Chronic Lymphocytic Leukemia: Methods and Protocols

Description

This book aims to provide scientists with tools and well-researched protocols to enable their research and to facilitate further progress in this common leukemia. 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. Authoritative and cutting-edge, Chronic Lymphocytic Leukemia: Methods and Protocols aims to accelerate research on chronic lymphocytic leukemia and further improvements in patient outcomes. Front Matter ....Pages i-xii Ex-Vivo Signal Transduction Studies in Chronic Lymphocytic Leukemia (Karly-Rai Rogers-Broadway, Laura I. Karydis, Rachel C. Dobson, Andrew J. Steele)....Pages 1-17 Ex Vivo Pharmacological Profiling in Chronic Lymphocytic Leukemia Cells (Burcu Aslan, Mary L. Ayres, Varsha Gandhi)....Pages 19-25 Culture and Harvest of CpG-Stimulated Peripheral Blood or Bone Marrow in Chronic Lymphocytic Leukemia (Cecelia R. Miller, Nyla A. Heerema)....Pages 27-34 Analysis of Common Abnormalities Seen in Chronic Lymphocytic Leukemia Using Fluorescence In Situ Hybridization (Reid G. Meyer, Daniel L. Van Dyke)....Pages 35-49 Immunoglobulin Gene Analysis in Chronic Lymphocytic Leukemia (Andreas Agathangelidis, Richard Rosenquist, Frederic Davi, Paolo Ghia, Chrysoula Belessi, Anastasia Hadzidimitriou et al.)....Pages 51-62 Detection and Functional Analysis of TP53 Mutations in CLL (Sarka Pavlova, Jana Smardova, Nikola Tom, Martin Trbusek)....Pages 63-81 The Development and Use of Scalable Systems for Studying Aberrant Splicing in SF3B1-Mutant CLL (Tushar Murthy, Kiran V. Paul, Alexander C. Minella, Manoj M. Pillai)....Pages 83-99 Methods for Investigating VLA-4 (CD49d/CD29) Expression and Activation in Chronic Lymphocytic Leukemia and Its Clinical Applications (Antonella Zucchetto, Erika Tissino, Alexander Chigaev, Tanja Nicole Hartmann, Valter Gattei)....Pages 101-112 In Vitro Assay to Study CLL and Monocyte Interactions (Maria Teresa Sabrina Bertilaccio, Ronghua Zhang, Priyanka Banerjee, Varsha Gandhi)....Pages 113-119 Extracellular Flux Assays to Determine Oxidative Phosphorylation and Glycolysis in Chronic Lymphocytic Leukemia Cells (Hima V. Vangapandu, Varsha Gandhi)....Pages 121-128 Measurement of Leukemic B-Cell Growth Kinetics in Patients with Chronic Lymphocytic Leukemia (Andrea N. Mazzarello, Mark Fitch, Marc K. Hellerstein, Nicholas Chiorazzi)....Pages 129-151 Assays on DNA Damage and Repair in CLL (Tzung-Huei Lai, Deepa Sampath)....Pages 153-163 Method for Generating a Patient-Derived Xenograft Model of CLL (Shih-Shih Chen)....Pages 165-171 Immunological Methods to Study Monoclonal Antibody Activity in Chronic Lymphocytic Leukaemia (M. J. Carter, L. N. Dahal, K. L. S. Cleary, M. J. E. Marshall, R. R. French, S. A. Beers et al.)....Pages 173-184 CRISPR/Cas9-Based Gene Dropout Screens (Kai Wu, Sami N. Malek)....Pages 185-200 Gene Disruption Using CRISPR-Cas9 Technology (Nan Hu, Sami N. Malek)....Pages 201-209 Minimal Residual Disease Quantification in Chronic Lymphocytic Leukemia: Clinical Significance and Flow Cytometric Methods (Sebastian Böttcher)....Pages 211-238 Rare Variant Quantitation Using Droplet Digital PCR (Brian Parkin)....Pages 239-251 Methods for Measuring ctDNA in Lymphomas (Davide Rossi, Adalgisa Condoluci, Valeria Spina, Gianluca Gaidano)....Pages 253-265 Measurement of miRNAs in Chronic Lymphocytic Leukemia Patient Samples by Quantitative Reverse Transcription PCR (Katrien Van Roosbroeck, Recep Bayraktar, George A. Calin)....Pages 267-276 Bioinformatics Analysis of Whole Exome Sequencing Data (Peter J. Ulintz, Weisheng Wu, Chris M. Gates)....Pages 277-318 Genome Sequencing and Analysis Methods in Chronic Lymphocytic Leukemia (Víctor Quesada, Miguel Araujo-Voces, José G. Pérez-Silva, Gloria Velasco, Carlos López-Otín)....Pages 319-325 Characterization of Somatically-Acquired Copy Number Alterations in Chronic Lymphocytic Leukaemia Using Shallow Whole Genome Sequencing (Helen Parker, Louise Carr, Sharma Syeda, Dean Bryant, Jonathan C. Strefford)....Pages 327-353 High-Throughput Sequencing of the T-Cell Receptor Beta Chain Gene Repertoire in Chronic Lymphocytic Leukemia (E. Vlachonikola, A. Vardi, K. Stamatopoulos, A. Hadzidimitriou)....Pages 355-363 Back Matter ....Pages 365-373