title: CTLPScanner: a web server for chromothripsis-like pattern detection.
abstract: Chromothripsis is a recently observed phenomenon in cancer cells in which one or several chromosomes shatter into pieces with subsequent inaccurate reassembly and clonal propagation. This type of event generates a potentially vast number of mutations within a relatively short-time period, and has been considered as a new paradigm in cancer development. Despite recent advances, much work is still required to better understand the molecular mechanisms of this phenomenon, and thus an easy-to-use tool is in urgent need for automatically detecting and annotating chromothripsis. Here we present CTLPScanner, a web server for detection of chromothripsis-like pattern (CTLP) in genomic array data. The output interface presents intuitive graphical representations of detected chromosome pulverization region, as well as detailed results in table format. CTLPScanner also provides additional information for associated genes in chromothripsis region to help identify the potential candidates involved in tumorigenesis. To assist in performing meta-data analysis, we integrated over 50 000 pre-processed genomic arrays from The Cancer Genome Atlas and Gene Expression Omnibus into CTLPScanner. The server allows users to explore the presence of chromothripsis signatures from public data resources, without carrying out any local data processing. CTLPScanner is freely available at http://cgma.scu.edu.cn/CTLPScanner/.
authors.affiliation: Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Yang
authors.affiliation: Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China.
authors.forename: Jixiang
authors.initials: J
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Ouyang
authors.affiliation: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, Sichuan, China liubo2400@scu.edu.cn.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu 610064, Sichuan, China haoyang.cai@scu.edu.cn.
authors.forename: Haoyang
authors.initials: H
authors.lastname: Cai
mesh_terms: D001271:Atlases as Topic; D002471:Cell Transformation, Neoplastic / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000737:chemistry*; D000072837:Chromothripsis; D003196:Computer Graphics; D030541:Databases, Genetic; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D059645:Mutation Rate; D009363:Neoplasm Proteins / Q000235:genetics* / Q000378:metabolism; D009369:Neoplasms / Q000145:classification / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D014584:User-Computer Interface
chemical_list: D009363:Neoplasm Proteins