Digital PCR: Methods and Protocols

Preface...Table of Contents...Contributing Authors...
Part I Background Concepts
1. Entering the Pantheon of 21st Century Molecular Biology Tools: A Perspective on Digital PCRGeorge Karlin-Neumann and Frank Bizouarn
2. Basic Concepts and Validation of Digital PCR MeasurementsLeonardo Pinheiro and Kerry R. Emslie
3. Fundamentals of Counting Statistics in Digital PCR: I Just Measured Two Target Copies, What Does it Mean?Svilen Tzonev
4. 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. Devonshire
Part II Absolute Quantification
5. Multiplex Droplet Digital PCR Protocols for Quantification of GM Maize EventsDavid Dobnik, Bj rn Spilsberg, Alexandra Bogozalec, Dejan Stebih, Dany Morisset, Arne Holst-Jensen and Jana Zel
6. 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 Jacobson
7. Biomarkers in Cerebrospinal Fluid: Analysis of Cell-Free Circulating Mitochondrial DNA by Digital PCRPetar Podlesniy and Ramon Trullas
8. Testing of General and Human-Associated Fecal Contamination in WatersYiping Cao, Mereditch R. Raith, and John F. Griffith
Part III Copy Number Variation
9. Analyzing Copy Number Variation with Droplet Digital PCRAvery Davis Bell, Christina L. Usher, and Steven A. McCarroll
10. Assessing HER2 Amplification in Plasma cfDNAIsaac Garcia-Murillas and Nick Turner
11. 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. Urban
Part IV Rare Mutation and Rare Allele Detection
12. 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. Paweletz
13. Detection of Cancer DNA in Early Stage and Metastatic Breast Cancer PatientsArielle J. Medford, Riaz N. Gillani, and Ben Ho Park
14. Droplet Digitial PCR for Miniaml Residual Disease Detection in Mature Lymphoproliferative DisordersDaniela Drandi, Simone Ferrero, and Marco Ladetto
15. Quantitation of JAK2 V617F Allele Burden by using the QuantStudio(TM) 3D Digitial PCR SystemElena Kinz and Axel Muendlein
16. Novel Multiplexing Strategies for Quantification of Rare Alleles using ddPCRMiguel Alcaide and Ryan Morin
17. Identification and Use of Personalized Genomic Markers for Monitoring Circulating Tumor DNAYilun Chen, Anthony George, Eleonor Olsson, and Lao H. Saal
18. Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant GenotypingChristina Wood and Hanlee P. Ji
19. A Universal Droplet Digital PCR Approach for Monitoring of Graft Health after Transplantation using a Pre-Selected SNP SetJulia Beck, Michael Oellerich, and Ekkehard Sch?tz
20. Detection and Quantification of HDR and NHEJ Induced by Genome Editi