Part I: Core Techniques 1. Fluorescence in situ Hybridization (FISH), Basic Principles, and Methodology Elisa Garimberti and Sabrina Tosi 2. Fluorescence in situ Hybridization on DNA Halo Preparations and Extended Chromatin Fibers Lauren S. Elcock and Joanna M. Bridger 3. Detection of Nascent RNA Transcripts by Fluorescence in situ Hybridization Jill M. Brown and Veronica J. Buckle 4. Fluorescence in situ Hybridization Analysis of Formalin Fixed Paraffin Embedded Tissues, Including Tissue Microarrays Brenda M. Summersgill and Janet M. Shipley 5. Fluorescence in situ Hybridization (FISH) on Tissue Cryosections Irina Solovei 6. Multiplex Fluorescence in situ Hybridization (M-FISH) Rhona Anderson 7. Optical Mapping of Protein-DNA Complexes on Chromatin Fibers Beth Sullivan 8. 3D-FISH on Cultured Cells Combined with Immunostaining Irina Solovei and Marion Cremer Part II: Technical Advancements and Novel Adaptations 9. The Comet-FISH Assay for the Analysis of DNA Damage and Repair Graciela Spivak 10. Direct in situ Hybridization with Oligonucleotide Functionalized Quantum Dot Probes Laurent A. Bentolila 11. LNA-FISH for Detection of microRNAs in Frozen Sections Asli N. Silahtaroglu 12. Chromosome Orientation Fluorescence in situ Hybridization (CO-FISH) or Strand-Specific FISH Susan M. Bailey, Eli S. Williams, Michael N. Cornforth, and Edwin H. Goodwin 13. Combinatorial Oligo FISH: Directed Labeling of Specific Genome Domains in Differentially Fixed Cell Material and Live Cells Eberhard Schmitt, Jutta Schwarz-Finsterle, Stefan Stei, Carmen Boxler, Patrick Muller, Andriy Mokhir, Roland Kramer, Christoph Cremer, and Michael Hausmann 14. Simultaneous Visualization of FISH Signals and Bromo-deoxyuridine Incorporation by Formamide-Free DNA Denaturation Daniela Moralli and Zoia L. Monaco 15. CryoFISH: Fluorescence in situ Hybridization on Ultrathin Cryosections Sheila Q. Xie, Liron-Mark Lavitas, and Ana Pombo 16. Characterization ofChromosomal Rearrangements Using Multicolor-Banding (MCB/m-band) Thomas Liehr, Anja Weise, Sophie Hinreiner, Hasmik Mkrtchyan, Kristin Mrasek, and Nadezda Kosyakova 17. Visualizing Nucleic Acids in Living Cells by Fluorescence in vivo Hybridization Joop Wiegant, Anneke K. Brouwer, Hans J. Tanke, and Roeland W. Dirks Part III: Translational FISH: Applications for Human Genetics and Medicine 18. Quality Control in FISH as Part of a Laboratory's Quality Management System Ros Hastings 19. FlashFISH: Same Day Prenatal Diagnosis of Common Chromosomal Aneuploidies Sherry Ho and Mahesh A. Choolani 20. FISH for Pre-Implantation Genetic Diagnosis Paul N. Scriven and Caroline Mackie Ogilvie 21. PNA-FISH on Human Sperm Franck Pellestor, Cecile Monzo, and Samir Hamamah 22. POD-FISH: A New Technique for Parental Origin Determination Based on Copy Number Variation Polymorphism Anja Weise, Madeleine Gross, Sophie Hinreiner, Vera Witthuhn, Hasmik Mkrtchyan, and Thomas Liehr 23. Sequence-Based High Resolution Chromosomal Comparative Genomic Hybridization (CGH) Agata Kowalska, Eva Bozsaky, and Peter F. Ambros 24. ImmunoFISH on Isolated Nuclei from Paraffin-Embedded Biopsy Material Soo-Yong Tan and Goran Mattsson 25. Fluorescence in situ Hybridization on 3D Cultures of Tumor Cells Karen J. Meaburn 26. Simultaneous Ultrasensitive Subpopulation Staining/Hybridization in situ (SUSHI) in HIV-1 Disease Monitoring Bruce Patterson Part IV: Protocols for Model Organisms 27. Detection of Prokaryotic Cells with Fluorescence in situ Hybridization Katrin Zwirglmaier 28. FISH as a Tool to Investigate Chromosome Behavior in Budding Yeast Harry Scherthan and Josef Loidl 29. FISH on Chromosomes Derived from the Snail Model Organism Biomphalaria glabrata Edwin C. Odoemelam, Nithya Raghavan, Wannaporn Ittiprasert, Andre Miller, Joanna M. Bridger, and Matty Knight 30. Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (BACs) to Mitotic