Table Of ContentP M P
RINCIPLES OF OLECULAR ATHOLOGY
P
RINCIPLES
M
OF OLECULAR
P
ATHOLOGY
By
A A. K , , ,
NTHONY ILLEEN MB BCh PhD
Department of Laboratory Medicine and Pathology,
University of Minnesota, Minneapolis, MN
SPRINGER SCIENCE+BUSINESS MEDIA, LLC
© 2004 Springer Science+Business Media New York
Originally published by Humana Press Inc. in 2004
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Cover Illustrations: Figures 23 and 25A–D from Chapter 4, “Methods in Molecular Pathology”; Figure 5
from Chapter 3, “Mutation”; and Figure 9 from Chapter 2, “Genetic Inheritance.”
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ISBN 978-1-61737-348-0
Library of Congress Cataloging-in-Publication Data
Killeen, Anthony A.
Principles of molecular pathology / by Anthony A. Killeen.
p. cm.
Includes bibliographical references and index.
ISBN 978-1-61737-348-0 ISBN 978-1-59259-431-3 (eBook)
DOI 10.1007/978-1-59259-431-3
1. Pathology, Molecular. 2. Genetic disorders. I. Title.
RB113.K47 2003
616.07’56--dc21
2003041737
D
EDICATION
In memoriam parentium, Professor James Francis and Joyce Killeen.
v
P
REFACE
Principles of Molecular Pathology provides a comprehensive, but concise
introduction to this rapidly growing subject. It will be useful to a wide readership
including residents and fellows in laboratory medicine and pathology, practicing
pathologists who have not had a formal exposure to this relatively new field, and
our medical and scientific colleagues in related laboratory and clinical disciplines.
Only a few years ago, experts debated whether molecular pathology was a
bona fide academic discipline, or merely the application of new laboratory tech-
niques that would find their roles in existing areas of the clinical laboratories.
Now it is clear that this field is far more than just a set of novel techniques.
Molecular pathology has a grand theme, and that theme is the study of genetic
mutations, both inherited and acquired, and their effects on the structure and
function of the cell. Within this theme, molecular pathology brings together
concepts from molecular biology, genetics, and traditional pathology to provide
new insights into human diseases, new ways of classifying certain types of dis-
eases, and the technologies to provide new diagnostic and prognostic informa-
tion. There is no doubt that the practice of laboratory medicine and pathology will
be significantly altered by the principles and laboratory methods of molecular
pathology.
The topics in Principles of Molecular Pathology were chosen to provide a
broad overview of the field. Basic concepts of human molecular biology and
genetics are followed by a description of the most commonly used analytical
methods. This background is followed by a discussion of the acquired genetic
abnormalities that underlie human malignancies. Chapters on pharmacogenetics
and identity testing emphasize the growing importance of these areas in clinical
practice. The application of molecular methods to the detection of microbial
pathogens has assumed an essential role in clinical laboratory practice, and this
important area is illustrated using common viral infections as examples.
I hope that Principles of Molecular Pathology will stimulate interest in this
exciting field. I welcome comments from readers at [email protected].
Acknowledgments
First and foremost, I thank my wife, Randee, for her love and support, and for
her patience during the course of my writing this book. It would never have been
completed without the time she afforded me to write. Our children, Olivia and
Trevor, were a constant source of energy and enthusiasm during this project.
I acknowledge with gratitude the excellent support of my colleagues at the
University of Minnesota and my former colleagues at the University of Michi-
vii
viii Preface
gan. Several have read and commented on chapters, including Matt Bower,
Charlotte Brown, Michelle Dolan, Betsy Hirsch, Mark Linder, Elizabeth Petty,
and Rima Tinawi-Aljundi. I thank them sincerely for their suggestions.
Anthony A. Killeen
C
ONTENTS
Preface............................................................................................... vii
1 Basic Concepts in Molecular Pathology.....................................1
2 Genetic Inheritance ...................................................................31
3 Mutation ....................................................................................57
4 Methods in Molecular Pathology..............................................89
5 Inherited Disorders..................................................................141
6 Molecular Origins of Cancer ..................................................185
7 Familial Cancer Syndromes....................................................211
8 Molecular Pathology of Hematological Malignancies...........239
9 Pharmacogenetics.....................................................................279
10 Identity Testing .......................................................................297
11 Molecular Diagnoses of Human Immunodeficiency
Virus and Hepatitis C Virus...........................................309
Index.................................................................................................327
ix
1
Basic Concepts in Molecular
Pathology
BASIC TERMINOLOGY
Human diseases that have a genetic basis, whether hereditary or
acquired, arise from changes in the sequence or pattern of expres-
sion of genes. A gene, which is the unit of heredity, is a piece of
DNA that encodes a protein or RNA. The position at which a given
gene is found on a chromosome is known as its locus. Sequence
variants of a gene are known as alleles,and the most common func-
tional allele at a locus is known as the wild-type allele. Changes in
the sequence of DNA are known as mutations. In genetic use, the
term mutation does not necessarily mean that the effect of the
change in sequence is deleterious to the organism. By definition, a
sequence change that is present in at least 1% of the population is
known as a polymorphism.
In the haploid cell, the human genome is composed of approxi-
mately 3 × 109 bp of DNA, the sequence of which has largely been
determined through the efforts of the public and commercial human
genome projects (1,2).Most of the genome is located in the nucleus,
but mitochondria also contain a small genome that is approximately
16.5 kb in length. The set of genes that is expressed in a cell deter-
mines the structure and functions of the cell.
STRUCTURE OF NUCLEIC ACIDS
Both DNA and RNA are polymers composed of repeating units
of sugars (deoxyribose or ribose, respectively) with attached bases.
The sugars are joined by phosphodiester linkages between the 3′
carbon of one sugar and the 5′ carbon of the next sugar in the poly-
mer (Fig. 1). A strand of DNA or RNA therefore has polarity: the
end with the terminal 5′-carbon is known as the 5′end,and the other
end of the strand, which has an unlinked 3′-hydroxyl group, is
From:Principles of Molecular Pathology
Edited by:A. A. Killeen©Humana Press Inc.,Totowa,NJ
1
2 Killeen
Fig. 1. Structure of a strand of nucleic acid (DNA shown). The strand is com-
posed of a polymer of sugar residues joined by phosphate linkages between the 3′-
carbon of one sugar and the 5′-carbon of the next sugar. Each sugar is attached to a
base. The 5′and 3′ends of the polymer are shown by arrows.
known as the 3′end. Ribose and deoxyribose differ at the 2′-carbon,
which has a hydroxyl group in ribose (Fig. 2). Both DNA and RNA
are composed of purine and pyrimidine bases (Fig. 3). The standard
base composition differs between DNA and RNA:in DNA the bases
adenine (A), cytidine (C), guanine (G), and thymidine (T) are pre-
sent. In RNA,uracil (U) is present in place of thymidine. The struc-
tures of these are shown in Figs. 4 and 5. In addition to these
standard bases, other bases are found in DNA and RNA. The most
frequent modification is methylation of cytidine at carbon 5, giving
rise to 5-methylcytidine.
A strand of DNA forms interstrand hydrogen bonds with another
DNA strand of complementary sequence. In this arrangement, A
forms a base pair with T on the complementary strand,and C forms
Fig. 2. The numbering of carbon atoms in ribose and deoxyribose in nucleic acids
is shown at the top. The structures of ribose and deoxyribose differ at the 2′-car-
bon, which is linked to a hydroxyl group in ribose. In DNA and RNA, the bases
are joined at the 1′carbon.
Fig. 3. Basic structure and numbering of carbon atoms in purine and pyrimidine.
Fig. 4. Structures of the purines adenine and guanine.
