Inhaltsverzeichnis

Vorwort

Foreword

In 1994 I coedited a book, Molecular Pathology: Approaches to Diagnosing Human Disease in the Clinical Laboratory, that coined the phrase "molecular pathology" to refer to applications of molecular biology in the traditional areas of laboratory medicine. That compilation of clinical molecular techniques included 11 chapters and an epilogue on "New Directions for the Clinical Laboratory." Chapter headings included: automation, neoplasia, heritable diseases, and infectious diseases.

Three years later, in 1997, Bill Coleman and Greg Tsongalis edited Molecular Diagnostics: For the Clinical Laboratorian, which contained 18 chapters and introduced the new areas of RT-PCR and In Situ PCR, and included a section on gene therapy. Now, ten years after the introduction of molecular pathology, we are looking at the second edition of Bill Coleman and Greg Tsongalis' text.

This second edition now comprises 44 chapters, and contains new chapters on bioinformatics, microarrays, methylation assays, FISH, laser capture microdissection, quality assurance, chimerism studies for bone marrow transplantation, and separate chapters on genetic counseling and ELSI (ethical, legal, and social issues). These new chapters represent developments in the past decade that have fundamentally changed the scope from molecular pathology to molecular diagnostics, highlighting the changing role of the clinical laboratorians who direct these efforts. It should be evident that molecular pathology and diagnostics impact almost every conceivable subspecialty in laboratory medicine and, particularly in the case of pharmacogenomics, have led to the development of new areas of investigation.

What is less evident is the burden placed upon the laboratorians directing these efforts. Issues regarding training, certification, continuing education, and reimbursement (just to name a few) have demanded enormous time and effort from professional organizations and governmental agencies. In addition, because conventional approaches cannot always be applied to molecular diagnostics, unique solutions for quality assurance and quality control must be developed. These challenges have engendered committees, subcommittees, taskforces, and workgroups from regulatory agencies and professional organizations, representing worldwide constituencies. As in any situation involving so many players, consensusbuilding and communication are mandatory. To these ends, professional journals and textbooks are our best hope for remaining current with this rapidly changing field. One needs only to compare the wealth of knowledge in this current edition with our efforts of only ten years ago to appreciate the magnitude of this challenge.

Lawrence M. Silverman, PhD

Klappentext

Molecular Diagnostics

For the Clinical Laboratorian

SECOND EDITION

Edited by William B. Coleman

Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC

Gregory Tsongalis

Department of Pathology, Dartmouth Medical School, Dartmouth-Hitchcock Medical Center, Lebanon, NH

Foreword by

Lawrence M. Silverman Department of Pathology and Laboratory Medicine, University of Virginia, Charlottesville, VA

From Reviews of the First Edition...

"...highly recommended...for those interested in clinical molecular diagnosis...will satisfy those who are more expert in certain areas of molecular diagnosis, but who have been unable to keep up with the wide range of recent advances in molecular diagnosis. " - AMERICAN JOURNAL OF CLINICAL PATHOLOGY

"...gives a good theoretical background for those with little experience in this field. It is readable, comprehensive, and...up-to-date. " - JOURNAL OF CLINICAL PATHOLOGY

"... well written, comprehensive... should bring even the reader with limited background knowledge up to speed on what is a rapidly progressing field. "

- TRENDS IN MOLECULAR MEDICINE

"...a timely and highly relevant book that will serve as a valuable resource to those practicing molecular diagnostics from the bench, as well as to basic

and clinical scientists... " - ENDOCRINE NEWS

"...a very good introduction to the basic elements of molecular pathology...excellent discussion of methods... " - CLINICAL CHEMISTRY

Taking advantage of the many major advances that have occurred since their groundbreaking first edition was published, William B. Coleman and Gregory J. Tsongalis have updated and expanded their highly praised tutorial guide to molecular diagnostic techniques to include not only improved traditional methods, but also totally new molecular technologies, some not yet in routine use. The authors offer cutting-edge molecular diagnostics for genetic disease, human cancers, infectious diseases, and identity testing, as well as new insights into the question of quality assurance in the molecular diagnostics laboratory. Additional chapters address other technologies found in the clinical laboratory that are complementary to molecular diagnostic methodologies, and also discuss genetic counseling and the ethical and social issues involved with nucleic acid testing. A value-added compact disk containing a companion eBook version of Molecular Diagnostics: For the Clinical Laboratorian, Second Edition, is included for downloading and use in the reader' s PC or PDA.

Authoritative and state-of-the-art, Molecular Diagnostics: For the Clinical Laboratorian, Second Edition is the essential textbook of choice for anyone working in molecular diagnostics and who wants to remain current with this rapidly changing field.

Features

Cutting-edge molecular diagnostics for genetic disease, human cancers, and infectious diseases

New applications of technology to specific problems in molecular diagnostics

Discussion of quality assurance issues in the molecular diagnostics laboratory

Advanced molecular technologies and their potential use in molecular diagnostics

• Inclusion of common technologies that can complement molecular diagnostics
• Introductory survey of basic molecular biology techniques and concepts
• Review of genetic counseling and the ethical issues involved in nucleic acid testing

ISBN 1-58829-356-4

Register

Index

A

ACE, see Angiotensin-Converting enzyme

Acute lymphoblastic leukemia (ALL),

- cytogenetics, 185
- epidemiology, 415
- flow cytometry immunophenotyping, 168
- pathogenesis, 427, 428
- precursor B-cell disease,

- - chromosomal translocations, 428-430
- - gene mutations, 430
- - ploidy, 428
- precursor T-cell disease,

- - chromosomal translocations, 430, 431
- - gene mutations, 430, 431
Acute myeloid leukemia (AML),

- chromosomal translocations and inversions,

- - acute megakaryoblastic leukemia, 423
- - acute promyelocytic leukemia translocations, 419, 420
- - inv(16)(pl3q22), 420, 421
- - mil translocations, 421, 422
- - pml-rara,

- - - detection, 418, 419
- - - overview, 417, 418
- - t(6;9), 422, 423
- classification, 184, 185, 415
- cytogenetics, 184, 185, 187
- epidemiology, 415
- flow cytometry immunophenotyping, 167, 168
- gene mutations,

- - c-kit, 416
- - p53, 416
- - Ras, 416
- - retinoblastoma gene, 416
- - Runxl, 416
- gene partial tandem duplications,

- - Flt3, 416, 417,

- - mll, 417
- induction by cancer treatment, 187
- treatment, 415
Adrenergic receptors, heart failure gene polymorphisms, 304, 305
Agarose gel electrophoresis, see Electrophoresis

AHO, see Albright's hereditary osteodystrophy

AIDS, see Human immunodeficiency virus-1
Albright's hereditary osteodystrophy (AHO), gene mutations, 288
ALCL, see Anaplastic large cell lymphoma

ALL, see Acute lymphoblastic leukemia
AML, see Acute myeloid leukemia
Amplification refractory mutation system (ARMS),
- advantages and limitations, 70
- double ARMS, 69
- MS-PCR, 69
- multiplex ARMS, 69, 70
- principles, 69
Anaplastic large cell lymphoma (ALCL),

- ALK1 immunohistochemistry, 213, 214
- chromosomal translocations, 408, 409
Andral, Gabriel, 6
Aneuploidy, see Cytogenetic analysis

Angiotensin-Converting enzyme (ACE), heart failure gene polymorphisms, 303, 304
Antithrombin, coagulation disorders, 313
Apolipoprotein E, gene alleles and cardiovascular disease risks, 302
ARMS, see Amplification refractory mutation system

Ataxia telangiectasia,
- features, 274
- genetics, 274
- molecular diagnosis, 274
ATM, T-cell prolymphocytic leukemia mutations, 433

B

B-cell,

- clonality,

- - overview, 393, 394
- - polymerase chain reaction analysis, 401-403
- Southern blot analysis, 399-401
- development, 394, 395
- surface immunoglobulin receptor gene rearrangement, 396-398
B-cell prolymphocytic leukemia, features, 432
Bioinformatics,

- candidate genes,

- - identification, 58, 59
- - mapping, 58
- clinical applications,
- - disease gene identification, 59
- - genetic databases, 60
- - personalized medicine, 59
- - pharmacogenetics, 59, 60
- - pharmacogenomics, 60
- drug discovery, 60
- tools,

- - BLAST, 57
- - dbEST, 58
- - Map Viewer, 57
- - sequence databases, 57
- - UniGene, 58
Bladder cancer, cytogenetics, 182
Bone marrow transplantation,

- allogeneic transplant types, 511
- engraftment monitoring,

- - clinical utility, 511
- - controls, 513
- - informative markers, 512, 513
- - overview of tests, 511, 512
- - quantitative fingerprinting, 513
- - reporting, 513
- - sensitivity, 513
- effects on later blood testing, 513
Boyle, Robert, 5
Breast cancer,
- cytogenetics, 183
- hereditary cancer, 362
- immunohistochemistry,

- - E-cadherin, 213
- - Her-2/Neu, 212
- prognostic value of molecular testing, 365
Bright, Richard, 6
Burkitt lymphoma, chromosomal translocations, 406, 407

C

Calcium-sensing receptor, gene mutations, 288
Cancer, see also specific cancers,

- cytogenetics,
- - chromosome number instability, 354, 355
- - chromosome structure instability, 355, 356
- DNA methylation changes, 150, 151
- DNA repair defects, 353
- early detection and genetics, 363-365
- genomic instability, 352, 353
- micro satellite instability,

- - determination, 256, 357
- - frequency in human cancer, 358
- - mismatch repair defects, 358, 359
- - molecular targets, 359, 360
- molecular alterations,

- - chromosomal abnormalities, 350, 353-356
- - DNA damage, 351
- - mutations, 349, 350
- - nucleotide sequence abnormalities, 350, 351
- multistep pathogenesis, 349
- mutation rates,

- - cancer cells, 352
- - spontaneous mutation rates in normal cells, 351, 352
- prognostic value of molecular testing, 365
- screening, 365, 366
Capillary electrophoresis, see Electrophoresis

Cardiovascular disease (CVD),

- apolipoprotein E gene alleles and risk, 302
- genetic association criteria, 295, 296
- heart failure markers,

- - adrenergic receptor gene polymorphisms, 304, 305
- - angiotensin-converting enzyme gene polymorphisms, 303, 304
- lipoprotein lipase gene alleles and risk, 300, 301
- methylene tetrahydrofolate reductase gene alleles and risk, 302, 303
- NADH/NADPH oxidase gene alleles and risk, 301
- nitric oxide synthase, endothelial enzyme gene alleles and risk, 301, 302
- paraoxonase gene alleles and risk, 301
- platelet glycoprotein gene alleles and risk, 297-300
- single nucleotide polymorphisms and risks, 297
- thrombotic gene alleles and risk,

- - factor II, 295, 296

- - factor V, 295, 296

- - factor VII, 296

- - fibrinogen, 296
- - plasminogen activator inhibitor-1, 296, 297
CCM, see Chemical cleavage of mismatched nucleotides

Central dogma, molecular biology, 13
Cervical cancer, see also Human papillomavirus, Pap test sensitivity, risk factors, 447
CF, see Cystic fibrosis

CGH, see Comparative genomic hybridization

Charcot-Marie-Tooth disease, see Hereditary motor and sensory neuropathy

Chemical cleavage of mismatched nucleotides (CCM), principles, 96
Chlamydia trachomatis,

- clinical features, 437
- conventional detection, 437, 438
- epidemiology, 437
- molecular assays,

- - commercial assays,
- - - Amplicor CT/NG, 442, 443
- - - Aptima Combo 2, 442
- - - Hybrid Capture II assays, 441, 442
- - - LCX, 440
- - - Pace 2C, 442
- - - Probe-Tec assay, 440, 441
- - overview, 439, 440
- - prospects, 443
Chromosomal aberrations, see Cytogenetic analysis

Chromosome banding, techniques, 189, 190
Chronic eosinophilic leukemia, features, 427
Chronic lymphocytic leukemia (CLL),

- chromosomal translocations, 431, 432
- classification, 431
- epidemiology, 415
- fluorescence in situ hybridization, 431
- gene expression profiling, 432
- immunoglobulin gene somatic hypermutation, 432
- transformation, 432
Chronic myelogenous leukemia (CML),

- accelerated phase, 426
- cytogenetics, 183-186
- epidemiology, 415
- imatinib mesylate,

- - resistance, 426
- - treatment, 415, 426
- Philadelphia chromosome, 423-426
Chronic myelomonocytic leukemia (CMML),

- chromosomal translocations, 426, 427
- Ras mutations, 427
c-kit,

- acute myeloid leukemia mutation, 416
- gastrointestinal stromal tumor immunohistochemistry, 212, 213
CLIA, see Clinical Laboratory Improvement Act

Clinical genetics,
- physician training, 533
- specialties, 530
Clinical Laboratory Improvement Act (CLIA), regulations, 227, 228, 237
CLL, see Chronic lymphocytic leukemia

Cloning, historical perspective, 8, 9
CML, see Chronic myelogenous leukemia

CMML, see Chronic myelomonocytic leukemia

CMV, see Cytomegalovirus

Coagulation,
- anticoagulant systems, 312
- hemostasis,

- - primary, 311
- - secondary, 311, 312
- history of testing, 311
- molecular defects in disorders,

- - antithrombin, 313
- - bleeding disorders, 313 factor V, 313
- - methylenetetrahydrofolate reductase, 314
- - platelet glycoproteins, 314
- - polymorphisms and mutations, 312
- - protein C, 313
- - protein S, 313, 314
- - prothrombin, 313
- - thrombomodulin, 314
- molecular testing,

- - advantages and disadvantages, 317
- - clinical applications, 317, 318
- - direct hybridization, 316
- - DNA microarray, 315, 316
- - Factor V Leiden, 315-317
- - general aspects, 314, 315
- - polymerase chain reaction techniques, 315
- - restriction fragment length polymorphism analysis, 315
Colorectal cancer, see also Hereditary nonpolyposis colorectal cancer,

- cytogenetics, 183
- early detection, 363, 364
- genetic model of development and progression, 360
- mismatch repair protein immunohistochemistry, 213
- prognostic value of molecular testing, 365
Comparative genomic hybridization (CGH), principles, 132
Congestive heart failure, see Heart failure

Coronary artery disease, see Cardiovascular disease

CVD, see Cardiovascular disease

Cystic fibrosis (CF),

- anatomic pathology,

- - bones and joints, 323, 324
- - gastrointestinal system, 323
- - hepatobiliary system, 323
- - pancreas, 323
- - reproductive system, 324
- - respiratory system, 323
- - vascular system, 324
- carrier screening, 324, 326
- clinical testing, 321, 322
- cystic fibrosis transmembrane conductance regulator gene mutations, 321
- genetic counseling, 533, 534
- molecular diagnostics and result reporting, 324, 326
- pathophysiology, 322
Cytogenetic analysis, see also Fluorescence in situ hybridization,

- acquired abnormalities, 181-187
- aneuploidy,

- - autosomal aneuploidy, 177, 178
- - cancer, 355
- - monosomy, 176, 177
- - prevalence, 176
- - sex chromosomes, 176, 177
- deletions, 179-181, 356
- duplications, 179-181
- genetic disorder classification, 260, 261
- historical perspective, 173
- insertions, 181
- inversions, 179
- laboratory considerations, 173, 174
- polyploidy, 177, 178
- samples,

- - amniotic fluid, 174, 175
- - blood, 175
- - bone marrow, 176
- - solid tissues, 175, 176
- translocations, 178, 179
Cytomegalovirus (CMV),

- detection,

- - assays and performance, 473-475, 477, 478
- - clinical utility,

- - - opportunistic infection, 476, 477
- - - transplant recipients, 475, 476
- - - treatment monitoring, 475
- - prospects, 479, 480
- drug resistance mutations and testing, 478-480
- opportunistic infection, 473, 476, 477

D

Denaturing gradient gel electrophoresis (DGGE), bisulfite modification for DNA methylation identification, 153
- mutation detection, 94-96
Dentatorubral-pallidoluysian atrophy (DRPLA),

- features, 269
- genotype-phenotype correlation, 269, 270
- molecular diagnosis, 271, 272
- molecular mechanisms, 270, 271
- parental transmission bias, 270
- repeat instability, 269
DGGE, see Denaturing gradient gel electrophoresis

Diabetes, see also Maturity onset diabetes of the young,

- genetics,
- - type 1 diabetes, 290, 291
- - type 2 diabetes, 291
- history of testing, 6, 7
Diffuse large B-cell lymphoma, chromosomal translocations, 408
Direct molecular diagnostic tests, overview, 264, 265
DMD, see Duchenne muscular dystrophy

DNA,

- blotting, see Southern blot
- central dogma, 13
- chemical nature, 13, 14
- extraction, see Nucleic acid extraction
- genetic code, 17
- genomic DNA organization, 15
- mutagenesis and consequences, 20-22
- recombination, 16
- repair, 16, 17
- replication, 15, 16
- structure,
- - elucidation, 8, 517
- - overview, 14, 517, 518
- transcription of RNA, 15
DNA methylation,

- functions, 149, 150
- human diseases,

- - cancer changes, 150, 151
- - clinical applications,

- - - hereditary nonpolyposis colorectal cancer, 156, 157
- - - imprinting disorder diagnosis, 156
- - - marker of malignant disease, 155
- - - prognostic/predictive markers, 156
- - - prospects, 157
- - - quality control, 157
- - - tumor clonality determination, 155, 156
- - syndromes, 150
- normal cells, 149, 150
- polymerase chain reaction-based methods,

- - bisulfite modification, 151
- - bisulfite PCR followed by restriction analysis, 152
- - DNA melting analysis, 153
- - enzymatic regional methylation assay, 152, 153
- - genomic sequencing, 151
- - methylation-sensitive single-nucleotide primer extension assay, 152
- - methylation-sensitive single-strand conformation
- - analysis, 153
- - methylation-specific PCR, 151, 152
- - primer design, 154, 155
- - profiling and arrays, 154
- - real-time polymerase chain reaction, 153, 154
DNA microarray,

- applications, 121, 122
- DNA arrays,

- - chip production, 123
- - image acquisition and analysis, 124-126
- - sample preparation and hybridization, 123, 124
- clinical applications, 145, 146
- coagulation disorder analysis, 315, 316
- historical perspective, 122, 123
- hypothesis testing, 135, 136
- interpretation,

- - gene filtering, 136
- - gene space, 136
- - machine learning, 136, 137
- - supervised learning,

- - - k-nearest neighbors, 139, 140
- - - limitations and special considerations, 142
- - - method selection, 140
- - - overview, 139
- - - support vector machine, 140
- - - validation, 140-142
- - unsupervised learning,

- - - clustering and dendrograms, 137, 138
- - - limitations and special considerations, 142
- - - method selection, 139
- - - overview, 137
- - - partitioning methods, 138, 139
- normalization of data, 134, 135
- oligonucleotide arrays,

- - Affymetrix platform and chip production, 126, 127
- - Agilent system, 128, 129
- - image acquisition and analysis, 128
- - sample preparation and hybridization, 128
- RNA extraction, 28, 29
- RNA measurement rationale, 130
- sample selection, 129, 130
- software, 144, 145
- standardization, 142-144
- study design and error sources, 130, 134
DNA repair,

- cancer defects, 353, 358, 359
- mismatch repair defects in cancer,

- - epigenetic silencing of repair genes, 359
- - gene defects, 359
- - hereditary nonpolyposis colorectal cancer,

- - - comparative sequence analysis, 384
- - - immunohistochemical analysis of protein expression, 377, 378
- - - mutation detection strategy, 386
- - - point mutation detection, 384
- - - whole-exon mutation detection, 384-386
- microsatellite instability induction, 358
- mutation rates, 358
- overview, 377
- oxidative stress role, 359
DNA sequencing,

- clinical applications, 105, 106
- data analysis software, 104, 105
- genomic sequencing, 14, 15, 151
- human leukocyte antigen typing, 489, 491
- Maxam and Gilbert method, 100, 101
- mitochondrial DNA sequencing for human identity testing, 504, 505
- overview, 99, 100
- Sanger sequencing,

- - capillary array electrophoresis, 103, 104
- - dideoxynucleotide terminated fragment labeling, 101-103
- - enzymes, 101
- - principles, 100, 101
Down's syndrome,

- acute megakaryoblastic leukemia susceptibility, 423

- features, 177
DRPLA, see Dentatorubral-pallidoluysian atrophy

Drugs,
- metabolism and distribution,

- - phase I metabolism, 341, 342
- - phase II metabolism, 341, 342
- - single nucleotide polymorphism effects, 341
- - transporters, 342, 343
- pharmacogenetics,
- - clinical applications, 344
- - drug development, 343, 344
- - overview, 343
Duchenne muscular dystrophy (DMD),

- features, 276
- genetics, 276, 277
- molecular diagnosis, 277, 278

E

EBV, see Epstein-Barr virus

Edward syndrome, features, 177
Ehrlich, Paul, 6
Electrophoresis,

- agarose gel electrophoresis, 86, 87
- applications,

- - chemical cleavage of mismatched nucleotides, 96
- - denaturing gradient gel electrophoresis, 94-96
- - DNA fragment sizing, 90
- - DNA sequencing, 99-107
- - heteroduplex analysis, 93, 94
- - restriction fragment length polymorphism analysis, 98, 99
- - ribonuclease cleavage assays, 96-98
- - single-stranded conformational polymorphism, 90-93
- capillary electrophoresis, 88-90, 103, 104
- Polyacrylamide gel electrophoresis, 87, 88
- principles, 86
- trinucleotide repeat measurements,

- - capillary electrophoresis, 244
- - Polyacrylamide gel electrophoresis, 244
Enzymatic regional methylation assay (ERMA), principles, 152, 153
Epstein-Barr virus (EBV), immunohistochemistry, 208
ERMA, see Enzymatic regional methylation assay

Ethics,
- confidentiality and discrimination, 526, 528, 548-550
- genetic counseling dilemmas, 526, 528, 530
- informed consent, acquisition, 546, 547
- - contents of form, 547, 553, 554
- - definition, 546
- - overview, 545, 546
- - research informed consent, 547, 548
- patent infringement, see Patents

F

Factor II, gene alleles and cardiovascular disease risks, 295, 296
Factor V,

- coagulation disorders, 313
- Factor V Leiden testing, 315-317
- gene alleles and cardiovascular disease risks, 295, 296
Factor VII, gene alleles and cardiovascular disease risks, 296
Familial medullary thyroid carcinoma (FMTC), gene mutations, 288, 289
Fibrinogen, gene alleles and cardiovascular disease risks, 296
FISH, see Fluorescence in situ hybridization

Flow cytometry,
- clinical applications,

- - acute lymphoblastic leukemia immunophenotyping, 168
- - acute myeloid leukemia immunophenotyping, 167, 168
- - CD4+ T-cell enumeration in immune deficiency, 164-167
- - CD34+ hematopoietic stem cell enumeration, 167
- - DNA content/ploidy analysis, 170
- - minimal residual disease analysis, 170, 172
- - non-Hodgkin's lymphoma immunophenotyping, 168-170
- principles, data analysis and gating, 164 fluidics, 163
- - fluorescence and extrinsic properties, 163
- - light source and scatter, 163
- - multicolor analysis, 163, 164
- - spectral overlap and compensation, 164
Flt3, gene partial tandem duplication, 416, 417
Fluorescence in situ hybridization (FISH),

- cell cycle phase of target cell, 191, 192
- clinical implications of cytogenetic assessment,

- - monitoring of disease, 198
- - pathobiology of disease, 196, 197
- - prognosis, 197, 198
- - treatment response, 198
- comparative genomic hybridization, 194, 195
- comparison with other cytogenetic analysis techniques, 198-200
- DNA probes, 192, 193

- fiber-FISH, 195

- historical perspective, 189
- multiplex FISH and spectral karyotyping, 193, 194
- principles, 191, 192
- prospects, 200
- signal amplification,

- - in situ polymerase chain reaction, 195, 196
- - primed in situ labeling, 195
- - tyramide signal amplification, 196
- signal enumeration, 193
- troubleshooting, 193, 195
FMTC, see Familial medullary thyroid carcinoma

Follicular lymphoma, chromosomal translocations, 405, 406
Forensics, see Human identity testing

Fragile X syndrome, features, 267
- genotype-phenotype correlation, 269, 270
- molecular diagnosis, 271, 272
- molecular mechanisms, 270, 271
- parental transmission bias, 270
- repeat instability, 269
- trinucleotide repeat measurements,

- - allele size analysis, 244
- - capillary electrophoresis, 244
- - overview, 243, 244
- - Polyacrylamide gel electrophoresis, 244
Friedreich's ataxia,

- features, 269
- genotype-phenotype correlation, 269, 270
- molecular diagnosis, 271, 272
- molecular mechanisms, 270, 271
- parental transmission bias, 270
- repeat instability, 269

G

Gastrointestinal stromal tumor (GIST), c-kit immunohistochemistry, 212, 213
Gene mutations, features, 261, 262
Genetic counseling,

- assumptions, 529
- candidates, 426
- case studies,
- - cystic fibrosis, 533, 534

- - familial cancer, 537, 538
- - hearing loss GJB2 gene mutation, 534, 535
- - Huntington's disease, 535-537
- communication, 526, 527, 531
- components, 528, 529
- counselors,

- - supply and projected need, 530
- - training, 530
- definitions, 529
- ethical dilemmas, 526, 528, 530
- expectations, 532

- family history collection, 529

- genetic testing,

- - benefits, 528
- - children, 528
- - counseling needs, 532
- - heterogeneity and misinterpretation, 532, 533
- - indications, 527
- - supplementation of results, 533
- - utility,

- - - diagnosis, 527
- - - information for relatives, 527, 528
- - - natural history of disorder, 527
- goals, 530, 532
- nondirectiveness, 531
- outcome evaluation, 531, 532
- overview, 525, 526
- philosophical and societal differences, 531
- privacy rights, 526, 528
- recurrence risks, 531, 532
- reproductive decision effects, 531
- trends, 531
- unequal access to genetic services, 533
GH, see Growth hormone

GIST, see Gastrointestinal stromal tumor

Growth hormone (GH),

- combined pituitary hormone deficiency,

- - HESX1 mutations, 286
- - LHX3 mutations, 286
- - overview, 286
- - PIT1 mutations, 286, 287
- - PROP1 mutations, 287
- - X-linked deficiency, 287
- isolated growth hormone deficiency,

- - autosomal dominant deficiency, 283, 284
- - autosomal recessive deficiency, 282, 283, 285
- - diagnosis, 282
- - features, 282
- - X-linked deficiency, 284
- pathway, 282
- resistance,
- - gene deletions, 285
- - gene point mutations, 285, 286
- - Laron dwarfism I, 285, 286
- - Laron dwarfism II, 286
- - receptor defects, 285
- - splicing defects, 286

H

HDN, see Hemolytic disease of the newborn

Heart failure,

- adrenergic receptor gene polymorphisms, 304, 305
- angiotensin-converting enzyme gene polymorphisms, 303, 304
Hemolytic disease of the newborn (HDN),

- human platelet antigens, 329, 330
- Kell red cell antigen system genotyping, 334
- Kidd red cell antigen system genotyping, 334, 335
- maternal contamination and sensitivity of genotyping, 336, 337
- Rhesus blood group,

- - genes, 330
- - RhC genotyping, 331, 333, 334
- - RhD genotyping, 330
Hepatitis C,

- clinical features, 462, 463
- clinical utility of tests,

- - acute disease, 466
- - blood donor testing, 468
- - chronic disease, 466, 467
- - interferon response, 466, 467
- - pretreatment evaluation, 467
- epidemiology, 461
- genotyping, 465, 466
- RNA detection,
- - qualitative assays, 464, 465
- - quantitative assays, 465
- - sample handling, 464
- - viral load, 464
- serological tests, 463, 464
- viral structure and function, 461, 462
Her-2/Neu, immunohistochemistry, 212
Hereditary motor and sensory neuropathy (HMSN),

- features, 274, 275
- genetics, 275, 276
- molecular diagnosis, 276
Hereditary nonpolyposis colorectal cancer (HNPCC),

- combination testing, 386, 387
- cost-effectiveness of tumor testing, 387-389
- diagnostic criteria, 375, 376
- DNA methylation analysis, 157, 156, 157
- DNA mismatch repair,

- - comparative sequence analysis, 384
- - immunohistochemical analysis of protein expression, 377, 378
- - mutation detection strategy, 386
- - overview, 377
- - point mutation detection, 384
- - whole-exon mutation detection, 384-386

- family selection for linkage studies, 375, 376

- gene mutations, 361, 362

- history of study, 375

- interpretation of tests, 389

- microsatellite instability,
- - categories, 378, 379, 381
- - clinical significance, 382
- - testing,

- - - number of markers, 381
- - - practical points, 382-384
- - - selection of markers, 381, 382
- tumor types and risks, 375, 376
HESX1, mutations, 286
Heteroduplex analysis,
- conformation-sensitive gel electrophoresis, 93, 94
- human leukocyte antigen typing, 492
- MDE™ gels, 93
- mutation detection, 93
HGP, see Human Genome Project

HIV-1, see Human immunodeficiency virus-1
HLA, see Human leukocyte antigen

HMSN, see Hereditary motor and sensory neuropathy

HNPCC, see Hereditary nonpolyposis colorectal cancer

Hodgkin' s lymphoma,

- cytogenetics, 186
- diagnosis, 409, 410
- immunohistochemistry, 209, 210
- prevalence, 393
HPV, see Human papillomavirus

Human Genome Project (HGP),

- bioinformatics, 57-60
- genome features, 259
- goals, 57
- historical perspective, 9
Human identity testing,

- case reports, 520, 521
- commercial labs in United States, 498
- DNA typing,
- - DNA isolation and quantification, 499, 500
- - historical perspective, 495-497
- - interpretation, 519, 520
- - mitochondrial DNA sequencing, 504, 505
- - prospects, 505-507
- - quality assurance, 497-499
- - sample collection, 499, 518
- - short tandem repeats,
- - - commercially available multiplexes, 501

- - - fragment separation and data analysis, 502-504

- - - polymerase chain reaction of loci, 500, 518, 519
- - - Y chromosome analysis, 505
- - Southern blot, 518

- floater contamination, 519, 520

- forensic cases, 495
Human immunodeficiency virus-1 (HIV-1),

- cytomegalovirus opportunistic infection, see Cytomegalovirus

- drug resistance testing, 457, 458
- epidemiology, 453
- viral load testing,
- - clinical utility, 453, 454
- - commercial assays,
- - - Nucli-Sens assay, 454, 455
- - - QUANTIPLEX® assay, 454
- - - Roche Amplicor assay, 455
- - interpretation, 456, 457
- - specimen requirements, 456
- - TaqMan assay, 455, 456
- virology, 453
Human leukocyte antigen (HLA),

- major histocompatibility complex genetics, 487, 488
- nomenclature, 488
- structure and function, 487
- types, 485, 486
- typing,
- - clinical applications, 485, 492, 493
- - DNA sequencing, 489, 491
- - heteroduplex analysis, 492
- - polymerase chain reaction with sequence-specific
- - primers, 489
- - reference strand conformation analysis, 492
- - sequence-specific oligonucleotide probe hybridization, 489
- - single-stranded conformational polymorphism, 491, 492
Human papillomavirus (HPV),

- cervical cancer,

- - risks, 448
- - testing,

- - - ASCUS Low Grade Triage Study, 448, 449
- - - direct probe hybridization, 449
- - - Hybrid Capture II assay, 449, 450
- - - polymerase chain reaction, 450
- - - prospects, 450
- - - utility, 449
- immunohistochemistry, 208
- replication, 447
- types, 447
Huntington's disease,

- features, 269
- genetic counseling, 535-537
- genotype-phenotype correlation, 269, 270
- molecular diagnosis, 271, 272
- molecular mechanisms, 270, 271
- parental transmission bias, 270
- repeat instability, 269

I

Identity testing see Human identity testing

IHC, see Immunhistochemistry

Immunhistochemistry (IHC),

- antibodies, 204

- antigen retrieval, 204, 205

- artifacts, 206

- autzomation, 205, 206

- clinical applications,

- - infectious disease, 207, 208

- - oncogenic virus detection, 208

- - prospects, 215
- - tissue microarrays, 211, 212
- - tumor diagnosis, 208-212
- controls, 206, 207
- detection, 205
- hereditary nonpolyposis colorectal cancer analysis of mismatch repair protein expression, 377, 378
- historical perspective, 203
Indirect molecular diagnostic tests, overview, 264, 265
Informed consent,

- acquisition, 546, 547
- contents of form, 547, 553, 554
- definition, 546
- overview, 545, 546
- quality assurance, 230
- research informed consent, 547, 548
In situ hybridization (ISH), see also Fluorescence in situ hybridization,

- fixation of specimens, 190
- historical perspective, 189
- hybridization and visualization, 190, 191
- pretreatment of specimens, 190
- principles, 80, 81, 189
- signal amplification,

- - in situ polymerase chain reaction, 195, 196
- - primed in situ labeling, 195
- - tyramide signal amplification, 196
Invader™ assay, single nucleotide polymorphism typing, 113, 115
ISH, see In situ hybridization

K

Kell, red cell antigen system genotyping, 334
Kidd, red cell antigen system genotyping, 334, 335
Klinefelter syndrome, features, 177

L

Laboratory-developed assays (LDAs),
- Food and Drug Administration analyte-specific reagent rule, 248, 249
- genetic testing constraints, 255
- implementation,

- - assay design and development, 250-252
- - patent issues, 250
- - test selection, 249, 250
- kit assay comparison, 247, 248
- quality control and assurance of testing process, 255, 256
- validation, 252
- verification,

- - accuracy, 254
- - clinical verification, 255
- - overview, 252, 253
- - preanalytical consideration, 254, 255
- - precision, 253, 254
- - reportable range, 254
- - sensitivity, 254
- - specificity, 254
Laser capture microdissection (LCM),

- cell number requirements, 224
- instrumentation,

- - Arcturus, 219
- - Bio-Rad Clonis, 220
- - comparison of systems,

- - - pros and cons, 223, 224
- - - smallest microdissected area, 222
- - - specifications, 223
- - - specimen conditions, 221, 222, 224
- - - specimen visualization, 222, 223
- - Leica AS LMD, 219, 220
- - PALM, 220
- resources, 219
LCR, see Ligase chain reaction

LDAs, see Laboratory-developed assays

LHX3, mutations, 286
Li-Fraumeni syndrome, gene mutations, 361
Ligase chain reaction (LCR), principles, 78, 79
Linked linear amplification, principles, 79
Lipoprotein lipase (LPL), gene alleles and cardiovascular disease risks, 300, 301
LOH, see Loss of heterozygosity

Loss of heterozygosity (LOH),

- assays, 132
- cancer, 354
- endocrine disease, 288, 289
LPL, see Lipoprotein lipase

Lung cancer,
- early detection, 364
- small-cell carcinoma cytogenetics, 182, 183

M

Major histocompatibility complex, see Human leukocyte antigen

Mantle cell lymphoma,
- chromosomal translocations, 407, 408
- cyclin Dl immunohistochemistry, 214, 215
Maturity onset diabetes of the young (MODY), types and gene mutations, 289, 290
Melanoma, familial, 362
MEN, see Multiple endocrine neoplasia

Mendel, Gregor, 7, 8

Mendelian inheritance, patterns, 262-264
Metastasis, immunohistochemistry, 209
Methylene tetrahydrofolate reductase,

- coagulation disorders, 314
- gene alleles and cardiovascular disease risks, 302, 303
Microsatellite instability,

- cancer,
- - determination, 256, 357

- - frequency in human cancer, 358

- - mismatch repair defects, 358, 359

- - molecular targets, 359, 360

- hereditary nonpolyposis colorectal cancer,

- categories, 378, 379, 381
- clinical significance, 382
- testing,

- - number of markers, 381
- - practical points, 382-384
- - selection of markers, 381, 382
Minimal residual disease (MRD),

- flow cytometry analysis, 170, 172
- non-Hodgkin's lymphoma, 410
Mitochondrial DNA, sequencing for human identity testing, 504, 505

mll,

- chromosomal translocation, 421, 422
- gene partial tandem duplication, 417
MLPA, see Multiplex ligation-dependent probe amplification

MODY, see Maturity onset diabetes of the young

MRD, see Minimal residual disease

Muir-Torre syndrome, gene mutations, 362
Multiple endocrine neoplasia (MEN),

- genetic testing,

- - children, 289
- - resources, 289
- RET alleles, 289, 363
- type 1, 288
- type 2A, 288
- type 2B, 288
Multiplex ligation-dependent probe amplification (MLPA),

- advantages and uses, 71
- hereditary nonpolyposis colorectal cancer mismatch repair gene analysis, 385, 386
- limitations, 71
- principles, 70, 71
Muscular dystrophy, see Duchenne muscular dystrophy

Myotonic dystrophy type I,

- features, 267, 269
- genotype-phenotype correlation, 269, 270
- molecular diagnosis, 271, 272
- molecular mechanisms, 270, 271
- parental transmission bias, 270
- repeat instability, 269

N

NADH/NADPH oxidase, gene alleles and cardiovascular disease risks, 301
NAN, see Neonatal alloimmune neutropenia

NASBA, see Nucleic acid sequence based amplification

NATP, see Neonatal alloimmune thrombocytic purpura

Neisseria gonorrhoeae,

- clinical features, 438
- conventional detection, 439
- epidemiology, 438
- molecular assays,

- - commercial assays,

- - - Amplicor CT/NG, 442, 443
- - - Aptima Combo 2, 442
- - - Hybrid Capture II assays, 441, 442
- - - Pace 2, 442
- - - Probe-Tec assay, 440, 441
- - overview, 439, 440
- - prospects, 443
Neonatal alloimmune neutropenia (NAN), features and genotyping, 336
Neonatal alloimmune thrombocytic purpura (NATP), features and genotyping, 336
Neuroblastoma, cytogenetics, 182
Neurofibromatosis type 1

- features, 273
- genetics, 273, 362, 363
- molecular diagnosis, 273, 274
NHL, see Non-Hodgkin's lymphoma

Nitric oxide synthase (NOS), gene alleles and cardiovascular disease risks, 301, 302
Non-Hodgkin's lymphoma (NHL), see also specific lymphomas,

- chromosomal translocations,

- - anaplastic large-cell lymphoma, 408, 409
- - Burkitt lymphoma, 406, 407
- - diffuse large B-cell lymphoma, 408

- - follicular lymphoma, 405, 406

- - mantle cell lymphoma, 407, 408

- clonality of lymphocytes,

- - overview, 393, 394
- - polymerase chain reaction analysis, 401-403
- - Southern blot analysis, 399-401
- cytogenetics, 186
- flow cytometry immunophenotyping, 168-170

- fluorescence in situ hybridization, 403-405

- immunohistochemistry, 210

- minimal residual disease detection, 410

- prevalence, 393
Northern blot,
- agarose gel electrophoresis, 38, 39
- hybridization, factors affecting, 44
- interpretation, 39, 40
- membrane transfer, 39
- overview, 31, 37, 40, 45
- probe preparation,

- - nick translation, 41
- - nonradioactive probes, 43, 44
- - random primer extension, 41, 42
- - strand-specific probes, 42, 43
- probe removal, 44, 45
- ribonuclease inactivation, 38
- RNA isolation, 38
- total versus messenger RNA, 38
- troubleshooting, 41
- washing, 44
NOS, see Nitric oxide synthase

Nucleic acid extraction,

- DNA microarray samples, 28, 29
- inorganic extraction, 28
- leukocyte isolation from blood, 27
- lysis of tissue samples, 27
- organic extraction, 27, 28
- paraffin removal, 27
- quality assessment, 29
- quantification, 29
- RNA extraction, 28
- sample sources,

- - blood, 26, 27
- - forensic samples, 27
- - formalin/paraffin-embedded tissue, 26
- - fresh tissue, 25, 26
- storage of nucleic acid, 29
Nucleic acid sequence based amplification (NASBA), principles, 75, 76

O

OLA, see Oligonucleotide ligation assay

Oligonucleotide ligation assay (OLA),

- cystic fibrosis diagnostics, 326
- principles, 70

P

pS3
- acute myeloid leukemia mutation, 416
- cancer inactivation, 354
- immunohistochemistry, 211
- standards for mutation detection, 244-246
PAI-1, see Plasminogen activator inhibitor-1

Pancreatic cancer, early detection, 364, 365
Paraoxonase, gene alleles and cardiovascular disease risks, 301
Parentage testing, see Human identity testing Pateau syndrome, features, 177
Patents,
- gene patents,
- - examples of tests, 550, 551

- - filing by researchers, 551

- - research use and infringement, 551
- overview, 550
- polymerase chain reaction, 550
PCR, see Polymerase chain reaction

Pedigree analysis, Mendelian inheritance patterns, 262-264
Pendred syndrome, 287
Pharmacogenetics, see Bioinformatics; Drugs

Philadelphia chromosome, see Chronic myelogenous leukemia PIT1, mutations, 286, 287
Pituitary hormone, combined pituitary hormone deficiency,
- HESX1 mutations, 286
- LHX3 mutations, 286
- overview, 286
- PIT1 mutations, 286, 287
- PROP1 mutations, 287 

- X- linked deficiency, 287
Plasminogen activator inhibitor-1 (PAI-1), gene alleles and cardiovascular disease risks, 296, 297
Platelet glycoproteins,
- coagulation disorders, 314
- gene alleles and cardiovascular disease risk, 297-300
- human platelet antigens, 329, 330
Polyacrylamide gel electrophoresis, see Electrophoresis Polymerase chain reaction (PCR),

- coagulation disorder analysis techniques, 315
- comparison with fluorescence in situ hybridization for cytogenetic analysis, 198-200
- contaminants, 52
- DNA methylation detection, see DNA methylation

- enzymes, 48, 49
- historical perspective, 85
- human identity testing, 500, 518, 519
- human leukocyte antigen typing with sequence-specific primers, 489
- human papillomavirus detection, 450
- in situ polymerase chain reaction, 195, 196
- inhibitors, 53
- lymphocyte clonality analysis, 401-403
- mutation detection, see Amplification refractory mutation system; Multiplex ligation-dependent probe amplification; Oligonucleotide ligation assay; Primer extension assay; Quantitative fluorescent PCR; Real-time polymerase chain reaction

- optimization, 51
- patent, 550
- primer design, 49, 50
- principles, 47, 48, 85
- products,

- - analysis, 52, 53
- - verification, 53
- reaction mixtures, 50, 51
- reverse transcriptase-PCR,

- - amplification, 54
- - RNA isolation, 53, 54
- site-directed mutagenesis, 98, 99
- specificity and sensitivity improvement,

- - hot-start PCR, 51, 52
- - nested PCR, 52
- - Taq polymerase preparations, 51
- - touch-down PCR, 52
- templates, 48
Pregnancy, history of diagnosis, 4
Primer extension assay,
- advantages and limitations, 72
- applications, 72
- equipment, 72
- methylation-sensitive single-nucleotide primer extension assay, 152
- principles, 71, 72
PROP1, mutations, 287
Protein C, coagulation disorders, 313
Protein S, coagulation disorders, 313, 314
Proteomics, overview, 132-134
Prothrombin, coagulation disorders, 313

Q

QF-PCR, see Quantitative fluorescent PCR

Quality assurance, molecular diagnostics,

- analytical phase,

- - contamination, 231
- - controls, 231, 232
- - equipment maintenance, 232
- - indicators for assessment, 235
- - laboratory design, 231
- - laboratory practices, 231
- - nucleic acid extraction and specimen storage, 230, 231
- - personnel competency, 233
- - procedural manual, 230
- - proficiency testing and accreditation, 233
- - validation of tests, 232, 240
- Clinical Laboratory Improvement Act regulations, 227, 228, 237
- human identity testing, 497-499
- laboratory-developed assays, see Laboratory-developed assays - personnel qualifications, 234
- postanalytical phase,

- - indicators for assessment, 235, 236
- - laboratory test reports, 233, 234
- - patient confidentiality, 234
- - timeliness of reporting, 234
- preanalytical phase,

- - error correction, 230
- - indicators for assessment, 235
- - informed consent, 230
- - overview, 228, 229
- - specimens,
- - - collection and handling, 229, 230
- - - rejection, 230
- - test requests, 229
- verification of molecular assays, accuracy, 240
- - laboratory-developed assays, 252-255
- - overview, 237
- - precision, 239, 240
- - reference range, 237, 238
- - reportable range, 239
- - sensitivity, 238
- - specificity, 238
Quantitative fluorescent PCR (QF-PCR),

- applications, 70
- principles, 70

R

Ras,

- acute myeloid leukemia mutation, 416
- chronic myelomonocytic leukemia mutations, 427
RCA, see Rolling circle amplification

READIT™ assay, single nucleotide polymorphism typing, 115, 116
Real-time polymerase chain reaction,

- advantages, 68
- applications, 68
- DNA methylation analysis, 153, 154
- equipment, 68
- labeled probes,

- - cleavage-based probes, 65, 66

- - fluorescence resonance energy transfer probes, 67

- - molecular beacons, 66, 67

- - scorpion primers, 67, 68

- limitations, 68
- nonspecific DNA-binding dyes, 65
- principles, 65
- resources, 68
Reference strand conformation analysis (RSCA), human leukocyte antigen typing, 492
Refractive anemia, cytogenetics, 184
Restriction fragment length polymorphism (RFLP),

- coagulation disorder analysis, 315
- principles of analysis, 98, 99, 261
RET, see Familial medullary thyroid carcinoma; Multiple endocrine neoplasia

Retinoblastoma gene (Rb),
- acute myeloid leukemia mutation, 416
- cytogenetics, 182
- retinoblastoma mutations, 361
Reverse transcriptase-polymerase chain reaction (RT-PCR),

- amplification, 54
- RNA isolation, 53, 54
RFLP, see Restriction fragment length polymorphism

Rhesus blood group,

- genes, 330
- RhC genotyping, 331, 333, 334
- RhD genotyping, 330
RNA, blotting, see Northern blot

- chemical nature, 17
- extraction, see Nucleic acid extraction

- reverse transcriptase-PCR,

- - amplification, 54
- - RNA isolation, 53, 54
- structure and function,

- - higher-order structures, 20
- - messenger RNA, 17-19
- - ribosomal RNA, 19, 20
- - transfer RNA, 19
- transcription, 15
Rolling circle amplification (RCA), principles, 77, 78
RSCA, see Reference strand conformation analysis

RT-PCR, see Reverse transcriptase-polymerase chain reaction

Runxl, acute myeloid leukemia mutation, 416

S

SAGE, see Serial analysis of gene expression

Sarcoma, immunohistochemistry, 210, 211

SBMA, see Spinal-bulbar muscular atrophy

SCCA, see Spinocerebellar ataxia

SDA, see Strand displacement amplification
Sequence-specific oligonucleotide probe hybridization, human leukocyte antigen typing, 489
Serial analysis of gene expression (SAGE), principles, 130, 131
Short tandem repeats (STRs),

- features, 261
- human identity testing, 497, 500-504
Signal amplification techniques,

- enzymatic amplification,

- - cleavage reactions, 81, 82
- - ramification amplification, 82
- limitations, 82, 83
- nonenzymatic amplification,

- - branched chain DNA, 80
- - hybrid capture, 79, 80
- - in situ hybridization, 80, 81
- overview, 79
Single nucleotide polymorphisms (SNPs),

- arrays, 132
- cardiovascular disease risks, 297
- disease-causing mutation testing and mapping, 111, 112
- identification, 111
- typing,

- - Aff metrix microchips, 116, 117
- - Invader™ assay, 113, 115
- - prospects, 118
- - READIT™ assay, 115, 116
- - TaqMan assay, 117, 118
- - traditional approaches, 112, 113
Single-stranded conformational polymorphism (SSCP),

- human leukocyte antigen typing, 491, 492
- principles, 90-93, 111
SMA, see Spinal muscular atrophy

SNPs, see Single nucleotide polymorphisms

Southern blot,
- agarose gel electrophoresis, 32-34
- DNA preparation, 32
- human identity testing, 518
- hybridization, factors affecting, 44
- interpretation, 36, 37
- lymphocyte clonality analysis, 399-401
- overview, 31, 32, 34, 45
- probe preparation,

- - nick translation, 41
- - nonradioactive probes, 43, 44
- - random primer extension, 41, 42
- - strand-specific probes, 42, 43
- probe removal, 44, 45
- solutions, 35
- transfer to blot,
- - capillary transfer, 35, 36
- - electrophoretic transfer, 36 fixation, 36
- - membrane selection, 34, 35
- - vacuum blotting, 36
- troubleshooting, 37
- washing, 44
Spinal-bulbar muscular atrophy (SBMA),

- features, 269
- genotype-phenotype correlation, 269, 270
- molecular diagnosis, 271, 272
- molecular mechanisms, 270, 271
- parental transmission bias, 270
- repeat instability, 269
Spinal muscular atrophy (SM A),
- genetics, 272, 273
- molecular diagnosis, 273
- types and features, 272
Spinocerebellar ataxia (SCA),
- features, 269
- genotype-phenotype correlation, 269, 270
- molecular diagnosis, 271, 272
- molecular mechanisms, 270, 271
- parental transmission bias, 270
- repeat instability, 269
SSCP, see Single-stranded conformational polymorphism

Strand displacement amplification (SDA), principles, 76, 77
STRs, see Short tandem repeats

T

TaqMan assay, single nucleotide polymorphism typing, 117, 118
T-cell,

- clonality,
- - overview, 393, 394
- - polymerase chain reaction analysis, 401-403
- - Southern blot analysis, 399-401
- development, 395, 396
- receptor gene rearrangement, 396-398
T-cell prolymphocytic leukemia,

- ATM mutations, 433
- chromosomal aberrations, 432, 433
Thrombomodulin, coagulation disorders, 314
Thyroid hormone, resistance, 287, 288
Tissue microarray, overview, 211, 212
TMA, see Transcription-mediated amplification

Transcription-mediated amplification (TMA), principles, 75, 76
Turcot' s syndrome, gene mutations, 362
Turner syndrome, features, 176

U

Urinalysis, historical perspective, 4-6

V

Variable number of tandem repeats (VNTRs),
- features, 261
- human identity testing, 495-497
- maternal contamination analysis of fetal samples, 336, 337
Verification, see Quality assurance, molecular diagnostics

Vesalius, Andreas, 5
VNTRs, see Variable number of tandem repeats

W

Wilms' tumor,
- cytogenetics, 182
- gene mutations, 363
Wolcott-Rallison syndrome, gene mutations, 290
Wolfram syndrome, gene mutations, 290

Autor

CONTRIBUTORS

TERRY AMISS, PhD • BD Technologies/Biosensors, Research Triangle Park, NC 

JEAN A. AMOS, PhD • Scientific Director, Molecular Genetics, Specialty Laboratorie, Inc., Santa Monica,CA

MARK J. ARENDS, MA, MB ChB(Hons), BSc(Hons), PhD, FRCPath • Department of Pathology, Addenbrooke 's Hospital, University of Cambridge, Cambridge, UK

C. ROBERT BAGNELL, JR., PhD • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 

MARIA BAIULESCU, MD • Department of Pathology and Laboratory Medicine, Charlotte-Hungerford Hospital, Torrington, CT 

ENRIQUE BALLESTEROS, MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

SELWYN J. BAPTIST, MD • Department of Pathology, Saint Barnabas Medical Center, Livingston, NJ

PAUL N. BOGNER, MD • Department of Pathology, University of Michigan, Ann Arbor, MI 

JESSICA BOOKER, PhD, FACMG • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 

ULRICH BROECKEL, MD • Department of Medicine and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 

RACHEL BUTLER, BSC(HONS), MRCPath • Molecular Genetics Laboratory, Institute of Medical Genetics, Cardiff, UK 

ANGELA M. CALIENDO, MD, PhD • Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA

RICHARD W. CARTUN, PhD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT

WILLIAM B. COLEMAN, PhD • Department of Patholog and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 

TRACEY DAWSON CRUZ, PhD • Forensic Science Program & Department of Biology, Virginia Commonwealth University, Richmond, VA 

BRIAN R. CURTIS, MS, MT (ASCP)SBB • Platelet and Neutrophil Laboratory, The Blood Center of Southeastern Wisconsin, Milwaukee, WI

D. BRIAN DAWSON, PhD • Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN

LARISSA DAVYDOVA, MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

JOSEPH A. DIGIUSEPPE, MD, PhD • Director, Special Hematology Laboratory, Acting Director, Molecular Pathology Laboratory, Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

ALEXANDER DOBROVIC, PhD • Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia

D. ROBERT DUFOUR, MD • Pathology and Laboratory Medicine Service, Veterans Affairs Medical Center, Washington, DC 

ANDREA FERREIRA-GONZALEZ, PhD • Department of Pathology, Virginia Commonwealth University, Richmond, VA 

IAN M. FRAYLING, MA, MB, BChir, PhD, MRCPath • Clinical Genetics Laboratory, Institute of Medical Genetics University Hospital of Wales, Cardiff, UK 

CARLETON T. GARRETT, MD, PhD • Department o Pathology, Virginia Commonwealth University, Richmond, VA 

LISA HAPPERFIELD, FIBMS, MSC • Department of Histopathology, Addenbrooke's Hospital, Cambridge, UK 

DAVID NEIL HAYES, MD, MPH • Division of Hematology/ Oncology, Department of Internal Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC

JENNIFER L. HERBST, JD, M.Bioethics • Montgomery, McCracken, Walker & Rhoads, LLC, Philadelphia, PA

MARTIN J. HESSNER, PhD • Department of Pediatrics and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI

W. EDWARD HIGHSMITH, JR., PhD • Division of Laboratory Genetics, Department of Laboratory Medicine Pathology, Mayo Clinic, Rochester, MN 

CHARLES E. HILL, MD, PhD • Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA 

JOHN HUNT, MD • Department of Pathology, Bay state Medical Center, Springfield, MA 

JOHN P. JAKUPCIAK, PhD • DNA Technologies Group, Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD

MARTHA B. KEAGLE, MEd, CLSP(CG) • Diagnostic Cytogenetic Sciences, School of Allied Health, University of Connecticut, Storrs, CT

ANTHONY A. KILLEEN, MD, PhD • Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 

CHRISTOPHER J. KLEIN, MD • Department of Neurology, Mayo Clinic, Rochester, MN 

ROBERT J. KOSKA, BSMT (ASCP), MBA • Cepheid, Sunnyvale, CA

EUGENE H. LEWIS III, DO • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

MYRA J. LEWIS, DO • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

PEI LIN, MD • Department of Hematopathology,University of Texas M.D. Anderson Cancer Center,Houston, TX 

NELL S. LURAIN, PhD • Department of Immunology/Microbiology, Rush-Presbyterian-St. Luke's Medical-Center, Chicago, IL 

CHRISTOPHER MATTOCKS, BSc(Hons) • National Genetics-Reference Laboratory, Salisbury District Hospital, Salisbury, UK

KAREN MCCULLOUGH, PhD • Vanda Pharmaceuticals, Rockville, MD

L. JEFFREY MEDEIROS, MD • Department of Hematopathology, University of Texas M.D. Anderson Cancer Center, Houston, TX 

JON F. MERZ • Center for Bioethics, and Center for Clinical Epidemiology and Biostatistics, Department of Medical Ethics, University of Pennsylvania School of Medicine, Philadelphia PA. 

MATTHEW MEYERSON, MD, PhD • Division of Oncology, Dana Färber Cancer Institute, Harvard Medical School, Boston, MA 

EMMA MONK, BSC • East Anglian Regional Genetics Service, Molecular Genetics Laboratory, Addenbrooke's Hospital, Cambridge, UK 

ROBERT E. MOORE, PhD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT

SUNEEL D. MUNDLE, PhD • Rush Cancer Institute, Chicago, IL; Technical Services Manager, Vysis Inc., Downers Grove, IL 

NARASIMHAN NAGAN, PhD • Laboratory Director, Athena,Diagnostics, Worcester, MA

KIM OAKHILL, BSc(Hons), DipRCP • East Anglian Regional Genetics Service, Molecular Genetics Laboratory, Addenbrooke 's Hospital, Cambridge, UK 

CATHERINE D. O'CONNELL, PhD • Tetracore Inc., Gaithersburg, MD 

DEBORAH A. PAYNE, PhD, CLSP(MB), CLSDir(NCA) • Department of Pathology and Otolaryngology, Division of Molecular Diagnostics, The University of Texas Medical Branch, Galveston, TX

JOHN A. PHILLIPS III, MD • Division of Medical Genetics, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN 

AMY POTTER, MD • Division of Endocrinology and Metabolism, Departments of Pediatrics and Medicine, Vanderbilt University School of Medicine, Nashville, TN 

SHARON COLLINS PRESNELL, PhD • BD Technologies/ Biotherapy, Research Triangle Park, NC

TERESITA CUYEGKENG REDONDO, MD • Department of Pathology, Saint Barnabas Medical Center, Livingston, NJ

WILLIAM N. REZUKE JR., MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

ANDREW RICCI JR., MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

SHARON L. RICKETTS • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC

MYRA I. ROCHE, MS, CGC • Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC

MARLENE SABBATH-SOLITARE, PhD • Department of Pathology, Saint Barnabas Medical Center, Livingston, NJ

JOHN L. SCHMITZ, PhD • Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 

BRENT L. SEATON, PhD • Focus Technologies Inc., Cypress, CA

LAWRENCE M. SILVERMAN, PhD • Department of Pathology and Laboratory Medicine, University of Virginia, Charlottesville VA 

LAURIE E. SOWER, PhD • Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX

STEPHEN N. THIBODEAU, PhD • Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 

GREGORY J. TSONGALIS, PhD • Department of Pathology, Dartmouth Medical School, Dartmouth-Hitchcock Medical Center, Lebanon, NH 

ALEXANDRA VALSAMAKIS, MD, PhD • Department of Pathology, Division of Microbiology, Johns Hopkins University School of Medicine, Baltimore, MD 

THERESA M. VOYTEK, MD • Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, CT 

ELAINE WEIDENHAMMER, PhD • Senior Manager, Strategic Development, Nanogen, San Diego, CA 

MYRA J. WICK, PhD • Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN

ALAN H. B. WU, PhD • Department of Laboratory Medicine, University of California, San Francisco, CA

Reviews

"This is a great book to have handy for ready reference in this rapidly evolving field. While the reader may not use this reference daily, there is no question that it will be needed for those occasions when such testing is ordered and a clinical consultation between the clinical laboratory and the healthcare provider is necessary." - Doody's Health Sciences Book Review Journal "...the textbook of choice for anyone working in molecular diagnostics who wants to remain current with this rapidly changing field. -Clinical Laboratory International From Reviews of the First Edition... "...a very good introduction to the basic elements of molecular pathology...a clear, enjoyable read...an excellent discussion of methods." -Clinical Chemistry "...highly recommended...for those interested in clinical molecular diagnosis...will satisfy those who are more expert in certain areas of molecular diagnosis, but who have been unable to keep up with the wide range of recent advances in molecular diagnosis." -American Journal of Clinical Pathology "...gives a good theoretical background for those with little experience in this field. It is readable, comprehensive, and...up-to-date." -Journal of Clinical Pathology "...well written, comprehensive...should bring even the reader with limited background knowledge up to speed on what is a rapidly progressing field." -Trends in Molecular Medicine "...a timely and highly relevant book that will serve as a valuable resource to those practicing molecular diagnostics from the bench, as well as to basic and clinical scientists..." -Endocrine News