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Preface…Table of Contents…Contributing Authors…Part I Background Concepts1. Entering the Pantheon of 21st Century Molecular Biology Tools: A Perspective on Digital PCRGeorge Karlin-Neumann and Frank Bizouarn2. Basic Concepts and Validation of Digital PCR MeasurementsLeonardo Pinheiro and Kerry R. Emslie3. Fundamentals of Counting Statistics in Digital PCR: I Just Measured Two Target Copies, What Does it Mean?Svilen Tzonev4. Control Materials and Digital PCR Methods for Evaluation of Circulating Cell Free DNA Extractions from PlasmaAlexandra S. Whale, Ana Fernandez-Gonzalez, Alice Gutteridge, and Alison S. DevonshirePart II Absolute Quantification5. Multiplex Droplet Digital PCR Protocols for Quantification of GM Maize EventsDavid Dobnik, Bjørn Spilsberg, Alexandra Bogožalec, Dejan Štebih, Dany Morisset, Arne Holst-Jensen and Jana Žel6. Using Droplet Digital PCR to Detect Coinfection of Human Herpesviruses 6A and 6B (HHV-6A and HHV-6B) in Clinical SamplesAshlet Vellucci, Emily Leibovitch, and Steven Jacobson7. Biomarkers in Cerebrospinal Fluid: Analysis of Cell-Free Circulating Mitochondrial DNA by Digital PCRPetar Podlesniy and Ramon Trullas8. Testing of General and Human-Associated Fecal Contamination in WatersYiping Cao, Mereditch R. Raith, and John F. GriffithPart III Copy Number Variation9. Analyzing Copy Number Variation with Droplet Digital PCRAvery Davis Bell, Christina L. Usher, and Steven A. McCarroll10. Assessing HER2 Amplification in Plasma cfDNAIsaac Garcia-Murillas and Nick Turner11. Detection and Quantification of Mosaic Genomic DNA Variation in Primary Somatic Tissues using ddPCR: Analysis of Mosaic Transposable-Element Insertions, Copy-Number Variants, and Single-Nucleotide VariantsBo Zhou, Michael S. Haney, Xiaowei Zhu, Reenal Pattni, Alexej Abyzov, and Alexander E. UrbanPart IV Rare Mutation and Rare Allele Detection12. Monitoring of Response and Resistance in Plasma of EGFR-Mutant Lung Cancer using Droplet Digital PCRYanan Kuang, Adrian G. Sacher, Allison O’Connell, Nora Feeney, Ryan S. Alden, Geoffrey R. Oxnard, and Cloud P. Paweletz13. Detection of Cancer DNA in Early Stage and Metastatic Breast Cancer PatientsArielle J. Medford, Riaz N. Gillani, and Ben Ho Park14. Droplet Digitial PCR for Miniaml Residual Disease Detection in Mature Lymphoproliferative DisordersDaniela Drandi, Simone Ferrero, and Marco Ladetto15. Quantitation of JAK2 V617F Allele Burden by using the QuantStudio™ 3D Digitial PCR SystemElena Kinz and Axel Muendlein16. Novel Multiplexing Strategies for Quantification of Rare Alleles using ddPCRMiguel Alcaide and Ryan Morin17. Identification and Use of Personalized Genomic Markers for Monitoring Circulating Tumor DNAYilun Chen, Anthony George, Eleonor Olsson, and Lao H. Saal18. Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant GenotypingChristina Wood and Hanlee P. Ji19. A Universal Droplet Digital PCR Approach for Monitoring of Graft Health after Transplantation using a Pre-Selected SNP SetJulia Beck, Michael Oellerich, and Ekkehard Schütz20. Detection and Quantification of HDR and NHEJ Induced by Genome Editing at Endogenous Gene Loci using Droplet Digital PCRYuichiro Miyaoka, Steven J. Mayer, Amanda H. Chan, and Bruce R. Conklin21. DNA Methylation Analysis Using Droplet Digital PCRMing Tu, Tai J. Heinzerling, and William M. GradyPart V Gene Expression and RNA Quantification22. Simultaneous Quantification of Multiple Alternatively Spliced mRNA Transcripts using Droplet Digital PCRBing Sun and Yun-Ling Zheng23. Using Droplet Digital PCR to Analyze Allele-Specific RNA ExpressionNolan Kamitaki, Christina L. Usher, and Steven A. McCarroll24. Very Low Abundance Single-Cell Transcript Quantification with 5-Plex ddPCR™ AssaysGeorge Karlin-Neumann, Bin Zhang, and Claudia Litterst25. Quantification of Circulating MicroRNAs by Droplet Digital PCR using EvaGreen Probeless ChemistryManuela Ferracin and Massimo Negrini26. Droplet Digital PCR for Absolute Quantification of Extracellular MicroRNAs in Plasma and Serum: Quantification of the Cancer Biomarker has-miR-141Maria D. Giraldez, John R. Chevillet, and Muneesh TewaruPart VI Other Usses of Partitioning27. Droplet Digital™ PCR Next-Generation Sequencing Library QC AssayNick Heredia28. Phasing DNA Markers using Digital PCRJack Regan and George Karlin-Neumann29. ddTRAP: A Method for Sensitive and Precise Quantification of Telomerase ActivityAndrew T. Ludlow, Dawne Shelton, Woodring E. Wright, and Jerry W. Shay30. Highly Efficient and Reliable DNA Aptamer Selection Using the Partitioning Capabilities of ddPCR: The Hi-Fi SELEX MethodAaron Ang, Eric Quellet, Karen C. Cheung, and Charles Haynes