Chromothripsis: Methods and Protocols

Part I: Genesis and Impact of Chromothripsis

1. The Genomic Characteristics and Origin of Chromothripsis

Alessio Marcozzi, Franck Pellestor, and Wigard P. Kloosterman

2. Clinical Consequences of Chromothripsis and Other Catastrophic Cellular Events

Maki Fukami and Hiroki Kurahashi

3. Potential Role of Chromothripsis in the Genesis of Complex Chromosomal Rearrangements in Human Gametes and Preimplantation Embryo

Franck Pellestor and Vincent Gatinois

4. Chromothripsis and the Macroevolution Theory

Franck Pellestor

Part II: The Identification of Chromothripsis

5. Analysis of Chromothripsis by Combined FISH and Microarray Analysis

Ruth N. MacKinnon

6. Chromothripsis Detectable in Small Supernumerary Marker Chromosomes (sSMC) Using Fluorescence In Situ Hybridization (FISH)

Thomas Liehr

7. Identification of Chromothripsis in Biopsy Using SNP-Based Microarray

Veronica Ortega, Christina Mendiola, and Gopalrao Velagaleti

8. Detection of Chromothripsis in Plants

Isabelle M. Henry, Luca Comai, and Ek Han Tan

9. RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis

Part III: The Causal Mechanisms of Chromothripsis

10. Experimental Determination of Checkpoint Adaptation by Mitotic Shake-Off and Microscopy

Lucy H. Swift and Roy M. Golsteyn

11. A Role for Retrotransposons in Chromothripsis

Dustin C. Hancks

12. Generation of Micronuclei and Detection of Chromosome Pulverization

Monique N.H. Luijten, Jeannie X.T. Lee, Sixun Chen, and Karen C. Crasta

13. Detection of Impaired DNA Replication and Repair in Micronuclei as Indicators of Genomic Instability and Chromothripsis

Mariona Terradas, Marta Mart?n, and Anna Genesc?

14. Study of Telomere Dysfunction in TP53 Mutant LoVo Cell Lines as a Model for Genomic Instability

Oumar Samassekou, Nathalie Bastien, Ju Yan, Sabine Mai, and R?gen Drouin

15. Genes, Proteins, and Biological Pathways Preventing Chromothripsis

Martin Poot

16. 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, and R?gen Drouin

Part IV: The Bioinformatic Tools for Chromothripsis Analysis

17. Chromothripsis Detection and Characterization Using the CTLPScanner Web Server

18. ChromothripsisDB: A Curated Database for the Documentation, Visualization, and Mining of Chromothripsis Data

Haoyang Cai

Part V: The Experimental Models

19. Time-Lapse Imaging for the Detection of Chromosomal Abnormalities in Primate Pre-Implantation Embryos

Brittany L. Daughtry and Shawn L. Chavez

20. Correlative Live Imaging and Immunofluorescence for Analysis of Chromosome Segregation in Mouse Preimplantation Embryos