Molecular Pathology Protocols

488 Pages·2001·4.328 MB·English

by  Hongxin Fan, Margaret L. Gulley (auth.), Anthony A. Killeen MB, BCh, PhD, FFPathRCPI (eds.)

Molecular Pathology Protocols
M E T H O D S I N M O L E C U L A R M E D I C I N F .
John M. Walker, SERIESE DITOR
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Molecular Pathology
Protocols
Edited by
Anthony A. Killeen
MB, BCh, PhD, FFPathRCPl
Department of P~fholog U~P^, i versidy of Michigan, Ann Arbor, MI
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Library of Congress Caraloglng in Publication Data
Main entry under title:
Mcthcds in molecular medicinem.
MoIecular pathology protocols I ed~cedb y Anthony A. KiIleen
p. cm. - (Methods in molecular medicinen ; 49)
Includes bibliogtaphrcal references and tndcx.
ISBN 0-89603-68 1-2 (alk. paper).
I. Molecular diagnosikLaboratory manuals 2. Pathology, Molecular-Laboratory manuals.
1. Killeen, Anthony A. 1 I. Series.
[DNLM: I. Pathology, Clmical-methodsLaboratory Manuals. 2. Genetic Technique*
Laboratory Manuals, 3 Zrnmunolog~cT ests-Laboratory Manuals.
QY 25M7183 20011
RB43.7.M646 200 1
616.07'5--dc21 00-024928
Preface
The era of molecular pathology has arrived. From its promising begin-
nings in research laboratories, the field has grown, and continues to grow, to
become a vital part of the care of an ever-increasing number of patients.
Because of its recent emergence from the research taboratory, many
molecuIar pathology protocols we still to be found in the primary litcramre,
and have not appeared in a text. MO~PCUPa~dhQo~io gy Protocob contains labo-
ratory protocoIs that have been developed by many of the authors for use in
clinical molecular pathology laboratories and describe in detail Row to
perform these assays. This book is therefore intended for clinical laboratory
use by medical technologists and pathologists. It will dso be of interest to
research workers who are performing these assays.
In its broadest meaning, pathology is the study of disease, and therefore
it follows that any disease for which the molecular basis is understood would
be suitable as a topic for inclusion in this work. When seiecting protocols, it
was necessary to place limits on the number of chapters that could be feasibly
presented in a single work. Those protoculs that were selected are performed
more frequently, or have achieved recognition as having important diagnostic
utility in contemporary practice. A decision was made to exclude inherited
genetic diseases with certain exceptions, such as those diseases that are
associated with thrombotic states and are part of the traditional dumain
of pathology. Undoubtedly their etiology would have been of much interest to
the great pathologists of the past. A small number of chapters describe meth-
ods that are availabie as commercial assays. These chapters, particularly
in certain methodological details described in the notes, offer much Mler
description of the rnethodk than is often available.
As wiI1 be apparent, many of the protocols described have been devel-
oped as in-house methods by the authors. This point highlights a charactcris-
tic of the field of molecular pathology: the hck of standardization of most
assays, even those in reasonably wide clinica! practice, IJnlike some other
areas of clinical Iaboratoy analysis, there are no definitive methods available
for moiecular pathology. It would be of advantage to the field, if only to
provide consistency among laboratories, if there were to be agreement on
vi Preface
analytical issucs such as probes and primer sets for various assays. These pro-
tocols offer methods that the authors have found to work in their laboratories.
As with all clinical laboratory testing, the results should be interpreted in con-
junction with other laboratoly data and clinical findings.
Anthony A. Killean
Ma, BCh, PhD, FFPafhRCPl
Contents
Preface .................................................................................................v.. .......
Contributors .................... ........... .............................................................x..i. ...
DNA Extraction from Paraff in-f mbedded Tissues
Hongxin Fan and Margaret L. Gulley .............................. ........... I
DNA Extraction from Fresh or Frozen Tissues
fiongxin Fan and Margaret L. Gulley ................... .. ........................ 5
RNA Extraction from Fresh or Frozen Tissues
Hongxin Fan and Margaret L. Gulley .............................................f. .I.
Single-Strand Conformation Polymorphism Analysis of
Mutations in Exons 4-8 of the TP53 Gene
Kirsi H. Viihifkangas, Katariina Casfkn, and Judith A. Welsh ...... 15
CleavasemF ragment Length Polymorphism Analysis for
Genotyping and Mutation Detection
Laura Heisler and Chao-Hung Lee ....................................................2 9
Detection of Telomerase by In Sifu Hybridization and by the
Polymerase Chain Reaction-Based Telomerase Activity Assay
Carmela P. Morales and Shawn E. Holt .......................................... 43
Detection of Microsatellite Instability
Karin 13. Berg, Constance A. Griffin,a nd James R. Eshleman ......5 9
Polymerase Chain Reaction Clonality Assays Based on
X-Linked Genes
Langxing Pan and Huaizheng Peng .................................................. 73
Fluorescent In Situ Hybridization: Evaluation for Ploidy and Gene
Amplification
Susan Sheldon ...............................................................................8..1...
HER-zlne~Ol ncogene Amplification Determined by Fluorescence
In Situ Hybridization
Jeffrey S. Ross, Christine E. Sheehan,
and Jonathan A. Fletcher ............................................................... 93
A Nested Reverse Transcription-Polym erase Chain Reaction Assay
to Detect 8CRlabl
Linda M. Wasserman .....................................................................1..0..5
Contents
12 Detection of t(l5;17)(q24;q21), inv(l6)/t(16;16)(pt 3;q22),
and t(8;21 )(q22;q22) Anomalies in Acute Myeloid Leukemia
Dav/d S. Viswanatha. .........................................................................1 15
13 Detection of t(14;18)(q32;q21 )-Associated BCL-Z/J,Gene
Fusion in Non-Hodgkin Lymphoma
David S. Visw anatha ........................................................................1..4 7
14 Detection of Breast Cancer Cells Using lmmunomagnetic Beads
and Reverse Transcriptase Polymerase Chain Reaction
Scott Luke and Karen L. Kaul ...................... .. ...............................1 65
1 5 Molecular Detection of Circulating Prostate Cancer Cells
Karen L. Kaul .....................................................................................1. 77
16 Methods to Detect Clonal Gene Rearrangements in Lymphomas
and Leukemias
Naheed Mitha and Ronald C. McGIennen .......................................1 89
17 Monitoring of Bone Marrow Transplant Engraftment
Kristine P. Woronzoff-Dashkof f and Ronald C. McGlennen ....... .21 1
18 Direct Molecular Diagnosis of Multiple Endocrine Neoplasia Type t
Elizabeth M Petty, Michael Glynn, and Allen E. Bale ................... 227
19 Molecular Detection of Multiple Endocrine Neoplasia Type 2
Edward H. Rowsell and Myra J. Wick... .......................................... 243
20 Assay for Detecting the 11307K Susceptibility Allele within the
Adenomatous Polyposis Coli Gens
Stephen 6. Gruber ............................................................................. 263
21 Detection of Human Papitlomaviruses by Poty merase Chain
Reaction and In Situ Hybridization
Eiizabeth R. Unger and Suzanne DmV ernon... ................................ 271
22 Molecular Methods for Detecting Epstein-Barr Virus
(Part 1) : I n Situ Hybridization to Epstein-B arr Virus-Encoded RNA
(EBE RJ Transcripts
Hongxin Fan and Margaret L. Gutley .............................................3. 0 1
23 Molecular Methods for Detecting Epstein-Barr Virus (Part Ill:
Strucrural Analysis of Epstein-Barr Virus DNA as a Marker
of Cionaljty
Hongxin Fan and Margaret L. Gulley ............................................ 3 13
24 Molecular ~ethocisfo r Detecting Epstein-Barr Virus (Part Ill):
EBV Viral Load by Competitive Polymerase Chain Reaction
Hongxin Fan and Margaret L. Gulley .............................................. 32 1
Contents
25 Molecular Detection of Kaposi's Sarcoma-Associated Herpesvirus1
Human Herpesvirus-8
Ethel Cesarman .................................................................................. 33 1
26 Diagnostic Applications of Quantitative Polymerase Chain Reaction
for Cytomegatovirus
Richard H. Scheuermann and Xin Bai ..................... ......... ......... 337
27 A Coiorimetric Microtiter Plate Polymerase Chain Reaction System
That Detects Herpes Simplex Virus in Cerebrospinal Fluid and
Discriminates Genotypes 1 and 2
Yi- Wei Tang ..................................................................................... 353
28 Detection and Typing of Hepatitis C Virus
Frederick S. Nolfe ........................ ... ..........................................3..6 3
29 Detection and Speciation of Mycobacteria in Formalin-Fixed,
Paraffin-Embedded Tissue Sections
Diana Mohl and Thomas J. Giordano ..........................................3..7 ..9
30 Ultrasensitive Quantitation of Human Immunodeficiency Virus
Type t RNA in Plasma by the AMPLICOR and COBAS
AMPLICOR HIV-1 MON ITORTMT ests
Sfeven Herman, James Novokny, and Maurice Rosensfraus ...... 389
3 1 Molecular Diagnosis of Hereditary Thrombotic Disorders
James G. Donnelly .......................................................................... 4 13
32 Prenatal Genotyping of the RhD Locus to Identify Fetuses at Risk
for Hemolytic Disease of the Newborn
Martin J. Hessner and Daniel 8. Bellissirno .................................4.2. 7
33 Molecular Diagnosis of Hereditary Hemochromatosis
Suzanne Huber and Karl V. Voelkerding ...................................... 439
34 Genotyping of Apolipoprotein E
I. Cefin Orturk, Nahida Akel, and Anthony A. Kilieen .................4..5 1
35 Genotyping for Functionally Important Human CYP2D6"4 (0)
Mutation Using TaqMan Probes
Michael M. Shi, Scott P. Myrand, Michael R. Bleavins, and
Felix A. de la Iglesia ................................................................... 459
Index .......................... .. ...................................................................... 473