Whole Genome Amplification Methods and Protocols

This volume mirrors the holistic feature of whole genome amplification (WGA) technology by combining reviews, detailed basic methods and advanced sample workflows. The first part of the book covers an overview of the development of WGA techniques throughout recent years including general considerations on bias in WGA, possible sample pre-enrichment strategies and how to run a single-cell lab. The second part focuses on major WGA methods and protocols that allow the assessment of WGA product quality. The final chapters contain advanced protocols and address issues such as sample preparation using laser-micro dissection; WGA from partially degraded DNA (formalin-fixed paraffin embedded samples); circulating tumor cells; and ancient samples. 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, Whole Genome Amplification: Methods and Protocols will serve as a rich source of detailed information and inspiration and will help researchers, both new and experienced, yield successful results.

1. Principles of Whole Genome Amplification
Zbigniew Tadeusz Czyz, Stefab Kirsch, and Bernhard Polzer

2. Bias in Whole Genome Amplification: Causes and Considerations
Jeffrey X. Sabina and John H. Leamon

3. The Single-Cell Lab or How to Perform Single-Cell Molecular Analysis
Roland Kirchner and Marianna Alunni-Fabbroni

4. Sample Preparation Methods Following CellSearch Approach Compatible of Single-Cell Whole Genome Amplification: An Overview
Joost F. Swennenhuis and Leon W.M.M. Terstappen

5. Deterministic Whole Genome Amplification of Single Cells
Zbigniew T. Czyz and Christoph A. Klein

6. Construction of a DNA Library on Microbeads Using Whole Genome Amplification
Kojima T., Zhu B., and Nakano H.

7. Heat-Induced Fragmentation and Adapter-Assisted Whole Genome Amplification Using GenomePlex® Single Cell Whole Genome Amplification Kit (WGA4)
Amin El-Heliebi, Shukun Chen, and Thomas Kroneis

8. Whole Genome Amplification by Isothermal Multiple Strand Displacement Using Phi29 DNA Polymerase
Thomas Kroneis and Amin El-Heliebi

9. Using Multiplex-PCR for Assessing the Quality of Whole Genome Amplified DNA
Amin El-Heliebi, Shukun Chen, and Thomas Kroneis

10. Quality Control of Isothermal Amplified DNA Based on Short Tandem Repeat Analysis
Thomas Kroneis and Amin El-Heliebi

11. Laser-Microdissection of FFPE Tissue Areas and Subsequent Whole Genome Amplification by Ampli1^TM
Zbigniew T. Czyz, Nikolas H. Stoecklein, and Bernhard Polzer

12. Whole Genome Amplification from Blood Spot Samples
Karina Meden Sørensen

13. Analysis of Whole Mitogenomes from Ancient Samples
Gloria G. Fortes and Johanna L.A. Paijmans

14. Copy Number

15. Whole Genome Amplification in Genomic Analysis of Single Circulating Tumor Cells
Christin Gasch, Klaus Pantel, and Sabine Riethdorf

16. Whole Genome Amplification of Labeled Viable Single Cells Suited for Array Comparative Genomic Hybridization
Thomas Kroneis and Amin El-Heliebi

17. Low-Volume On-Chip Single-Cell Whole Genome Amplification for Multiple Subsequent Analyses
Thomas Kroneis, Shukun Chen, and Amin El-Heliebi

18. Detection and Characterization of Circulating Tumor Cells by the CellSearch Approach
Frank Coumans and Leon W.M.M. Terstappen