Main description:

This volume details applications, methods, and protocols on nucleic acid amplification. Chapters detail the management of organ and stem cell transplantation, constitutional genetics and genomics, epidemiology, public health, nucleic acid detection, methods for amplification and sequencing, nuclease-assisted mutant allele enrichment, isothermal, and high-throughput sequencing. 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.

Cutting-edge and thorough, Clinical Applications of Nucleic Acid Amplification is a valuable resource for both novice and expert scientists in this developing field.

Contents:

Part I. Foundations for Successful Assays

1. A Brief Practical Guide to PCR

Page B. McKinzie and Meagan B. Myers

2. Managing a PCR Contamination Event in a Molecular Pathology Laboratory

Julie Woolworth Hirschhorn, Alexandria Avery, and Cynthia A. Schandl

3. Next Generation Sequencing Informatic Architecture Considerations

W. Bailey Glen and Cynthia A. Schandl

Part II. Applications in Oncology

4. Nuclease Enrichment and qPCR Detection of Rare Nucleotide Variants

Ieva Keraite, Virginia Alvarez-Garcia, and Nicholas R. Leslie

5. MYD88 L265P Mutation Detection by ddPCR: Recommendations for Screening and Minimal Residual Disease Monitoring

Daniela Drandi, Martina Ferrante, Michela Borriero, and Simone Ferrero

6. Capture Methylation-Sensitive Restriction Enzyme Sequencing (Capture MRE-Seq) for Methylation Analysis of Highly Degraded DNA Xiaoyun Xing, Jennifer A. Karlow, Daofeng Li, Hyo Sik Jang, Hyung Joo Lee, and Ting Wang

7. LT-RPA: An Isothermal DNA Amplification Approach for Improved Microsatellite Genotyping and Microsatellite Instability Detection

Sophie I. Jeanjean, Victor Renault, Antoine Daunay, Yimin Shen, Lise M. Hardy, Jean-Francois Deleuze, and Alexandre How-Kit

8. Liquid Biopsy for Advanced Cancer: An Amplicon Based Massively Parallel Sequencing Panel Approach to Precision Oncology

Kristen Maurer and Cynthia A. Schandl

9. Mate Pair Sequencing: Next Generation Sequencing for Structural Variant Detection

Beth A. Pitel, Eric Zimmerman Zuckerman, and Linda B. Baughn

Part III. Applications in the Management of Organ and Stem Cell Transplantation

10. Cell Subset-Specific Chimerism Testing by Short Tandem Repeats Analysis for Engraftment Monitoring After Hematopoietic Stem Cell Transplantation

Louise Pagaduan, Thea dela Cruz, Lain Tan, Cassie Wu, Jack Lai, Young Cho, Denice Kong, and Raja Rajalingam

11. Immune Cell Lineage-Specific Chimerism Testing by Next-Generation Sequencing for Engraftment Monitoring After Allogeneic Hematopoietic Stem Cell Transplantation

Cassie Wu, Thea dela Cruz, Jack Lai, Denice Kong, and Raja Rajalingam

Part IV. Applications in Constitutional Genetics and Genomics

12. Rapid Whole Genome Sequencing for Diagnosis of Single Locus Genetic Diseases in Critically Ill Children

Mallory J. Owen, Sergey Batalov, Katarzyna A. Ellsworth, Meredith Wright, Sylvia Breeding, Kwon Hugh, Stephen F. Kingsmore, and Yan Ding

13. EOSAL-CNV for Easy and Rapid Detection of CNVs by Fragment Analysis

Francisco Lara, Jessica Cortez, Soraya Garcia-Sorribes, Sebastian Blesa, M. Dolores Olivares, Andy S Alic, Ana-Barbara Garcia-Garcia, and F. Javier Chaves

Part V. Applications in Epidemiology and Public Health

14. Rapid Cycle and Extreme Polymerase Chain Reaction

Carl T. Wittwer

15. CRISPR-Cas12-Based Diagnostic Applications in Infectious and Zoonotic Diseases

Linxian Li, Shiyuan Li, Dayong Gu, Yong X, and Jin Wang

16. SARS-CoV-2 Sequencing for Variant Surveillance

Julie Woolworth Hirschhorn and Jaclyn Dunne

Part VI. Applications in Resource-Limited Medicine

17. Tuberculosis Diagnosis Using Isothermal Nucleic Acid Amplification in a Paper-and-Plastic Device

Navjot Kaur and Bhushan J. Toley

18. Loop-Mediated Isothermal Amplification on Paper Microfluidic Chips for Highly Sensitive and Specific Zika Virus Detection Using Smartphone

Kattika Kaarj and Jeong-Yeol Yoon

19. Ultrasensitive Reverse Transcriptase Loop-Mediated Isothermal Amplification (US-LAMP) Based Detection of Malaria Infection from Dried Blood Spots

Abu Naser Mohon, Noah Toppings, Daniel Castaneda-Mogollon, Claire Kamaliddin, Dylan R. Pillai