COSINE:A web server for clonal and subclonal structure inference and evolution in cancer genomics

作     者：Xi-Guo Yuan Yuan Zhao Yang Guo Lin-Mei Ge Wei Liu Shi-Yu Wen Qi Li Zhang-Bo Wan Pei-Na Zheng Tao Guo Zhi-Da Li Martin Peifer Yu-Peng Cun Xi-Guo Yuan;Yuan Zhao;Yang Guo;Lin-Mei Ge;Wei Liu;Shi-Yu Wen;Qi Li;Zhang-Bo Wan;Pei-Na Zheng;Tao Guo;Zhi-Da Li;Martin Peifer;Yu-Peng Cun

作者机构：School of Computer Science and TechnologyXidian UniversityXi'anShaanxi 710071China iFlora Bioinformatics CenterGermplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunan 650201China Yuxi Rongjian Information Technology Co.Ltd.YuxiYunan 653100China Center for Molecular Medicine Cologne(CMMC)University of CologneCologne 50931Germany Pediatric Research InstituteMinistry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory DisordersChildren’s Hospital of Chongqing Medical UniversityChongqing 400014China 

出 版 物：《Zoological Research》 (动物学研究（英文）)

年 卷 期：2022年第43卷第1期

页      面：75-77页

核心收录：

学科分类：0831[工学-生物医学工程（可授工学、理学、医学学位）] 0711[理学-系统科学] 1002[医学-临床医学] 07[理学] 08[工学] 100214[医学-肿瘤学] 10[医学] 

基　　金：supported by the CAS Pioneer Hundred Talents Program and National Natural Science Foundation of China(32070683)to Y.P.C the Science and Technology Planning Project of XI'AN(GXYD6.2) National Natural Science Foundation of China(61771369)to X.G.Y 

主　　题：.net server COSINE 

摘      要：Cancer cell genomes originate from single-cell mutation with sequential clonal and subclonal expansion of somatic mutation acquisition during pathogenesis,thus exhibiting a Darwinian evolutionary process(Gerstung et al.,2020;Nik-Zainal et al.,2012).Through next-generation sequencing of tumor tissue,this evolutionary process can be characterized by statistical modelling,which can identify the clonal state,somatic mutation order,and evolutionary process(Gerstung et al.,2020;Mcgranahan&Swanton,2017).Inference of clonal and subclonal structure from bulk or single-cell tumor genomic sequencing data has a huge impact on studying cancer *** state and mutation order can provide detailed insight into tumor origin and future *** the past decade,various methods for subclonal reconstruction using bulk tumor sequencing data have been ***,these methods had different programming languages and data input formats,which limited their use and ***,we established a web server for Clonal and Subclonal Structure Inference and Evolution(COSINE)of cancer genomic data,which incorporated twelve popular subclonal reconstruction *** deconstructed each method to provide a detailed workflow of single processing steps with a user-friendly *** the best of our knowledge,this is the first web server providing online subclonal inference based on the integration of most popular subclonal reconstruction *** is freely accessible at ***.