Single Nucleotide Polymorphisms: Methods and Protocols

283 Pages·2003·3.004 MB·English

by  Lisa D. Brooks (auth.), Pui-Yan Kwok MD, PhD (eds.)

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M E T H O D S I N M O L E C U L A R B I O L O G YTM
Single Nucleotide
Polymorphisms
Methods and Protocols
Edited by
Pui-Yan Kwok, ,
MD PhD
Cardiovascular Research Institute
and Department of Dermatology
University of California, San Francisco
San Francisco, CA
Humana Press Totowa, New Jersey
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Single nucleotide polymorphisms ; methods and protocols / edited by Pui-Yan Kwok.
p. cm. -- (Methods in molecular biology ; 212)
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ISBN 0-89603-968-4 (alk. paper)
1. Chromosome polymorphism--Laboratory manuals. 2. Human genetics--
Variation--Laboratory manuals. 3. Genetic markers--Laboratory manuals. I.
Kwok, Pui-Yan, 1956– II. Methods in molecular biology (Totowa, N.J.) ; v. 212
QH447.6.S565 2002
611'.01816--dc21
2002024055
Preface
With the near-completion of the human genome project, we
are entering the exciting era in which one can begin to elucidate
the relationship between DNA sequence variation and susceptibility
to disease, as modified by environmental factors. Single nucleotide
polymorphisms (SNPs) are by far the most prevalent of all DNA
sequence variations. Although the vast majority of the SNPs are
found in noncoding regions of the genome, and most of the SNPs
found in coding regions do not change the gene products in
deleterious ways, SNPs are thought to be the basis for much of the
genetic variation found in humans. As explained eloquently by Lisa
Brooks in Chapter 1 of Single Nucleotide Polymorphisms: Methods
and Protocols, SNPs are the markers of choice in complex disease
mapping and will be the focus of the next phase of the human
genome project. Besides the obvious applications in human disease
studies, SNPs are also extremely useful in genetic studies of all
organisms, from model organisms to commercially important plants
and animals.
Identification of SNPs has been a laborious undertaking. In
Single Nucleotide Polymorphisms: Methods and Protocols, the
inventors of the most successful mutation/SNP detection methods
(including denaturing high-performance liquid chromatography
[dHPLC], single-strand conformation polymorphism [SSCP],
conformation-sensitive gel electrophoresis [CSGE], chemical
cleavage, and direct sequencing) describe the most current protocols
for these methods. In addition, a chapter on computational
approaches to SNP discovery in sequence data found in public
databases is also included.
Genotyping SNPs has been a particularly fruitful area of
research, with many innovative methods developed over the last
v
vi Preface
decade. The second half of Single Nucleotide Polymorphisms:
Methods and Protocols contains chapters written by the inventors
of the most robust SNP genotyping methods, including the
molecular beacons, Taqman assay, single-base extension
approaches, pyrosequencing, ligation, Invader assay, and primer
extension with mass spectrometry detection. Since the projected
need for SNP genotyping is in the order of 200 million genotypes
per genome-wide association study, methods described in this
volume will form the basis of ultrahigh-throughput genotyping
approaches of the future.
I am indebted to a most talented group of friends and colleagues
who have put together easy-to-follow protocols of the methods they
invented for this volume. It is my hope that Single Nucleotide
Polymorphisms: Methods and Protocols will serve as a guidebook
to all interested in SNP discovery and genotyping and will inspire
innovative minds to develop even more robust methods to make
complex disease mapping and molecular diagnosis a reality in the
near term.
Pui-Yan Kwok, MD, PhD
Contents
Preface ................................................................................ v
Contributors........................................................................ ix
1 SNPs: Why Do We Care?
Lisa D. Brooks.............................................................1
2 Denaturing High-Performance Liquid Chromatography
Andreas Premstaller and Peter J. Oefner..............15
3 SNP Detection and Allele Frequency Determination
by SSCP
Tomoko Tahira, Akari Suzuki, Yoji Kukita,
and Kenshi Hayashi..............................................37
4 Conformation-Sensitive Gel Electrophoresis
Arupa Ganguly...........................................................47
5 Detection of Mutations in DNA by Solid-Phase
Chemical Cleavage Method: A Simplified Assay
Chinh T. Bui, Jeffrey J. Babon, Andreana
Lambrinakos, and Richard G. H. Cotton...............59
6 SNP Discovery by Direct DNA Sequencing
Pui-Yan Kwok and Shenghui Duan.........................71
7 Computational SNP Discovery in DNA Sequence Data
Gabor T. Marth...........................................................85
8 Genotyping SNPs With Molecular Beacons
Salvatore A. E. Marras, Fred Russell Kramer,
and Sanjay Tyagi.................................................111
9 SNP Genotyping by the 5'-Nuclease Reaction
Kenneth J. Livak......................................................129
vii
viii Contents
10 Genotyping SNPs by Minisequencing Primer
Extension Using Oligonucleotide Microarrays
Katarina Lindroos, Ulrika Liljedahl, and
Ann-Christine Syvänen........................................149
11 Quantitative Analysis of SNPs in Pooled DNA
Samples by Solid-Phase Minisequencing
Charlotta Olsson, Ulrika Liljedahl,
and Ann-Christine Syvänen...............................167
12 Homogeneous Primer Extension Assay
With Fluorescence Polarization Detection
Tony M. Hsu and Pui-Yan Kwok............................177
13 Pyrosequencing for SNP Genotyping
Mostafa Ronaghi.....................................................189
14 Homogeneous Allele-Specific PCR
in SNP Genotyping
Søren Germer and Russell Higuchi......................197
15 Oligonucleotide Ligation Assay
Jonas Jarvius, Mats Nilsson,
and Ulf Landegren...............................................215
16 Invader Assay for SNP Genotyping
Victor Lyamichev and Bruce Neri.........................229
17 MALDI-TOF Mass Spectrometry-Based
SNP Genotyping
Niels Storm, Brigitte Darnhofer-Patel,
Dirk van den Boom, and Charles P. Rodi..........241
Index .................................................................................263
Contributors
JEFFREY J. BABON • Genomic Disorders Research Centre,
St. Vincent’s Hospital, Melbourne, Victoria, Australia
DIRK VAN DEN BOOM • Sequenom Inc., San Diego, CA
LISA D. BROOKS • National Human Genome Research Institute,
National Institutes of Health, Bethesda, MD
CHINH T. BUI • Genomic Disorders Research Centre,
St. Vincent’s Hospital, Melbourne, Victoria, Australia
RICHARD G. H. COTTON • Genomic Disorders Research Centre,
St. Vincent’s Hospital, Melbourne, Victoria, Australia
BRIGITTE DARNHOFER-PATEL • Sequenom Inc., San Diego, CA
SHENGHUI DUAN • Division of Dermatology, Washington
University, St. Louis, MO
ARUPA GANGULY • Department of Genetics, University
of Pennsylvania, Philadelphia, PA
SØREN GERMER • Roche Molecular Systems, Alameda, CA
KENSHI HAYASHI • Division of Genome Analysis, Research Center
for Genetic Information, Medical Institute of Bioregulation,
Kyushu University, Higashi-ku, Fukuoka, Japan
RUSSELL HIGUCHI • Roche Molecular Systems, Alameda, CA
TONY M. HSU • Division of Dermatology, Washington
University, St. Louis, MO
JONAS JARVIUS • Rudbeck Laboratory, Unit of Molecular
Medicine, Department of Genetics and Pathology,
Uppsala University, Uppsala, Sweden
FRED RUSSELL KRAMER • Department of Molecular Genetics,
Public Health Research Institute, Newark, NJ
YOJI KUKITA • Division of Genome Analysis, Research Center
for Genetic Information, Medical Institute of Bioregulation,
Kyushu University, Higashi-ku, Fukuoka, Japan
ix
x Contributors
PUI-YAN KWOK • Cardiovascular Research Institute
and Department of Dermatology, University of California,
San Francisco, San Francisco, CA
ANDREANA LAMBRINAKOS • Genomic Disorders Research Centre,
St. Vincent’s Hospital, Melbourne, Victoria, Australia
ULF LANDEGREN • Rudbeck Laboratory, Unit of Molecular
Medicine, Department of Genetics and Pathology,
Uppsala University, Uppsala, Sweden
ULRIKA LILJEDAHL • Department of Medical Sciences, Uppsala
University; Uppsala University Hospital, Uppsala, Sweden
KATARINA LINDROOS • Department of Medical Sciences, Uppsala
University; Uppsala University Hospital, Uppsala, Sweden
KENNETH J. LIVAK • Applied Biosystems, Foster City, CA
VICTOR LYAMICHEV• Third Wave Technologies Inc., Madison, WI
SALVATORE A. E. MARRAS • Department of Molecular Genetics,
Public Health Research Institute, Newark, NJ
GABOR T. MARTH • National Center for Biotechnology
Information, National Library of Medicine, National Institutes
of Health, Bethesda, MD
BRUCE NERI • Third Wave Technologies, Inc., Madison, WI
MATS NILSSON • Rudbeck Laboratory, Unit of Molecular
Medicine, Department of Genetics and Pathology,
Uppsala University, Uppsala, Sweden
PETER J. OEFNER • Stanford Genome Technology Center,
Palo Alto, CA
CHARLOTTA OLSSON • Department of Medical Sciences, Uppsala
University; Uppsala University Hospital, Uppsala, Sweden
ANDREAS PREMSTALLER • Stanford Genome Technology Center,
Palo Alto, CA
CHARLES P. RODI • Rodi Pharma, San Diego, CA
MOSTAFA RONAGHI • Stanford Genome Technology Center,
Palo Alto, CA
NIELS STORM • Sequenom GmbH, Hamburg, Germany
AKARI SUZUKI • Division of Genome Analysis, Research Center
for Genetic Information, Medical Institute of Bioregulation,
Kyushu University, Higashi-ku, Fukuoka, Japan