Molecular Analysis and Genome Discovery

314 Pages·2011·7.712 MB·English

by  Ralph Rapley, Stuart Harbron

Molecular Analysis
and
Genome Discovery
Second edition
Molecular Analysis
and
Genome Discovery
Second edition
Edited by
Ralph Rapley
University of Hertfordshire, UK
and
Stuart Harbron
The Enzyme Technology Consultancy, UK
A John Wiley & Sons, Ltd., Publication
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LibraryofCongressCataloguing-in-PublicationData
Molecularanalysisandgenomediscovery/editedbyRalphRapleyandStuartHarbron. –2nded.
p.;cm.
Includesbibliographicalreferencesandindex.
ISBN978-0-470-75877-9 (cloth)
1.Moleculardiagnosis.2.Genomics.3.Proteomics.4.Pharmacogenomics.5.Polymerasechainreaction.
6.DNAmicroarrays.I.Rapley,Ralph.II.Harbron,Stuart.
[DNLM:1.Genomics–methods.2.DrugDesign.3.GeneticTechniques.4.Metabolomics–methods.
5.Proteomics–methods.QU58.5]
RB43.7.M5952011
615(cid:2).7–dc23
2011019770
AcataloguerecordforthisbookisavailablefromtheBritishLibrary.
Thisbookispublishedinthefollowingelectronicformats:ePDF9781119977445; WileyOnlineLibrary
9781119977438; ePub9781119978442; Mobi9781119978459
Setin10.5/13ptTimesbyLaserwordsPrivateLimited,Chennai,India
PrintedinSingaporebyMarkonoPrintMediaPteLtd.
FirstImpression2012
Contents
Preface ix
Contributors xi
1 Overview of Genotyping 1
Mo´nica Baye´s and Ivo Glynne Gut
Introduction 1
Methods for interrogating SNPs 3
Commercial platforms for SNP genotyping 7
Practical recommendations 11
SNP databases 14
Methylation analysis 15
Copy number variation analysis 16
Second generation sequencing technologies 17
Conclusions 18
References 19
2 DNA Chip Analysis in Genome Discovery 24
Ross N. Nazar and Jane Robb
Introduction 24
Interrogating a genome 25
Cross-species hybridization 28
Comparative genomic hybridization and microarray-based genotyping 31
Barcodes, DNA microarrays and organism identification 34
Concluding remarks 36
References 37
3 qPCR, Theory, Reliability and Use in Molecular Analysis 43
Jamie Murphy and Stephen A. Bustin
Sample preparation 44
RNA quality 45
Reagents 46
Assay design 47
Transparency of published data 51
vi CONTENTS
Further considerations 52
Conclusion 52
References 52
4 DNA Analysis in Droplet-Based Microfluidic Devices 56
Pinar Ozdemir and Yonghao Zhang
Introduction 56
Continuous-flow microPCR chips 58
PCR inhibition and carryover contamination 62
PCR in droplets 65
Conclusions 73
References 75
5 High-Resolution Melt Profiling 81
Steven F. Dobrowolski and Carl T. Wittwer
Introduction 81
Basic concepts of melt profiling 82
HRMP and polymerase chain reaction 84
DNA specimens and HRMP 89
Determining a temperature window for melting 90
Dyes and platforms for melt profiling 92
Scanning PCR products for sequence variation 93
Genotyping with high-resolution melt profiling 102
Other applications of HRMP 108
Final notes 109
References 110
6 Massively Parallel Sequencing 114
Tracy Tucker, Marco Marra and Jan M. Friedman
Sanger sequencing 114
Massively parallel sequencing 114
Commercially available massively parallel sequencers 115
Future technologies 122
Paired-end or mate-paired reads 123
Target-enrichment strategies for MPS 124
Applications of MPS 125
Summary 131
References 132
7 Aptamers for Analysis: Nucleic Acids Ligands in the
Post-Genomic Era 135
Pedro Nadal, Alessandro Pinto, Marketa Svobodova
and Ciara K. O’Sullivan
Introduction 135
SELEX 136
Aptamers in analysis 147
CONTENTS vii
Imaging with aptamers 157
Conclusions, outlooks and perspectives 160
References 161
8 Use of Nanotechnology for Enhancing of Cancer Biomarker
Discovery and Analysis: A Molecular Approach 175
Farid E. Ahmed
Introduction 175
Proteomics and nanotechnology 176
Nanoscale multicomponent separation 176
Nanoscale protein detection strategies 178
Surface-enhanced Raman scattering (SERS) 182
References 188
9 Chip-Based Proteomics 193
Julian Bailes, Andrew Milnthorpe, Sandra Smieszek
and Mikhail Soloviev
Introduction 193
Lab-on-a-chip 194
Arrays 196
Chip-based mass spectrometry 203
Surface plasmon resonance (SPR) and quartz crystal
microbalance (QCM) chip instruments 205
Microfluidics 207
Conclusion 209
References 211
10 Antibody Microarrays in Proteome Profiling 219
Mohamed Saiel Saeed Alhamdani and Jo¨rg D. Hoheisel
Introduction 219
Technical aspects 220
Antibody array applications 226
Summary 229
Acknowledgements 229
References 229
11 Biomarker Detection and Molecular Profiling by Multiplex
Microbead Suspension Array Based Immunoproteomics 244
V. V. Krishhan, Imran H. Khan and Paul A. Luciw
Introduction 244
Principles of microbead-based multiplexing 245
Experimental aspects of the multiplex microbead assay 247
Multiplex microbead assay design and comparison with other methods 250
Applications of the multiplex microbead assay system for biomedical
research and clinical studies 252
viii CONTENTS
Selected investigational fields for multiplex analysis and
examples of applications 255
Challenges and current limitations 255
Summary and future directions 259
Acknowledgements 261
References 261
12 Mass Spectrometry in Metabolomics 271
William J. Griffiths and Yuqin Wang
Introduction 271
Sample collection and preparation 272
Data acquisition 274
Data analysis 279
Applications 283
Conclusion 294
Acknowledgement 294
References 295
Index 299
Preface
In our preface to the first edition of Molecular Analysis and Genome Discovery
we indicated that the face of diagnostics and drug discovery had changed beyond
recognition over the past decade. With the publication of this second edition this
statement is even more apposite. There have been numerous advances in the tech-
nologyandinthediscoveryofbiologicalsystemsyieldingnewareasofanalysissuch
as transcriptomics and metabolomics. There can be no doubt that these continued
advances will lead to the ultimate goal of the development and use of personalized
and stratified medicines.
Thisbookaimstobuilduponthediscoveryandanalysisaspectsofthefirstedition
by detailing the way in which techniques have been further developed or new meth-
odsimplementedintheareasofmolecularanalysisandgenomediscovery.Following
an updated overview of the important areas of genotyping, there are a number of
chapters dealing with the methods of DNA analysis. These include the further use
of DNA chips and qPCR, two mainstays of the area. Further analysis methods are
presented including the use of microfluidic devices, high resolution melt profiling
and the ability to analyse DNA on a large scale with parallel sequencing systems.
Analysisofnucleicacidsusingaptamershasalsobeenrevisitedandupdated,provid-
ing further exciting analytical approaches for the post-human genome era. A chapter
onnanotechnologyincancerbiomarkerdiscoveryessentiallybridgesthenucleicacid
analysis and discovery aspects and leads into chapters that are more orientated to
proteins. Indeed, the emergence of nanotechnology has been spectacular, typify-
ingouropeningstatement. Theadvancement ofquantumdots,carbonnanotubes and
nanoengineeringpresentedinthischapterisafacetwhichthirtyyearsagowouldhave
been in the realms of science fiction. Chip analysis follows on from the perspective
of protein analysis and discovery, after which antibody arrays in proteome profiling
and multiplex microbead suspension array based immunoproteomics are addressed.
The application of mass spectrometry as applied to metabolomics is detailed in
the final chapter.
x PREFACE
In compiling this second edition of Molecular Analysis and Genome Discovery
we have sought again to combine both current and emerging approaches to the
analysis of genomes and proteomes. This has been undertaken with an eye on how
they maybeofbenefitforareas suchasdrugandbiomarker discovery. Weareagain
indebted to the panel of expert and distinguished authors who have provided vital
insights into these important and exciting areas.
Ralph Rapley
Stuart Harbron
Contributors
Ahmed, Farid E.
GEM Tox Consultants & Labs, Inc., Greenville, NC 27834, USA
Alhamdani, Mohamed Saiel Saeed
Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum
(DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
Bailes, Julian
School of Biological Sciences, Royal Holloway, University of London, Egham,
Surrey, TW20 0EX, UK
Baye´s, Mo`nica
Centro Nacional de Ana´lisis Geno´mico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
Bustin, Stephen A.
Academic Surgical Unit, 3rd Floor Alexandra Wing, Royal London Hospital,
Whitechapel, London E1 1BB, UK
Dobrowolski, Steven F.
Department of Pathology, University of Utah, School of Medicine, Salt Lake City,
Utah, USA
Friedman, Jan M.
DepartmentofMedicalGenetics, UniversityofBritishColumbia, Vancouver,British
Columbia, V6H 3N1 Canada and Child & Family Research Institute, Vancouver,
British Columbia, V5Z 4H4 Canada
Griffiths, William J.
Institute of Mass Spectrometry, School of Medicine, Room 352 Grove Building,
Swansea University, Singleton Park, Swansea SA2 8PP, Wales, UK
Gut, Ivo Glynne
Centro Nacional de Ana´lisis Geno´mico, C/Baldiri Reixac 4, 08028 Barcelona, Spain