Neurogenetics: Methods and Protocols

390 Pages·2003·5.758 MB·English

by  Thomas W. Prior (auth.), Nicholas T. Potter (eds.)

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Neurogenetics
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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 Y ™
Neurogenetics
Methods and Protocols
Edited by
Nicholas T. Potter
University of Tennessee Medical Center,
Knoxville, Tennessee
Humana Press Totowa, New Jersey
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Neurogenetics / edited by Nicholas T. Potter
p. cm. -- (Methods in molecular biology ; v. 217)
Includes bibliographical references and index.
ISBN 0-89603-990-0 (alk. paper)
1. Neurogenetics--Laboratory manuals. 2. Genetic disorders--Diagnosis--Laboratory
manuals. I. Potter, Nicholas T. II. Series.
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Preface
The rapid identification and characterization of genes of neurological relevance
holds great potential for offering insight into the diagnosis, management, and under-
standing of the pathophysiologic mechanisms of neurological diseases. This volume
in the Methods in Molecular Biology™ series was conceived to highlight many of the
contemporary methodological approaches utilized for the characterization of neuro-
logically relevant gene mutations and their protein products. Although an emphasis
has been placed upon descriptions of methodologies with a defined clinical utility, it
is hoped that Neurogenetics: Methods and Protocols will appeal not only to clinical
laboratory diagnosticians, but also to clinicians, and to biomedical researchers with an
interest in advances in disease diagnosis and the functional consequences of neuro-
logically relevant gene mutations.
To meet this challenge, more than 60 authors graciously accepted my invitation
to contribute to the 32 chapters of this book. Through their collective commitment
and diligence, what has emerged is a comprehensive and timely treatise that covers
many methodological aspects of mutation detection and screening, including discus-
sions on quantitative PCR, trinucleotide repeat detection, sequence-based mutation
detection, molecular detection of imprinted genes, fluorescence in situ hybridization
(FISH), in vitro protein expression systems, and studies of protein expression and
function. I would like to take this opportunity to formally thank my colleagues for
their effort and dedication to this work.
This book would not have been possible without the guidance and wisdom of the
Series Editor, Professor John M. Walker, whose intimate knowledge of the nuances of
the editorial process made my job somewhat less intimidating. I would also like to
thank Thomas Lanigan, President of Humana Press, who enthusiastically embraced
the book concept and my original prospectus from the very beginning, and Craig Adams,
also at Humana Press, for transforming the individual chapters into their final form.
Nicholas T. Potter
v

Contents
Preface ..........................................................................................................................v
Color Plates...................................................................................................................x
Contributors..................................................................................................................xi
PART I. QUANTITATIVE PCR
1 Determination of Gene Dosage:
Utilization of Endogenous and Exogenous Internal Standards
Thomas W. Prior............................................................................................................3
2 Semiquantitative PCR for the Detection of Exon Rearrangements
in the Parkin Gene
Christoph B. Lücking and Alexis Brice................................................................13
PART II. TRINUCLEOTIDE REPEAT DETECTION
3 Detection of FMR1 Trinucleotide Repeat Expansion Mutations
Using Southern Blot and PCR Methodologies
Jack Tarleton................................................................................................................29
4 Extreme Expansion Detection in Spinocerebellar Ataxia Type 2 and Type 7
Karen Snow and Rong Mao......................................................................................41
5 Repeat Expansion Detection (RED) and the RED Cloning Strategy
Qiu-Ping Yuan, Kerstin Lindblad-Toh, and Martin Schalling........................51
6 Repeat Analysis Pooled Isolation and Detection (RAPID) Cloning
of Microsatellite Expansions
Laura P. W. Ranum.....................................................................................................61
7 DIRECT Technologies for Molecular Cloning of Genes Containing
Expanded CAG Repeats
Kazuhiro Sanpei, Takeshi Ikeuchi, and Shoji Tsuji..........................................73
8 Antibody-Based Detection of CAG Repeat Expansion Containing Genes
Yvon Trottier.................................................................................................................83
9 Detection of Trinucleotide Repeat Containing Genes
by Matrix-Assisted Laser Desorption/Ionization (MALDI)
Mass Spectrometry
Chung-Hsuan Chen, Nicholas T. Potter, and Nelly T. Taranenko................91
10 Fluorescence PCR and GeneScan® Analysis for the Detection
of CAG Repeat Expansions Associated with Huntington’s Disease
Cindy L. Vnencak-Jones.........................................................................................101
PART III. SEQUENCE-BASED MUTATION DETECTION
11 Molecular Detection of Galactosemia Mutations by PCR-ELISA
Kasinathan Muralidharan and Wei Zhang.........................................................111
12 Denaturing High-Performance Liquid Chromatography
and Sequence Analyses for MECP2 Mutations in Rett Syndrome
Inge M. Buyse and Benjamin B. Roa...................................................................119
vii
viii Contents
13 Multiplexed Fluorescence Analysis for Mutations Causing
Tay-Sachs Disease
Tracy L. Stockley and Peter N. Ray.....................................................................131
14 Single-Strand Conformational Polymorphism Analysis (SSCP)
and Sequencing for Ion Channel Gene Mutations
Kylie A. Scoggan and Dennis E. Bulman...........................................................143
15 Pulse Field Gel Electrophoresis for the Detection of Facioscapulohumeral
Muscular Dystrophy Gene Rearrangements
Luciano Felicetti and Giuliana Galluzzi..............................................................153
16 Denaturing Gradient Gel Electrophoresis (DGGE) for Mutation Detection
in Duchenne Muscular Dystrophy (DMD)
Luciana C. B. Dolinsky............................................................................................165
17 Genetic Diagnosis of Charcot-Marie-Tooth Disease
Frank Baas...................................................................................................................177
18 Analysis of Human Mitochondrial DNA Mutations
Antonio L. Andreu, Ramon Martí, and Michio Hirano....................................185
19 Detection of Mitochondrial DNA Mutations Associated
with Leber Hereditary Optic Neuropathy
Kasinathan Muralidharan........................................................................................199
PART IV. MOLECULAR DETECTION OF IMPRINTED GENES
20 PCR-Based Strategies for the Diagnosis of Prader-Willi/Angelman
Syndromes
Milen Velinov and Edmund C. Jenkins...............................................................209
PART V. FLUORESCENCEIN SITU HYBRIDIZATION (FISH)
21 Fluorescence In Situ Hybridization (FISH) for Identifying the Genomic
Rearrangements Associated with Three Myelinopathies:
Charcot-Marie-Tooth Disease, Hereditary Neuropathy with Liability
to Pressure Palsies, and Pelizaeus-Merzbacher Disease
Mansoor S. Mohammed and Lisa G. Shaffer....................................................219
PART VI. IN VITRO EXPRESSION SYSTEMS AND STUDIES
OF PROTEIN EXPRESSION AND FUNCTION
22 Drosophila Models of Polyglutamine Diseases
H. Y. Edwin Chan and Nancy M. Bonini.............................................................241
23 A Comparative Gene Expression Analysis
of Emery-Dreifuss Muscular Dystrophy Using a cDNA Microarray
Toshifumi Tsukahara and Kiichi Arahata..........................................................253
24 The COS-7 Cell In Vitro Paradigm to Study Myelin Proteolipid Protein 1
Gene Mutations
Alexander Gow...........................................................................................................263
25 In Vitro Expression Systems for the Huntington Protein
Shi-Hua Li and Xiao-Jiang Li.................................................................................277
26 Heterologous Expression of Ion Channels
Andrew R. Tapper and Alfred L. George, Jr.....................................................285
Contents ix
27 An Assay for Characterizing In Vitro the Kinetics
of Polyglutamine Aggregation
Valerie Berthelier and Ronald Wetzel.................................................................295
28 Characterization of Prion Proteins
Wenquan Zou, Monica Colucci, Pierluigi Gambetti,
and Shu G. Chen..................................................................................................305
29 Detection of NF1 Mutations Utilizing the Protein Truncation Test (PTT)
Meena Upadhyaya, Michael Osborn, and David N. Cooper.........................315
30 Application of the Protein Truncation Test (PTT) for the Detection
of Tuberosis Sclerosis Complex Type 1 and 2 (TSC1 and TSC2) Mutations
Karin Mayer.................................................................................................................329
31 Development and Characterization of Antibodies
that Immunoprecipitate the FMR1 Protein
Stephanie Ceman, Fuping Zhang, Tamika Johnson,
and Stephen T. Warren......................................................................................345
32 Immunological Methods for the Analysis of Protein Expression
in Neuromuscular Diseases
Mariz Vainzof, Maria Rita Passos-Bueno, and Mayana Zatz........................355
Index.........................................................................................................................379