Digital PCR: Methods and Protocols

ISBN-13: 9781493977765 / Angielski / Twarda / 2018 / 557 str.

George Karlin-Neumann; Frank Bizouarn

Opis

This volume explores and explains how digital PCRs (dPCRs) help in the study of numerous topics, such as infectious diseases, evolution of cancer and treatment responses, somatic mosaicism, genome editing and cell therapy, and food testing for GMOs and pathogens.

Recenzje

"The editors of the volume have succeeded in providing specialists in different sectors with a wide range of technology applications that can be adapted to other platforms or can provide the basis for creating new ones." (Paolo Catarsi, European Journal of Histochemistry, Vol. 63, 2019)

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Background Concepts

1. Entering the Pantheon of 21st Century Molecular Biology Tools: A Perspective on Digital PCR

George Karlin-Neumann and Frank Bizouarn

2. Basic Concepts and Validation of Digital PCR Measurements

Leonardo 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 Plasma

Alexandra 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 Events

David Dobnik, Bjørn Spilsberg, Alexandra Bogožalec, Dejan Štebih, Dany Morisset, Arne Holst-Jensen and Jana Žel

6. Using Droplet Digital PCR to Detect Coinfection of Human Herpesviruses 6A and 6B (HHV-6A and HHV-6B) in Clinical Samples

Ashlet Vellucci, Emily Leibovitch, and Steven Jacobson

7. Biomarkers in Cerebrospinal Fluid: Analysis of Cell-Free Circulating Mitochondrial DNA by Digital PCR

Petar Podlesniy and Ramon Trullas

8. Testing of General and Human-Associated Fecal Contamination in Waters

Yiping Cao, Mereditch R. Raith, and John F. Griffith

Part III Copy Number Variation

9. Analyzing Copy Number Variation with Droplet Digital PCR

Avery Davis Bell, Christina L. Usher, and Steven A. McCarroll

10. Assessing HER2 Amplification in Plasma cfDNA

Isaac 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 Variants

Bo 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 PCR

Yanan 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 Patients

Arielle J. Medford, Riaz N. Gillani, and Ben Ho Park

14. Droplet Digitial PCR for Miniaml Residual Disease Detection in Mature Lymphoproliferative Disorders

Daniela Drandi, Simone Ferrero, and Marco Ladetto

15. Quantitation of JAK2 V617F Allele Burden by using the QuantStudio™ 3D Digitial PCR System

Elena Kinz and Axel Muendlein

16. Novel Multiplexing Strategies for Quantification of Rare Alleles using ddPCR

Miguel Alcaide and Ryan Morin

17. Identification and Use of Personalized Genomic Markers for Monitoring Circulating Tumor DNA

Yilun Chen, Anthony George, Eleonor Olsson, and Lao H. Saal

18. Single Color Multiplexed ddPCR Copy Number Measurements and Single Nucleotide Variant Genotyping

Christina Wood and Hanlee P. Ji

19. A Universal Droplet Digital PCR Approach for Monitoring of Graft Health after Transplantation using a Pre-Selected SNP Set

Julia Beck, Michael Oellerich, and Ekkehard Schütz

20. Detection and Quantification of HDR and NHEJ Induced by Genome Editing at Endogenous Gene Loci using Droplet Digital PCR

Yuichiro Miyaoka, Steven J. Mayer, Amanda H. Chan, and Bruce R. Conklin

21. DNA Methylation Analysis Using Droplet Digital PCR

Ming Tu, Tai J. Heinzerling, and William M. Grady

Part V Gene Expression and RNA Quantification

22. Simultaneous Quantification of Multiple Alternatively Spliced mRNA Transcripts using Droplet Digital PCR

Bing Sun and Yun-Ling Zheng

23. Using Droplet Digital PCR to Analyze Allele-Specific RNA Expression

Nolan Kamitaki, Christina L. Usher, and Steven A. McCarroll

24. Very Low Abundance Single-Cell Transcript Quantification with 5-Plex ddPCR™ Assays

George Karlin-Neumann, Bin Zhang, and Claudia Litterst

25. Quantification of Circulating MicroRNAs by Droplet Digital PCR using EvaGreen Probeless Chemistry

Manuela Ferracin and Massimo Negrini

26. Droplet Digital PCR for Absolute Quantification of Extracellular MicroRNAs in Plasma and Serum: Quantification of the Cancer Biomarker has-miR-141

Maria D. Giraldez, John R. Chevillet, and Muneesh Tewaru

Part VI Other Usses of Partitioning

27. Droplet Digital™ PCR Next-Generation Sequencing Library QC Assay

Nick Heredia

28. Phasing DNA Markers using Digital PCR

Jack Regan and George Karlin-Neumann

29. ddTRAP: A Method for Sensitive and Precise Quantification of Telomerase Activity

Andrew T. Ludlow, Dawne Shelton, Woodring E. Wright, and Jerry W. Shay

30. Highly Efficient and Reliable DNA Aptamer Selection Using the Partitioning Capabilities of ddPCR: The Hi-Fi SELEX Method

Aaron Ang, Eric Quellet, Karen C. Cheung, and Charles Haynes

Blurb

This volume explores and explains how digital PCRs (dPCRs) help in the study of numerous topics, such as infectious diseases, evolution of cancer and treatment responses, somatic mosaicism, genome editing and cell therapy, and food testing for GMOs and pathogens. 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 thorough, Digital PCR: Methods and Protocols is a valuable resource for specialists in various fields, including geneticists, neurologists, immunologists, oncologists, and researchers who are interested in environmental sciences.”