","article-title":"A Hippo and fibroblast growth factor receptor autocrine pathway in cholangiocarcinoma","volume":"291","author":"Rizvi","year":"2016","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.ygeno.2024.110916_bb0170","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1159\/000463390","article-title":"Altered expression of Hippo signaling pathway molecules in intrahepatic cholangiocarcinoma","volume":"93","author":"Sugimachi","year":"2017","journal-title":"Oncology"},{"key":"10.1016\/j.ygeno.2024.110916_bb0175","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/ng.3101","article-title":"Genome-wide analysis of noncoding regulatory mutations in cancer","volume":"46","author":"Weinhold","year":"2014","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ygeno.2024.110916_bb0180","article-title":"Wnt\/beta-catenin signaling as an emerging potential key pharmacological target in cholangiocarcinoma","volume":"40","author":"Zhang","year":"2020","journal-title":"Biosci. Rep."},{"key":"10.1016\/j.ygeno.2024.110916_bb0185","doi-asserted-by":"crossref","DOI":"10.1016\/j.biopha.2020.110851","article-title":"WNT\/beta-catenin signaling in the development of liver cancers","volume":"132","author":"He","year":"2020","journal-title":"Biomed. Pharmacother."},{"key":"10.1016\/j.ygeno.2024.110916_bb0190","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.ygeno.2024.110916_bb0195","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.cell.2010.11.055","article-title":"Massive genomic rearrangement acquired in a single catastrophic event during cancer development","volume":"144","author":"Stephens","year":"2011","journal-title":"Cell"},{"key":"10.1016\/j.ygeno.2024.110916_bb0200","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1038\/nature10910","article-title":"Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes","volume":"483","author":"Molenaar","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2024.110916_bb0205","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.ygeno.2024.110916_bb0210","doi-asserted-by":"crossref","DOI":"10.3390\/diagnostics12112704","article-title":"Genetic analyses of cell-free DNA in pancreatic juice or bile for diagnosing pancreatic duct and biliary tract strictures","volume":"12","author":"Nagai","year":"2022","journal-title":"Diagnostics"},{"key":"10.1016\/j.ygeno.2024.110916_bb0215","article-title":"Bile is a reliable and valuable source to study cfDNA in biliary tract cancers","volume":"12","author":"Li","year":"2022","journal-title":"Front. Oncol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0220","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1016\/j.ejca.2019.07.022","article-title":"Therapeutic relevance of targeted sequencing in management of patients with advanced biliary tract cancer: DNA damage repair gene mutations as a predictive biomarker","volume":"120","author":"Chae","year":"2019","journal-title":"Eur. J. Cancer"},{"key":"10.1016\/j.ygeno.2024.110916_bb0225","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.cancergen.2014.02.003","article-title":"22q11-q13 as a hot spot for prediction of disease-free survival in bile duct cancer: integrative analysis of copy number variations","volume":"207","author":"Kang","year":"2014","journal-title":"Cancer Gene Ther."},{"key":"10.1016\/j.ygeno.2024.110916_bb0230","doi-asserted-by":"crossref","first-page":"23825","DOI":"10.18632\/oncotarget.8183","article-title":"Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations","volume":"7","author":"Kim","year":"2016","journal-title":"Oncotarget"},{"key":"10.1016\/j.ygeno.2024.110916_bb0235","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/s41588-019-0576-7","article-title":"Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing","volume":"52","author":"Cortes-Ciriano","year":"2020","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ygeno.2024.110916_bb0240","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.gde.2012.02.012","article-title":"Mechanisms for recurrent and complex human genomic rearrangements","volume":"22","author":"Liu","year":"2012","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.ygeno.2024.110916_bb0245","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41586-020-03064-z","article-title":"Chromothripsis drives the evolution of gene amplification in cancer","volume":"591","author":"Shoshani","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.ygeno.2024.110916_bb0250","doi-asserted-by":"crossref","first-page":"652","DOI":"10.21037\/jgo.2018.08.18","article-title":"Molecular profiling of biliary cancers reveals distinct molecular alterations and potential therapeutic targets","volume":"10","author":"Weinberg","year":"2019","journal-title":"J. Gastrointest. Oncol."},{"key":"10.1016\/j.ygeno.2024.110916_bb0255","doi-asserted-by":"crossref","DOI":"10.3389\/fonc.2020.567289","article-title":"Case report: BAP1 mutation and RAD21 amplification as predictive biomarkers to PARP inhibitor in metastatic intrahepatic cholangiocarcinoma","volume":"10","author":"Sabbatino","year":"2020","journal-title":"Front. Oncol."}],"container-title":["Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S088875432400137X?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S088875432400137X?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T06:59:08Z","timestamp":1728370748000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S088875432400137X"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9]]},"references-count":51,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2024,9]]}},"alternative-id":["S088875432400137X"],"URL":"https:\/\/doi.org\/10.1016\/j.ygeno.2024.110916","relation":{},"ISSN":["0888-7543"],"issn-type":[{"value":"0888-7543","type":"print"}],"subject":[],"published":{"date-parts":[[2024,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Identification of whole-genome mutations and structural variations of bile cell-free DNA in cholangiocarcinoma","name":"articletitle","label":"Article Title"},{"value":"Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ygeno.2024.110916","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"110916"}}