Chromothripsis

Description

This detailed book presents an up-to-date view on methods and experimental approaches developed to identify and explore the chromothripsis phenomenon. Beginning with a section exploring the genesis and impact of chromothripsis, the collection continues by covering the identification of chromothripsis, the causal mechanisms of chromothripsis, the bioinformatics tools for chromothripsis analysis, and experimental systems recently developed for the in vitro investigation of chromothripsis. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Chromothripsis: Methods and Protocols serves as a vital resource for cell biologists, molecular biologists, cytogeneticists, and geneticists investigating chromothripsis, but also for students and researchers new to the field of chromothripsis and genomic instability. Front Matter ....Pages i-xi Front Matter ....Pages 1-1 The Genomic Characteristics and Origin of Chromothripsis (Alessio Marcozzi, Franck Pellestor, Wigard P. Kloosterman)....Pages 3-19 Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events (Maki Fukami, Hiroki Kurahashi)....Pages 21-33 Potential Role of Chromothripsis in the Genesis of Complex Chromosomal Rearrangements in Human Gametes and Preimplantation Embryo (Franck Pellestor, Vincent Gatinois)....Pages 35-41 Chromothripsis and the Macroevolution Theory (Franck Pellestor)....Pages 43-49 Front Matter ....Pages 51-51 Analysis of Chromothripsis by Combined FISH and Microarray Analysis (Ruth N. MacKinnon)....Pages 53-77 Chromothripsis Detectable in Small Supernumerary Marker Chromosomes (sSMC) Using Fluorescence In Situ Hybridization (FISH) (Thomas Liehr)....Pages 79-84 Identification of Chromothripsis in Biopsy Using SNP-Based Microarray (Veronica Ortega, Christina Mendiola, Gopalrao V. N. Velagaleti)....Pages 85-117 Detection of Chromothripsis in Plants (Isabelle M. Henry, Luca Comai, Ek Han Tan)....Pages 119-132 RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis (Anne-Laure Bougé, Florence Rufflé, Sébastien Riquier, Benoit Guibert, Jérôme Audoux, Thérèse Commes)....Pages 133-156 Front Matter ....Pages 157-157 Experimental Determination of Checkpoint Adaptation by Mitotic Shake-Off and Microscopy (Lucy H. Swift, Roy M. Golsteyn)....Pages 159-168 A Role for Retrotransposons in Chromothripsis (Dustin C. Hancks)....Pages 169-181 Generation of Micronuclei and Detection of Chromosome Pulverization (Monique N. H. Luijten, Jeannie X. T. Lee, Sixun Chen, Karen C. Crasta)....Pages 183-195 Detection of Impaired DNA Replication and Repair in Micronuclei as Indicators of Genomic Instability and Chromothripsis (Mariona Terradas, Marta Martín, Anna Genescà)....Pages 197-208 Study of Telomere Dysfunction in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability (Oumar Samassekou, Nathalie Bastien, Ju Yan, Sabine Mai, Régen Drouin)....Pages 209-230 Genes, Proteins, and Biological Pathways Preventing Chromothripsis (Martin Poot)....Pages 231-251 Expression of Genes Associated with Telomere Homeostasis in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability (Oumar Samassekou, Nathalie Bastien, Ju Yan, Sabine Mai, Régen Drouin)....Pages 253-262 Front Matter ....Pages 263-263 Chromothripsis Detection and Characterization Using the CTLPScanner Web Server (Jian Yang, Bo Liu, Haoyang Cai)....Pages 265-278 ChromothripsisDB: A Curated Database for the Documentation, Visualization, and Mining of Chromothripsis Data (Haoyang Cai)....Pages 279-289 Front Matter ....Pages 291-291 Time-Lapse Imaging for the Detection of Chromosomal Abnormalities in Primate Preimplantation Embryos (Brittany L. Daughtry, Shawn L. Chavez)....Pages 293-317 Correlative Live Imaging and Immunofluorescence for Analysis of Chromosome Segregation in Mouse Preimplantation Embryos (Cayetana Vázquez-Diez, Greg FitzHarris)....Pages 319-335 Experimental Induction of Genome Chaos (Christine J. Ye, Guo Liu, Henry H. Heng)....Pages 337-352 Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Change Analysis in Complex Chromosomal Rearrangements and Chromothripsis (Kevin Yauy, Vincent Gatinois, Thomas Guignard, Satish Sati, Jacques Puechberty, Jean Baptiste Gaillard et al.)....Pages 353-361 Back Matter ....Pages 363-367