Lymphoma: Methods and Protocols

Description

This second edition volume expands on the previous edition with descriptions of recent developments in the field. The new and updated chapters discuss the latest approaches for studying single cell RNA sequencing, whole genome sequencing data, CRISPR/Cas9-mediated gene knockout, protein interactions by a proximity ligation assay, and detection of circulating cell-free tumor DNA in lymphomas. Written in the highly successful Methods in Molecular Biology series format, 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. Innovative and thorough, Lymphoma: Methods and Protocols, Second Edition is a valuable resource for hematologists, hematopathologists, and any scientists interested in cancer research, human genetics, and immunology. Front Matter ....Pages i-xii Origin and Pathogenesis of B Cell Lymphomas (Marc Seifert, René Scholtysik, Ralf Küppers)....Pages 1-33 Flow Cytometry for Non-Hodgkin and Hodgkin Lymphomas (Emily Glynn, Lori Soma, David Wu, Brent L. Wood, Jonathan R. Fromm)....Pages 35-60 Laser-Based Microdissection of Single Cells from Tissue Sections and PCR Analysis of Rearranged Immunoglobulin Genes from Isolated Normal and Malignant Human B Cells (Ralf Küppers, Markus Schneider, Martin-Leo Hansmann)....Pages 61-75 PCR GeneScan and Heteroduplex Analysis of Rearranged Immunoglobulin or T-Cell Receptor Genes for Clonality Diagnostics in Suspect Lymphoproliferations (Elke Boone, Kim C. Heezen, Patricia J. T. A. Groenen, Anton W. Langerak, On behalf of the EuroClonality Consortium)....Pages 77-103 Expression Cloning of Antibodies from Single Human B Cells (Hedda Wardemann, Christian E. Busse)....Pages 105-125 Studying the Replication History of Human B Lymphocytes by Real-Time Quantitative (RQ-)PCR (Menno C. van Zelm)....Pages 127-138 Stereotyped B Cell Receptor Immunoglobulins in B Cell Lymphomas (Andreas Agathangelidis, Fotis Psomopoulos, Kostas Stamatopoulos)....Pages 139-155 Flow Cytometric MRD Detection in Selected Mature B-Cell Malignancies (Sebastian Böttcher)....Pages 157-197 MRD Detection in B-Cell Non-Hodgkin Lymphomas Using Ig Gene Rearrangements and Chromosomal Translocations as Targets for Real-Time Quantitative PCR (Christiane Pott, Monika Brüggemann, Matthias Ritgen, Vincent H. J. van der Velden, Jacques J. M. van Dongen, Michael Kneba)....Pages 199-228 Generation of Whole Genome Bisulfite Sequencing Libraries from Very Low DNA Input (Dieter Weichenhan, Charles D. Imbusch, Qi Wang, Benedikt Brors, Christoph Plass)....Pages 229-248 FISH and FICTION in Lymphoma Research (Maciej Giefing, Reiner Siebert)....Pages 249-267 NGS-Based High-Throughput Screen to Identify MicroRNAs Regulating Growth of B-Cell Lymphoma (Joost Kluiver, Fubiao Niu, Ye Yuan, Klaas Kok, Anke van den Berg, Agnieszka Dzikiewicz-Krawczyk)....Pages 269-282 RNA Sequencing in B-Cell Lymphomas (Da Wei Huang, Moez Dawood, Calvin A. Johnson, Roland Schmitz)....Pages 283-303 Studying Cancer Heterogeneity by Single-Cell RNA Sequencing (Johannes W. Bagnoli, Lucas E. Wange, Aleksandar Janjic, Wolfgang Enard)....Pages 305-319 Evaluation of Whole Genome Sequencing Data (Daniel Hübschmann, Matthias Schlesner)....Pages 321-336 Protocols for CRISPR-Cas9 Screening in Lymphoma Cell Lines (Daniel E. Webster, Sandrine Roulland, James D. Phelan)....Pages 337-350 Lymphoma and Leukemia Cell Vulnerabilities and Resistance Identified by Compound Library Screens (Katarzyna Tomska, Sebastian Scheinost, Thorsten Zenz)....Pages 351-362 Proximity Ligation Assay (Ryan M. Young)....Pages 363-370 Phosphoproteomic Analysis of Signaling Pathways in Lymphomas (Björn Häupl, Henning Urlaub, Thomas Oellerich)....Pages 371-381 Ultrasensitive Detection of Circulating Tumor DNA in Lymphoma via Targeted Hybridization Capture and Deep Sequencing of Barcoded Libraries (Miguel Alcaide, Christopher Rushton, Ryan D. Morin)....Pages 383-435 Back Matter ....Pages 437-439