基因分析入门：生物信息学第二版

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"Bioinformatics for Geneticists, Second Edition" 是一本专为遗传学家设计的生物信息学入门书籍，由Michael R. Barnes撰写，他在GlaxoSmithKline Pharmaceuticals担任生物信息学工作。本书主要目的是帮助读者理解和应用生物信息学工具来分析遗传数据。书中分为五个部分，涵盖从基础的生物信息学概念到基因、基因组和遗传变异数据的掌握，再到从关联基因到疾病等位基因的分析，以及遗传和基因组数据接口的综合分析。在第一部分"AN INTRODUCTION TO BIOINFORMATICS FOR THE GENETICIST"中，作者可能会介绍生物信息学的基本定义、历史发展以及它在遗传学研究中的重要性。这部分可能涉及DNA序列比对、基因预测、进化分析等基础知识，帮助读者建立对生物信息学的初步理解。第二部分"MASTERING GENES, GENOMES AND GENETIC VARIATION DATA"将深入探讨基因、基因组和遗传变异数据的处理。可能涵盖的内容包括全基因组测序技术、SNP（单核苷酸多态性）分析、基因表达谱研究、基因功能注释以及基因组组装和比较。第三部分未在提供的信息中提及，但从标题推断，这部分可能是连接前两部分与后续部分的桥梁，可能涉及遗传学和生物信息学方法的综合应用。第四部分"MOVING FROM ASSOCIATED GENES TO DISEASE ALLELES"关注的是如何利用生物信息学方法从已知的基因关联性研究过渡到理解疾病的遗传基础。这部分可能讲解GWAS（全基因组关联研究）、因果推理方法、遗传风险评分计算以及复杂疾病基因网络的构建。第五部分"ANALYSIS AT THE GENETIC AND GENOMIC DATA INTERFACE"探讨了遗传数据与基因组数据的交互分析，可能涉及转录组学、表观遗传学、蛋白质组学和代谢组学的数据整合策略，以及多组学分析在疾病机制解析和药物发现中的应用。 "Bioinformatics for Geneticists, Second Edition"是一本全面介绍生物信息学在遗传学中应用的教材，旨在提升遗传学家在大数据时代进行复杂遗传分析的能力，对于想要了解或提高生物信息学技能的遗传学研究人员来说是一本宝贵的参考资料。

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FOREWORD

xiii

The data behind many of the bioinformatics tools described here are rapidly

changing and expanding. In response, the software tools and databases themselves

tend to be (infuriatingly) dynamic. A consequence of this ﬂuid state is that learning

to use existing programs by no means guarantees a knack for using those in the

future. Thus, one cannot expect long-term consistency in the tools and data-types

described here (or in most any other contemporary bioinformatics text). By learning

to use current tools more effectively, however, geneticists can not only capitalize on

technology available,but perhaps engagemorebioinformaticians in theexcitement of

genetics research. Bringing bioinformatics to geneticists is a crucial ﬁrst step towards

integrating the kindred ﬁelds and characterizing the frustratingly elusive genes that

inﬂuence complex phenotypes.

Lon R. Cardon

Professor of Bioinformatics

Wellcome Trust Centre for Human Genetics

University of Oxford

1. Doolittle, R. F. Of URFs and ORFs: A primer on how to analyze derived amino acid sequences

(University Science Books, Mill Valley, California, 1987).

2. von Heijne, G. Sequence analysis in molecular biology: Treasure trove or trivial pursuit

(Academic Press, London, 1987).

3. Wolfsberg, T. G., Wetterstrand, K. A., Guyer, M. S., Collins, F. S. & Baxevanis, A. D. A user’s

guide to the human genome. Nature Genetics 32 (suppl) (2002).

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Preface

I say ‘locus–locus’ instead of ‘gene–gene’ because if you work in human genetics long

enough, you realize that you may never have a gene. But you learn not to let that

put you off.

Peter A. Holmans

Making sense of the results of a genetic experiment is a challenge on any level.

Writing a book about the use of bioinformatics to achieve this goal might seem like

a somewhat vainglorious exercise. Individual perceptions of what is constituted by

bioinformatics vary widely. However, in the context of this book, bioinformatics

seeks to illuminate biological function, while disease genetics, our primary focus,

is essentially about understanding biological dysfunction. With this in mind, please

think of bioinformatics as a tool for improving the understanding of genetics.

Since the ﬁrst edition of this book, the reasons for thinking this way have

become more compelling. Human disease genetics is rapidly becoming a high-

throughput activity, and that means that making sense of a genetic experiment

now means making sense of millions of data points. Again this underlines the

need for genetics-focused bioinformatics. Quite simply, we need the informatics to

manipulate and analyse data on this scale, and we need the bio to make sense of

it all in the holistic biological system that is a human being.

This book could not have been realised without the insightful contributions of all

the chapter authors. I really feel they have helped to make this book worthy of both

the bio and the informatics monikers. I would also like to send my warmest thanks

to Ian C. Gray, who co-edited the ﬁrst edition with me, for providing helpful input

and support on this edition. All the exciting science you see here would not exist

without the incredibly dedicated team at Wiley, who have always kept things on

track, including Joan Marsh, Andrea Baier, Fiona Woods, Kate Pamphilon and Emilie

McDonough. I have a day job besides editing books, and so I would also really like to

thank Philippe Sanseau and David Searls at GSK for giving me the time, encourage-

ment and support to get this done. Finally, I would like to thank my wife, Aruna, for

her constant love, support, encouragement and superior punctuation. Without her,

I would not have had the will or punctuation skills to complete this magnum opus.

Michael R. Barnes

August 2006, Harlow, UK

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