A diverse collection of readily reproducible methods for use in cancer detection. Highlights include FISH-based methodologies currently used in the diagnosis of solid tumors, the molecular diagnosis of genetic abnormalities by DNA array technologies-including sequence-specific oligonucleotide arrays and CGH arrays-and methodologies directed at the detection of epigenetic events and at quantitative gene expression. The authors apply these novel diagnostic procedures to a broad range of cases taken from cytology, solid tumor pathology, hematology, and rare cell detection, paying special attention to potential future developments and the practical problems of dealing with quality control and accuracy.

Preface

v

Contributors

ix

1 Prognostic and Predictive Factors

Michael Scott and Peter A. Hall

1

(12)

2 Assessment of Predictive Values of Tumor Markers

Joseph E. Roulston

13

(16)

3 Quality Assurance of Predictive Markers in Breast Cancer

Anthony Rhodes and Diana M. Barnes

29

(30)

4 Extraction of Nucleic Acid Templates

John M.S. Bartlett and Helen Speirs

59

(12)

5 Microdissection and Extraction of DNA From Archival Tissue

Joanne Edwards, James J. Going, and John M.S. Bartlett

71

(6)

6 Fluorescence In Situ Hybridization: Technical Overview

John M.S. Bartlett

77

(12)

7 HER2 FISH in Breast Cancer

John M.S. Bartlett and Amanda Forsyth

89

(14)

8 Fluorescence In Situ Hybridization for BCR-ABL

Mark W. Drummond, Elaine K. Allan, Andrew Pearce, and Tessa L. Holyoake

103

(14)

9 UroVysion™ Multiprobe FISH in Urinary Cytology

Lukas Bubendorf and Bruno Grilli

117

(16)

10 Chromogenic In Situ Hybridization in Tumor Pathology

Jorma Isola and Minna Tanner

133

(12)

11 Comparative Genomic Hybridization and Fluorescence in Situ Hybridization in Chronic Lymphocytic Leukemia

Marie Jarosova

145

(14)

12 Molecular Characterization of Human Papillomaviruses by PCR and In Situ Hybridization

Suzanne D. Vernon and Elizabeth R. Unger

159

(22)

13 A Nested RT-PCR Assay to Detect BCR/abl

Linda M. Wasserman

181

(10)

14 TP53 Mutation Detection by SSCP and Sequencing

Jenni Hakkarainen, Judith A. Welsh, and Kirsi H. Vähäkangas

191

(18)

15 PCR Diagnosis of T-Cell Lymphoma in Paraffin-Embedded Bone Marrow Biopsies

Jean Benhattar and Sandra Gebhard

209

(8)

16 Circulating DNA Analysis: Protocols and Clinical Applications Using Taqman Assays

Kwan-Chee Allen Chan and Yuk-Ming Dennis Lo

217

(20)

17 Microsatellite Instability: Theory and Methods

Gillian Gifford and Robert Brown

237

(14)

18 The Diagnostic and Prognostic Significance of the Methylation Status of Myf-3 in Lymphoproliferative Disorders

Jeremy M.E. Taylor, Peter H. Kay, and Dominic V. Spagnolo

251

(16)

19 Quantitative Analysis of PRAME for Detection of Minimal Residual Disease in Leukemia

Maiko Matsushita, Rie Yamazaki, and Yutaka Kawakami

267

(10)

20 Determination of Cyclin D1 Expression by Quantitative Real-Time, Reverse-Transcriptase Polymerase Chain Reaction

Karen E. Bijwaard and Jack H. Lichy

277

(20)

21 Detection of Telomerase hTERT Gene Expression and Its Splice Variants by RT-PCR

W. Nicol Keith and Stacey F. Hoare

297

(14)

22 Detection of Telomerase Enzyme Activity by TRAP Assay

W. Nicol Keith and Aileen J. Monaghan

311

(12)

23 Identification of TP53 Mutations in Human Cancers Using Oligonucleotide Microarrays

Wen-Hsiang Wen and Michael F. Press

323

(14)

24 Detection of K-ras Mutations by a Microelectronic DNA Chip

Evelyne Lopez-Crapez, Thierry Livache, Patrice Caillat, and Daniela Zsoldos

337

(18)

25 Microarray-Based CGH in Cancer

Ekaterina Pestova, Kim Wilber, and Walter King

355

(22)

26 Tissue Microarrays

Ronald Simon, Martina Mirlacher, Guido Sauter

377

(14)

Index

391

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