Chromothripsis Detection and Characterization Using the CTLPScanner Web Server.

Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner ( http://cgma.scu.edu.cn/CTLPScanner/ ) is a web-based tool for identification and annotation of chromothripsis-like pattern (CTLP) in genomic array data. In this chapter, we illustrate the utility of CTLPScanner for screening chromosome pulverization regions and give interpretation of the results. The web interface offers a set of parameters and thresholds for customized screening. We also provide practical recommendations for effective chromothripsis detection. In addition to the user data processing module, CTLPScanner contains more than 50,000 preprocessed oncogenomic arrays, which allow users to explore the presence of chromothripsis signatures from public data resources.

[1]  J. Korbel,et al.  Criteria for Inference of Chromothripsis in Cancer Genomes , 2013, Cell.

[2]  N. Munshi,et al.  Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients. , 2011, Blood.

[3]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[4]  Sean R. Davis,et al.  NCBI GEO: archive for functional genomics data sets—update , 2012, Nucleic Acids Res..

[5]  P. Stankiewicz,et al.  Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements , 2011, Cell.

[6]  N. Carter,et al.  Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development , 2011, Cell.

[7]  Ni Ai,et al.  arrayMap 2014: an updated cancer genome resource , 2014, Nucleic Acids Res..

[8]  A. Børresen-Dale,et al.  Copynumber: Efficient algorithms for single- and multi-track copy number segmentation , 2012, BMC Genomics.

[9]  M. Robinson,et al.  Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens , 2014, BMC Genomics.

[10]  David T. W. Jones,et al.  Telomere dysfunction and chromothripsis , 2016, International journal of cancer.

[11]  Joachim Weischenfeldt,et al.  A cell-based model system links chromothripsis with hyperploidy , 2015, Molecular systems biology.

[12]  Stephen P. Jackson,et al.  Chromothripsis and cancer: causes and consequences of chromosome shattering , 2012, Nature Reviews Cancer.

[13]  Peter J. Campbell,et al.  Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia , 2014, Nature.

[14]  Markus J. van Roosmalen,et al.  Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer , 2011, Genome Biology.

[15]  C. Harrison,et al.  Blood Spotlight on iAMP21 acute lymphoblastic leukemia (ALL), a high-risk pediatric disease. , 2015, Blood.

[16]  Mingming Jia,et al.  COSMIC: exploring the world's knowledge of somatic mutations in human cancer , 2014, Nucleic Acids Res..

[17]  J. Naus.  The Distribution of the Size of the Maximum Cluster of Points on a Line , 1965 .

[18]  Emmanuel Barillot,et al.  Analysis of array CGH data: from signal ratio to gain and loss of DNA regions , 2004, Bioinform..

[19]  D. Zwijnenburg,et al.  Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes , 2012, Nature.

[20]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[21]  Jian Yang,et al.  CTLPScanner: a web server for chromothripsis-like pattern detection , 2016, Nucleic Acids Res..

[22]  David T. W. Jones,et al.  Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations , 2012, Cell.

[23]  Sean Davis,et al.  Chromothripsis and focal copy number alterations determine poor outcome in malignant melanoma. , 2013, Cancer research.

[24]  Pablo H. Hennings-Yeomans,et al.  ShatterProof: operational detection and quantification of chromothripsis , 2014, BMC Bioinformatics.