Next-Generation Sequencing and Sequence Data Analysis


by

Kuo Ping Chiu

DOI: 10.2174/97816810809251150101
eISBN: 978-1-68108-092-5, 2015
ISBN: 978-1-68108-093-2



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Nucleic acid sequencing techniques have enabled researchers to determine the exact order of base pairs - and by extension, the informa...[view complete introduction]

Table of Contents

About the Author

- Pp. i

Kuo Ping Chiu

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Foreword

- Pp. ii

Miao-Lin (Merlin) Hu

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Preface

- Pp. iii-iv (2)

Kuo Ping Chiu

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Acknowledgements

- Pp. v

Kuo Ping Chiu

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The Ultimate Frontier of Knowledge: the Mysterious Genomes and the Gene Expression and Regulation in the Upstream of Biological Information Flow

- Pp. 4-16 (13)

Kuo Ping Chiu

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Evolution of DNA Sequencing Technologies

- Pp. 17-24 (8)

Kuo Ping Chiu

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Mechanisms of Next-Generation Sequencing (NGS)

- Pp. 25-37 (13)

Kuo Ping Chiu

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Genome Assembly, the Genomic Era and the Rise of the Omics Era

- Pp. 38-48 (11)

Kuo Ping Chiu

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Laboratory Setup and Fundamental Works

- Pp. 50-56 (7)

Kuo Ping Chiu

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Sequencing Libraries and Basic Procedure for Sequencing Library Construction

- Pp. 57-61 (5)

Kuo Ping Chiu

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Paired-End (PE), Mate Pair (MP) and Paired-End Ditag (PED) Sequencing

- Pp. 62-76 (15)

Kuo Ping Chiu

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Genome Sequencing and Assembly

- Pp. 77-83 (7)

Kuo Ping Chiu

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Exome Sequencing: Genome Sequencing Focusing on Exonic Regions

- Pp. 84-87 (4)

Kuo Ping Chiu

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Transcriptome Analysis

- Pp. 88-96 (9)

Kuo Ping Chiu

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Single Cell Sequencing (SCS) and Single Cell Transcriptome (SCT) Sequencing

- Pp. 97-104 (8)

Kuo Ping Chiu

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ChIP-TFBS Analysis

- Pp. 105-111 (7)

Kuo Ping Chiu

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ChIP-EM Libraries

- Pp. 112-116 (5)

Kuo Ping Chiu

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MicroRNA Analysis

- Pp. 117-120 (4)

Kuo Ping Chiu

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Application of NGS in the Study of Sequence Diversity in Immune Repertoire

- Pp. 121-126 (6)

Kuo Ping Chiu

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Galaxy Pipeline for Transcriptome Library Analysis

- Pp. 128-146 (19)

Kuo Ping Chiu

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Subject Index

- Pp. 147-148 (2)

Kuo Ping Chiu

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Foreword

I have known Kuo Ping for almost thirty years. He is very fond of science, especially in developing or employing novel technologies for biological investigations. He and I often share ideas and have worked on common scientific interests, including the project to study the early anti-cancer activity of the medicinal fungus Antrodia cinnamomea using Next- Generation Sequencing (NGS) to sequence and compare the transcriptomes of cancer cells treated with or without the extract of A. cinnamomea. This work led to the discovery that this medicinal fungus was able to globally collapse the miRNA system.

It is his never-resting mind that has provided him a motivation to start writing this book some years ago, while he was still working for Genome Institute of Singapore when NGS was starting to take shape. During that time, there was nowhere to find a book to introduce advanced sequencing technologies and the potential applications to either students or laymen. This book evolves from his previous work on paired-end ditag technology and has a strong association with NGS which can be considered as the most fascinating technology of the 21st century. I am glad to see him accomplish this hard task. This book seems to be a good textbook for graduate students and a handbook for researchers who are interested in sequencing and biotechnologies.

It is worth mentioning that Kuo Ping is a scientist with a strong passion for outdoor activities. We did some interesting, and sometimes funny, things together. Back in California, we spent some weekends fishing at Pacifica Pier for perch and crabs, and then barbecued and talked over beer in my backyard. Here in Taiwan, we often tour around his “secret gardens” where he grew trees and raised domestic fish in a pond. The most interesting outdoor experience was a trip to find fossil stones in a wild countryside, where we found forgotten creeks running through the hillside. We tied a very heavy fossil stone with rope and carried it with a bamboo stick across water streams, making loud laughter in the wild. I actually believe that his passion for outdoor activities has contributed to the completion of this useful book.

Miao-Lin (Merlin) Hu, Ph.D.
Honorary Distinguished Professor,
National Chung Hsing University
Department of Food Science and Biotechnology
250 Kuo Kuang Road, Taichung 402
Taiwan


Preface

Many biological fields, including genetics, immunology, genomics, and epigenomics, can be readily integrated with bioinformatics and sequencing. In fact, sequencing is becoming an indispensable tool for biological and medical investigations, especially for the study of cancer, genetics, epigenetics, immunology, and developmental biology. Foreseeing the potential applications of sequencing technologies, we have initiated a sequence data analysis course at the Institute of Zoology, National Taiwan University to introduce sequencing technologies, genomics, epigenomics, bioinformatics, and biotechnologies to graduate and undergraduate students. At the same time, I started organizing the teaching materials to compose this book. Most of the materials were derived from my research at Academia Sinica and my teaching at National Taiwan University (NTU), National Central University (NCU), and National Yang Ming University (NYMU). Additionally, there are some from my previous work in the United States and Singapore.

Besides college students, this book is also written for people who already have some biological background, or with an interest in knowing more about DNA sequencing and its applications. With this effort, we hope to help develop sequence-associated knowledge among people from all walks of life, including researchers, professionals, and amateurs working in biology-related or -unrelated fields, with or without an ambition to apply sequencing technologies to biological or medical investigations. Extracting biological meaning from large quantities of sequence data is an art. We intend to help readers appreciate the various types of sequencing technologies, and learn how to use sequencing technologies to unravel the mystery of the biological system.

Sequence data analysis is not only an art, but also a tool to help researchers develop a constructive philosophy. When a diploma is awarded to a candidate, it may be treated by the recipient as a degree which can then help the graduate to find a better job, or achieve a higher social status. Some recipients may take it more seriously and use it for further, and possibly more advanced, studies. Similarly, sequence data analysis can be treated as either a course to be accomplished in class, or, alternatively, a process which will be a guide to the further understanding of the life of nanoscopic molecules within a cell. We gain many more experiences through the years of working in a lab, and, with those proficiencies, we build our philosophy. Sequencing and sequence data analysis can help us make sense of the activities which take place on a daily basis in the molecular world of our bodies, even though these activities are impalpable to the naked eye. Being able to “see” things that cannot “normally” be seen can help us build a philosophy, in which we travel between the macroscopic and molecular worlds.

A sincere attitude towards sequence data analysis is essential. Since omics sequence datasets are normally at large volumes, these data cannot be handled by traditional means, but by computer programs. Frequently we find bugs in computer programs which may produce erroneous or misleading results. A bug is a bug. No matter whether it is big or small, it has to be removed, so as to obtain the real molecular status of interest. Moreover, the author would like to emphasize the importance of practical exercise. Students are strongly encouraged to personally construct sequencing libraries, run sequencing, and analyze sequence libraries or related libraries whenever possible.

Although this book carries a mission, readers can treat it either as a novel, or a science fiction story. The development of sequencing technologies per se is science fiction, isn’t it? With limitations in man power and time, the contents of this edition may not be able to completely satisfy serious readers. Your opinions and suggestions are warmly welcomed!

Kuo Ping Chiu, Ph.D.
Genomics Research Center, Academia Sinica
National Taiwan University
National Central University
Taiwan

List of Contributors

Author(s):
Kuo Ping Chiu
Genomics Research Center, Academia Sinica
National Taiwan University
National Central University
Taiwan




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