9781904842187

Whole Genome Amplification

by
  • ISBN13:

    9781904842187

  • ISBN10:

    1904842186

  • Edition: 1st
  • Format: Hardcover
  • Copyright: 2005-11-01
  • Publisher: Scion Pub Ltd

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Summary

Whole genome amplification generates microgram quantities of genomic DNA starting from a sample of as little as a few femtograms and so is a vital technique when sample material is limited, as well as for high-throughput assays. Whole Genome Amplification: Methods Expressis a comprehensive up-to-date laboratory manual for this key technique. It provides detailed step-by-step protocols as well as hints and tips for success and troubleshooting, taking readers through all aspects of whole genome amplification. This book is an essential practical guide for any researcher currently using PCR for genomic amplification or who wishes to do so in future.

Table of Contents

Contributors ix
Preface xiii
Abbreviations xv
Color section xvii
Introduction to whole genome amplification
Jose M. Lage
Paul M. Lizardi
Introduction
1(1)
Methods and approaches
2(6)
References
8(3)
Single nucleotide polymorphism typing using degenerate-oligonucleotide-primed PCR-amplified products
Makoto Bannai
Katsushi Tokunaga
Introduction
11(1)
Methods and approaches
12(1)
Methodology of DOP-PCR
12(1)
Applications of DOP-PCR
12(1)
Recommended protocols
12(9)
Results
18(3)
Conclusion
21(1)
References
21(2)
Whole genome amplification by improved primer-extension pre-amplification PCR
Peter J. Wild
Wolfgang Dietmaier
Introduction
23(3)
Method of choice
23(3)
Methods and approaches
26(1)
Cell isolation
26(1)
Recommended protocols
27(5)
Downstream applications
29(3)
Troubleshooting
32(1)
References
32(1)
Global amplification using SCOMP: single-cell comparative genomic hybridization
Nona C.R. Arneson
Arezou A. Ghazani
Susan J. Done
Introduction
33(1)
Methods and approaches
34(1)
SCOMP
34(1)
Principles of SCOMP
34(1)
DNA template requirements
35(1)
Recommended protocols
35(9)
Downstream applications
40(4)
Troubleshooting
44(1)
References
45(2)
PRSG, a whole genome amplification method based on adaptor-ligation PCR of randomly sheared genomic DNA
Hiroki Sasaki
Kazuhiko Aoyagi
Introduction
47(1)
Methods and approaches
48(1)
Recommended protocols
48(9)
Downstream applications
55(2)
Troubleshooting
57(1)
References
57(2)
GenomePlex whole genome amplification
Simon Hughes
Gabrielle Sellick
Richard Coleman
John Langmore
Introduction
59(1)
Methods and approaches
60(2)
GenomePlex WGA
60(2)
Recommended protocols
62(12)
Downstream applications
68(6)
Troubleshooting
74(1)
References
75(2)
DNA linear amplification
Chih Long Liu
Bradley E. Bernstein
Stuart L. Schreiber
Introduction
77(2)
Methods and approaches
79(5)
DNA linear amplification
79(1)
General strategy
79(1)
Considerations for the starting dsDNA template
79(2)
Using this method for ChIP-chip experiments
81(1)
Controls for new users
82(2)
Recommended protocols
84(10)
Expected yields
91(1)
Composition of the amplification product
92(1)
Results
93(1)
ChIP-chip results
93(1)
Troubleshooting
94(4)
Poor amplification yield
94(2)
Poly(A) tracts in the amplified RNA
96(1)
DsRNA formation in the amplified RNA product
97(1)
References
98(1)
Multiple displacement amplification of genomic DNA
Roger Lasken
Introduction
99(7)
The challenge of amplifying an entire genome
100(2)
Reaction mechanisms and enzymology of MDA
102(4)
Methods and approaches
106(2)
Source of DNA template
106(2)
Amount of biological specimen required as DNA template source
108(1)
Source of MDA reagents
108(1)
Recommended protocols
108(9)
MDA reaction
108(2)
Expected yield of amplified DNA and storage
110(1)
Characteristics of amplified DNA and reaction optimization
110(7)
Troubleshooting
117(1)
References
117(2)
Multiple displacement amplification from single bacterial cells
Roger Lasken
Arumugham Raghunathan
Thomas Kvist
Thomas Ishoy
Peter Westermann
Birgitte K. Ahring
Robert Boissy
Introduction
119(1)
Methods and approaches
120(1)
Isolation of single cells by serial dilution
120(1)
Isolation of single cells by flow cytometry or micromanipulation
121(1)
Recommended protocols
121(25)
DNA sequencing with amplified DNA
123(3)
Characteristics of DNA amplified by MDA from single cells
126(5)
Isolation of single cells by micromanipulation and genomic DNA amplification by MDA
131(5)
Example of single-cell isolation and MDA
136(5)
Bioinformatic aspects of single-cell MDA for genome sequencing and assembly
141(5)
References
146(3)
Genome amplification tolerant to sample degradation: application to formalin-fixed, paraffin-embedded specimens
G. Mike Makrigiorgos
Introduction
149(1)
Methods and approaches
150(2)
Principles of RCA-RCA
150(1)
Advantages of RCA-RCA
150(2)
Recommended protocols
152(7)
Examples of results
154(5)
Troubleshooting
159(1)
References
160(3)
Pre-implantation genetic diagnosis using whole genome amplification
Alan H. Handyside
Mark D. Robinson
Francesco Fiorentino
Introduction
163(1)
Methods and approaches
164(5)
PGD using WGA
164(5)
Recommended protocols
169(14)
Downstream applications
170(13)
References
183(2)
Appendix 1 List of suppliers 185(4)
Index 189

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