Next-Generation Genome Sequencing E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 468

Veröffentlichungsjahr: 2011

Beschreibung

Written by leading experts from industry and academia, this first single comprehensive resource addresses recent developments in next generation DNA sequencing technology and their impact on genome research, drug discovery and health care. As such, it presents a detailed comparative analysis of commercially available platforms as well as insights into alternative, emerging sequencing techniques. In addition, the book not only covers the principles of DNA sequencing techniques but also social, ethical and commercial aspects, the concept of personalized medicine and a five-year perspective of DNA sequencing.

Leseprobe

Contents

Preface

List of Contributors

PART ONE: SANGER DNA SEQUENCING

1 SANGER DNA SEQUENCING

ARTEM E. MEN, PETER WILSON, KIRBY SIEMERING, AND SUSAN FORREST

1.1 THE BASICS OF SANGER SEQUENCING

1.2 INTO THE HUMAN GENOME PROJECT (HGP) AND BEYOND

1.3 LIMITATIONS AND FUTURE OPPORTUNITIES

1.4 BIOINFORMATICS HOLDS THE KEY

1.5 WHERE TO NEXT?

REFERENCES

PART TWO: NEXT-GENERATION SEQUENCING: TOWARD PERSONALIZED MEDICINE

2 ILLUMINA GENOME ANALYZER II SYSTEM

ABIZAR LAKDAWALLA AND HARPER VANSTEENHOUSE

2.1 LIBRARY PREPARATION

2.2 CLUSTER CREATION

2.3 SEQUENCING

2.4 PAIRED END READS

2.5 DATA ANALYSIS

2.6 APPLICATIONS

2.7 CONCLUSIONS

REFERENCES

3 APPLIED BIOSYSTEMS SOLID™ SYSTEM: LIGATION-BASED SEQUENCING

VICKI PANDEY, ROBERT C. NUTTER, AND ELLEN PREDIGER

3.1 INTRODUCTION

3.2 OVERVIEW OF THE SOLID™ SYSTEM

3.3 SOLID™ SYSTEM APPLICATIONS

3.4 CONCLUSIONS

REFERENCES

4 THE NEXT-GENERATION GENOME SEQUENCING: 454/ROCHE GS FLX

LEI DU AND MICHAEL EGHOLM

4.1 INTRODUCTION

4.2 TECHNOLOGY OVERVIEW

4.3 SOFTWARE AND BIOINFORMATICS

4.4 RESEARCH APPLICATIONS

REFERENCES

5 POLONY SEQUENCING: HISTORY, TECHNOLOGY, AND APPLICATIONS

JEREMY S. EDWARDS

5.1 INTRODUCTION

5.2 HISTORY OF POLONY SEQUENCING

5.3 POLONY SEQUENCING

5.4 APPLICATIONS

5.5 CONCLUSIONS

REFERENCES

PART THREE: THE BOTTLENECK: SEQUENCE DATA ANALYSIS

6 NEXT-GENERATION SEQUENCE DATA ANALYSIS

LEONARD N. BLOKSBERG

6.1 WHY NEXT-GENERATION SEQUENCE ANALYSIS IS DIFFERENT?

6.2 STRATEGIES FOR SEQUENCE SEARCHING

6.3 WHAT IS A “HIT,” AND WHY IT MATTERS FOR NGS?

6.4 SCORING: WHY IT IS DIFFERENT FOR NGS?

6.5 STRATEGIES FOR NGS SEQUENCE ANALYSIS

6.6 SUBSEQUENT DATA ANALYSIS

REFERENCES

7 DNASTAR’S NEXT-GENERATION SOFTWARE

TIM DURFEE AND THOMAS E. SCHWEI

7.1 PERSONALIZED GENOMICS AND PERSONALIZED MEDICINE

7.2 NEXT-GENERATION DNA SEQUENCING AS THE MEANS TO PERSONALIZED GENOMICS

7.3 STRENGTHS OF VARIOUS PLATFORMS

7.4 THE COMPUTATIONAL CHALLENGE

7.5 DNASTAR’S NEXT-GENERATION SOFTWARE SOLUTION

7.6 CONCLUSIONS

REFERENCES

PART FOUR: EMERGING SEQUENCING TECHNOLOGIES

8 REAL-TIME DNA SEQUENCING

SUSAN H. HARDIN

8.1 WHOLE GENOME ANALYSIS

8.2 PERSONALIZED MEDICINE AND PHARMACOGENOMICS

8.3 BIODEFENSE, FORENSICS, DNA TESTING, AND BASIC RESEARCH

8.4 SIMPLE AND ELEGANT: REAL-TIME DNA SEQUENCING

REFERENCES

9 DIRECT SEQUENCING BY TEM OF Z-SUBSTITUTED DNA MOLECULES

WILLIAM K. THOMAS AND WILLIAM GLOVER

9.1 INTRODUCTION

9.2 LOGIC OF APPROACH

9.3 IDENTIFICATION OF OPTIMAL MODIFIED NUCLEOTIDES FOR TEM VISUAL RESOLUTION OF DNA SEQUENCES INDEPENDENT OF POLYMERIZATION

9.4 TEM SUBSTRATES AND VISUALIZATION

9.5 INCORPORATION OF Z-TAGGED NUCLEOTIDES BY POLYMERASES

9.6 CURRENT AND NEW SEQUENCING TECHNOLOGY

9.7 ACCURACY

9.8 ADVANTAGES OF ZSG’S PROPOSED DNA SEQUENCING TECHNOLOGY

9.9 ADVANTAGES OF SIGNIFICANTLY LONGER READ LENGTHS

REFERENCES

10 A SINGLE DNA MOLECULE BARCODING METHOD WITH APPLICATIONS IN DNA MAPPING AND MOLECULAR HAPLOTYPING

MING XIAO AND PUI-YAN KWOK

10.1 INTRODUCTION

10.2 CRITICAL TECHNIQUES IN THE SINGLE DNA MOLECULE BARCODING METHOD

10.3 SINGLE DNA MOLECULE MAPPING

10.4 MOLECULAR HAPLOTYPING

10.5 DISCUSSION

REFERENCES

11 OPTICAL SEQUENCING: ACQUISITION FROM MAPPED SINGLE-MOLECULE TEMPLATES

SHIGUO ZHOU, LOUISE PAPE, AND DAVID C. SCHWARTZ

11.1 INTRODUCTION

11.2 THE OPTICAL SEQUENCING CYCLE

11.3 FUTURE OF OPTICAL SEQUENCING

REFERENCES

12 MICROCHIP-BASED SANGER SEQUENCING OF DNA

RYAN E. FORSTER, CHRISTOPHER P. FREDLAKE, AND ANNELISE E. BARRON

12.1 INTEGRATED MICROFLUIDIC DEVICES FOR GENOMIC ANALYSIS

12.2 IMPROVED POLYMER NETWORKS FOR SANGER SEQUENCING ON MICROFLUIDIC DEVICES

12.3 CONCLUSIONS

REFERENCES

PART FIVE: NEXT-GENERATION SEQUENCING: TRULY INTEGRATED GENOME ANALYSIS

13 MULTIPLEX SEQUENCING OF PAIRED END DITAGS FOR TRANSCRIPTOME AND GENOME ANALYSIS

CHIA-LIN WEI AND YIJUN RUAN

13.1 INTRODUCTION

13.2 THE DEVELOPMENT OF PAIRED END DITAG ANALYSIS

13.3 GIS-PET FOR TRANSCRIPTOME ANALYSIS

13.4 CHIP-PET FOR WHOLE GENOME MAPPING OF TRANSCRIPTION FACTOR BINDING SITES AND EPIGENETIC MODIFICATIONS

13.5 CHIA-PET FOR WHOLE GENOME IDENTIFICATION OF LONG-RANGE INTERACTIONS

13.6 PERSPECTIVE

REFERENCES

14 PALEOGENOMICS USING THE 454 SEQUENCING PLATFORM

M.THOMAS P. GILBERT

14.1 INTRODUCTION

14.2 THE DNA DEGRADATION CHALLENGE

14.3 THE EFFECTS OF DNA DEGRADATION ON PALEOGENOMICS

14.4 DEGRADATION AND SEQUENCING ACCURACY

14.5 SAMPLE CONTAMINATION

14.6 SOLUTIONS TO DNA DAMAGE

14.7 SOLUTIONS TO CONTAMINATION

14.8 WHAT GROUNDWORK REMAINS, AND WHAT DOES THE FUTURE HOLD?

REFERENCES

15 CHIP-SEQ: MAPPING OF PROTEIN–DNA INTERACTIONS

ANTHONY PETER FEJES AND STEVEN J.M. JONES

15.1 INTRODUCTION

15.2 HISTORY

15.3 CHIP-SEQ METHOD

15.4 SANGER DIDEOXY-BASED TAG SEQUENCING

15.5 HYBRIDIZATION-BASED TAG SEQUENCING

15.6 APPLICATION OF SEQUENCING BY SYNTHESIS

15.7 MEDICAL APPLICATIONS OF CHIP-SEQ

15.8 CHALLENGES

15.9 FUTURE USES OF CHIP-SEQ

REFERENCES

16 MICRORNA DISCOVERY AND EXPRESSION PROFILING USING NEXT-GENERATION SEQUENCING

EUGENE BEREZIKOV AND EDWIN CUPPEN

16.1 BACKGROUND ON MIRNAS

16.2 MIRNA IDENTIFICATION

16.3 EXPERIMENTAL APPROACH

16.4 VALIDATION

16.5 OUTLOOK

REFERENCES

17 DEEPSAGE: TAG-BASED TRANSCRIPTOME ANALYSIS BEYOND MICROARRAYS

KÅRE L. NIELSEN, ANNABETH H. PETERSEN, AND JEPPE EMMERSEN

17.1 INTRODUCTION

17.2 DEEPSAGE

17.3 DATA ANALYSIS

17.4 COMPARING TAG-BASED TRANSCRIPTOME PROFILES

17.5 FUTURE PERSPECTIVES

REFERENCES

18 THE NEW GENOMICS AND PERSONAL GENOME INFORMATION: ETHICAL ISSUES

JEANTINE E. LUNSHOF

18.1 THE NEW GENOMICS AND PERSONAL GENOME INFORMATION: ETHICAL ISSUES

18.2 THE NEW GENOMICS: WHAT MAKES IT SPECIAL?

18.3 INNOVATION IN ETHICS: WHY DO WE NEED IT?

18.4 A PROVISO: GLOBAL GENOMICS AND LOCAL ETHICS

18.5 MEDICAL ETHICS AND HIPPOCRATIC CONFIDENTIALITY

18.6 PRINCIPLES OF BIOMEDICAL ETHICS

18.7 CLINICAL RESEARCH AND INFORMED CONSENT

18.8 LARGE-SCALE RESEARCH ETHICS: NEW CONCEPTS

18.9 PERSONAL GENOMES

18.10 THE PERSONAL GENOME PROJECT: CONSENTING TO DISCLOSURE

REFERENCES

Index

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The Editor

Dr. Michal Janitz

Max Planck Institute for Molecular Genetics Fabeckstr. 60-62 14195 Berlin Germany

All books published by Wiley-VCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication DataA catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche NationalbibliothekDie Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at http://dnb.d-nb.de.

© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

ISBN: 978-3-527-32090-5

Preface

The development of the rapid DNA sequencing method by Fred Sanger and coworkers 30 years ago initiated the process of deciphering genes and eventually entire genomes. The rapidly growing demand for throughput, with the ultimate goal of deciphering the human genome, led to substantial improvements in the technique and was exemplified in automated capillary electrophoresis. Until recently, genome sequencing was performed in large sequencing centers with high automation and many personnel. Even when DNA sequencing reached the industrial scale, it still cost $10 million and 10 years to generate a draft of the human genome. With the price so high, population-based phenotype–genotype linkage studies were small in scale, and it was hard to translate research into statistically robust conclusions. As a consequence, most presumed associations between diseases and particular genes have not stood up to scientific scrutiny. The commercialization of the first massive parallel pyrosequencing technique in 2004 created the first opportunity for the cost-effective and rapid deciphering of virtually any genome. Shortly thereafter, other vendors entered the market, bringing with them a vision of sequencing the human genome for only $1000.

This is the topic of this book. We hope to provide the reader with a comprehensive overview of next-generation sequencing (NGS) techniques and highlight their impact on genome research, human health, and the social perception of genetics.

There is no clear definition of next-generation sequencing. There are, however, several features that distinguish NGS platforms from conventional capillary-based sequencing. First, it has the ability to generate millions of sequence reads rather than only 96 at a time. This process allows the sequencing of an entire bacterial genome within hours or of the Drosophila melanogaster genome within days instead of months. Furthermore, conventional vector-based cloning, typical in capillary sequencing, became obsolete and was replaced by direct subjecting of fragmented, and usually, amplified DNA for sequencing. Another distinctive feature of NGS are the sequenced products themselves, which are short-length reads between 30 and 400 bp. The limited read length has substantial impact on certain NGS applications, for instance, de novo sequencing. The following chapters will present several innovative approaches, which will combine the obvious advantages of NGS, such as throughput and simplified template preparation, with novel challenging features in terms of short read assembly and large sequencing data storage and processing.

This book arose from the recognition of the need to understand next-generation sequencing techniques and their role in future genome research by the broad scientific community. The chapters have been written by the researchers and inventors who participated in the development and applications of NGS technologies. The first chapter of the book contains an excellent overview on Sanger DNA sequencing, which still remains the gold standard in life sciences. The second and fourth parts of the book describe the commercially available and emerging sequencing platforms, respectively. The third part consists of two chapters highlighting the bottlenecks in the current sequencing: data storage and processing. Once the NGS techniques became available, an unprecedented explosion of applications could be observed. The fifth part of this book provides the reader with the insight into the ever-increasing NGS applications in genome research. Some of these applications are enhancements of existing techniques. Many others are unique to next-generation sequencing marked by its robustness and cost effectiveness, with the prominent example of paleogenomics.

The versatility and robustness of the NGS techniques in studying genes in the context of the entire genome surprised many scientists, including myself. We know that the processes that cause most diseases are not the result of a single genetic failure. Instead, they involve the interaction of hundreds if not thousands of genes. In the past, geneticists have concentrated on genes that have large individual effects when they go wrong, because those effects are so easy to spot. However, combinations of genes that are not individually significant may also be important. It has become evident that next-generation sequencing techniques, together with systems biology approaches, could elucidate the complex dependences of regulatory networks not only on the level of a single cell or tissue but also on the level of the whole organism.

We hope that this book will enrich the understanding of the dramatic changes in genome exploration and its impact not only on research itself but also on many aspects of our life, including healthcare policy, medical diagnostics, and treatment. The best example comes from the field of consumer genomics. Consumer genomics promises to inform people of their risks of developing ailments such as heart disease or cancer; it can even advise its customers how much coffee they can safely drink. This information is retrieved from the correlation of the single nucleotide polymorphism (SNP) pattern of the individual with the SNP haplotype linked to a particular disease. Recent public discussions on the challenges posed by the availability of personal genome information have revealed a new perception of genomic information and its uses. For the first time, a desire to understand the genome has become important and relevant to people outside of the scientific community. In addition to the benefits of having access to genetic information, the ethical and legal risks of making this information available are emerging. The last part of the book introduces the reader to the debate, which will only intensify in the years to come.

In conclusion, I would like to express my sincere gratitude to all of the contributors for their extraordinary effort to present these fascinating technologies and their applications in genome exploration in such a clear and comprehensive way. I also extend my thanks to Professor Hans Lehrach for his constant support.

Berlin, July 2008    

Michal Janitz

List of Contributors

Annelise E. BarronStanford University Department of Bioengineering W300B James H. Clark Center 318 Campus Drive Stanford, CA 94305 USA

Eugene BerezikovHubrecht Institute Uppsalalaan 8 3584 CT Utrecht The Netherlands

Leonard N. BloksbergSLIM Search Ltd. P.O. Box 106-367 Auckland 1143 New Zealand

Edwin CuppenHubrecht Institute Uppsalalaan 8 3584 CT Utrecht The Netherlands

Lei Du454 Life Sciences 20 Commercial Street Branford, CT 06405 USA

Tim DurfeeDNASTAR, Inc. 3801 Regent Street Madison, WI 53705 USA

Jeremy S. EdwardsUniversity of New Mexico Health Sciences Center Cancer Research and Treatment Center Department of Molecular Genetics and Microbiology Albuquerque, NM 87131 USA

University of New Mexico Department of Chemical and Nuclear Engineering Albuquerque, NM 87131 USA

Michael Egholm454 Life Sciences 20 Commercial Street Branford, CT 06405 USA

Jeppe EmmersenAalborg University Department of Health Science and Technology Fredrik Bajers Vej 3B 9000 Aalborg Denmark

Anthony P. FejesGenome Sciences Centre 570 West 7th Avenue, Suite 100 Vancouver, BC Canada V5Z 4S6

Susan ForrestUniversity of Queensland Level 5, Gehrmann Laboratories Australian Genome Research Facility St. Lucia, Brisbane, Queensland Australia

Ryan E. ForsterNorthwestern University Materials Science and Engineering Department 2220 Campus Drive Evanston, IL 60208 USA

Christopher P. FredlakeNorthwestern University Chemical and Biological Engineering Department 2145 North Sheridan, Tech E136 Evanston, IL 60208 USA

M. Thomas P. GilbertUniversity of Copenhagen Biological Institute Department of Evolutionary Biology Universitetsparken 10 2100 Copenhagen Denmark

William GloverZS Genetics 8 Hidden Pond Lane North Reading, MA 01864 USA

Susan H. HardinVisiGen Biotechnologies, Inc. 2575 West Bellfort, Suite 250 Houston, TX 77054 USA

Steven J.M. JonesGenome Sciences Centre 570 West 7th Avenue, Suite 100 Vancouver, BC Canada V5Z 4S6

Pui-Yan KwokUniversity of California, San Francisco Cardiovascular Research Institute San Francisco, CA 94143-0462 USA

University of California, San Francisco Department of Dermatology San Francisco, CA 94143-0462 USA

Abizar LakdawallaIllumina, Inc. 25861 Industrial Boulevard Hayward, CA 94545 USA

Jeantine E. LunshofVU University Medical Center EMGO Institute Section Community Genetics Van der Boechorststraat 7, MF D424 1007 MB Amsterdam The Netherlands

Artem E. MenUniversity of Queensland Level 5, Gehrmann Laboratories Australian Genome Research Facility St. Lucia, Brisbane, Queensland Australia

Kåre L. NielsenAalborg University Department of Biotechnology, Chemistry and Environmental Engineering Sohngaards-Holms vej 49 9000 Aalborg Denmark

Robert C. NutterApplied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA

Vicki PandeyApplied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA

Louise PapeUniversity of Wisconsin-Madison Biotechnology Center Departments of Genetics and Chemistry Laboratory for Molecular and Computational Genomics Madison, WI 53706 USA

Annabeth H. PetersenAalborg University Department of Biotechnology, Chemistry and Environmental Engineering Sohngaards-Holms vej 49 9000 Aalborg Denmark

Ellen PredigerApplied Biosystems 850 Lincoln Centre Drive Foster City, CA 94404 USA

Yijun RuanGenome Institute of Singapore 60 Biopolis Street Singapore 138672 Singapore

David C. SchwartzUniversity of Wisconsin-Madison Biotechnology Center Departments of Genetics and Chemistry Laboratory for Molecular and Computational Genomics Madison, WI 53706 USA

Thomas E. SchweiDNASTAR, Inc. 3801 Regent Street Madison, WI 53705 USA

Kirby SiemeringUniversity of Queensland Level 5, Gehrmann Laboratories Australian Genome Research Facility St. Lucia, Brisbane, Queensland Australia

William K. ThomasHubbard Center for Genome Studies 448 Gregg Hall, 35 Colovos Road Durham, NH 03824 USA

Harper VanSteenhouseIllumina, Inc. 25861 Industrial Boulevard Hayward, CA 94545 USA

Chia-Lin WeiGenome Institute of Singapore 60 Biopolis Street Singapore 138672 Singapore

Peter WilsonUniversity of Queensland Level 5, Gehrmann Laboratories Australian Genome Research Facility St. Lucia, Brisbane, Queensland Australia

Ming XiaoUniversity of California, San Francisco Cardiovascular Research Institute San Francisco, CA 94143-0462 USA

Shiguo ZhouUniversity of Wisconsin-Madison Biotechnology Center Departments of Genetics and Chemistry Laboratory for Molecular and Computational Genomics Madison, WI 53706 USA

PART ONE

SANGER DNA SEQUENCING

1

SANGER DNA SEQUENCING

Artem E. Men, Peter Wilson, Kirby Siemering, and Susan Forrest

1.1 The Basics of Sanger Sequencing

From the first genomic landmark of deciphering the phiX174 bacteriophage genome achieved by F. Sanger’s group in 1977 (just over a 5000 bases of contiguous DNA) to sequencing several bacterial megabase-sized genomes in the early 1990s by The Institute for Genomic Research (TIGR) team, from publishing by the European Consortium the first eukaryotic genome of budding yeast Saccharomyces cerevisiae in 1996 to producing several nearly finished gigabase-sized mammal genomes including our own, Sanger sequencing definitely has come a long and productive way in the past three decades. Sequencing technology has dramatically changed the face of modern biology, providing precise tools for the characterization of biological systems. The field has rapidly moved forward now with the ability to combine phenotypic data with computed DNA sequence and therefore unambiguously link even tiny DNA changes (e.g., single-nucleotide polymorphisms (SNPs)) to biological phenotypes. This allows the development of practical ways for monitoring fundamental life processes driven by nucleic acids in objects that vary from single cells to the most sophisticated multicellular organisms.

“Classical” Sanger sequencing, published in 1977 [1], relies on base-specific chain terminations in four separate reactions (“A”, “G”, “C”, and “T”) corresponding to the four different nucleotides in the DNA makeup (Figure 1.1a). In the presence of all four 2′- deoxynucleotide triphosphates (dNTPs), a specific 2′,3′-dideoxynucleotide triphosphate (ddNTP) is added to every reaction; for example, ddATP to the “A” reaction and so on. The use of ddNTPs in a sequencing reaction was a very novel approach at the time and gave far superior results compared to the 1975 prototype technique called “plus and minus” method developed by the same team. The extension of a newly synthesized DNA strand terminates every time the corresponding ddNTP is incorporated. As the ddNTP is present in minute amounts, the termination happens rarely and stochastically, resulting in a cocktail of extension products where every position of an “N” base would result in a matching product terminated by incorporation of ddNTP at the 3′ end.