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Cytogenetic Abnormalities
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Preface xiv Acknowledgments xv About the companion website xvi Introduction 1 Part 1: Constitutional Analyses 5 Section 1: Chromosome Analysis 7 1 Components of a standard cytogenetics report, normal results and culture failures 9 1.1 Components of a standard cytogenetics report 9 1.2 Prenatal normal results 17 1.3 Neonatal normal results 22 1.4 Normal variants in the population 23 1.5 Disclaimers and recommendations 29 1.6 Culture failures 30 1.7 Contamination 32 2 Mosaicism 35 2.1 Normal results with 30-50 cells examined 37 2.2 Normal and abnormal cell lines 37 2.3 Two or more abnormal cell lines 39 3 Autosomal trisomies - prenatal and livebirths 41 3.1 Introduction 41 3.2 Trisomy 21 - Down syndrome 42 3.3 Mosaic trisomy 21 - mosaic Down syndrome 43 3.4 Trisomy 13 - Patau syndrome 44 3.5 Trisomy 18 - Edwards syndrome 45 3.6 Trisomy 8 - mosaic 46 3.7 Trisomy 9 - mosaic 47 3.8 Trisomy 20 - mosaic, prenatal 47 3.9 Trisomy 22 - mosaic, prenatal 48 4 Translocations 51 4.1 Reciprocal (balanced) translocations 51 4.2 Robertsonian translocations 58 5 Inversions and recombinant chromosomes 67 5.1 Risks of spontaneous abortions and liveborn abnormal offspring 67 5.2 Pericentric inversions and their recombinants 67 5.3 Paracentric inversions and their recombinants 71 6 Visible deletions, duplications and insertions 75 6.1 Definitions 75 6.2 Visible duplications 79 6.3 Balanced insertions 80 7 Unidentifiable marker chromosomes, derivative chromosomes, chromosomes with additional material and rings 85 7.1 Marker chromosomes 85 7.2 Derivative chromosomes 87 7.3 Chromosomes with additional material 90 7.4 Ring chromosomes 91 7.5 Homogenously staining regions 94 8 Isochromosomes, dicentric chromosomes and pseudodicentric chromosomes 97 8.1 Isochromosomes/dicentric chromosomes 97 8.2 Pseudodicentric chromosomes 104 9 Composite karyotypes and other complex rearrangements 107 9.1 Composite karyotypes 107 9.2 Complex rearrangements 109 10 Sex chromosome abnormalities 115 10.1 X chromosome aneuploidies - female phenotypes 115 10.2 X and Y chromosome aneuploidies - male phenotypes 120 10.3 X chromosome structural abnormalities 122 10.4 Y chromosome structural abnormalities 128 10.5 46,XX males and 46,XY females 132 10.6 X chromosome translocations 135 11 Fetal demises/spontaneous abortions 143 11.1 Aneuploid rate 143 11.2 Confined placental mosaicism 144 11.3 Hydatidiform moles 145 11.4 Monosomy X in a fetus 146 11.5 Trisomies in a fetus 146 11.6 Double trisomy 149 11.7 Triploidy 150 11.8 Tetraploidy 151 12 Uniparental disomy 155 12.1 Uniparental disomy of chromosome 14 157 12.2 Uniparental disomy of chromosome 15 158 12.3 Uniparental disomy of chromosome 11p15 159 Section 2: Fluorescence In Situ Hybridization (FISH) Analysis 161 13 Metaphase analysis 163 13.1 Introduction 163 13.2 Reporting normal results 164 13.3 Common disclaimers 166 13.4 Microdeletions 167 13.5 Microduplications 190 13.6 Fluorescence in situ hybridization for chromosome identification 198 13.7 Subtelomere fluorescence in situ hybridization analysis 200 14 Interphase analysis 205 14.1 Introduction 205 14.2 Example report of interphase analysis 206 14.3 Common disclaimers 207 14.4 Reporting normal results 208 14.5 Abnormal prenatal/neonatal results 211 14.6 Abnormal product of conception FISH abnormalities 218 14.7 Molar pregnancies 222 14.8 Preimplantation genetic diagnosis 222 15 Integrated chromosome and FISH analyses 231 15.1 ISCN rules and reporting normal results by chromosomes and FISH 232 15.2 ISCN rules and reporting abnormal chromosomes and FISH 233 15.3 ISCN rules and reporting of chromosomes and subtelomere FISH 237 Section 3: Chromosomal Microarray Analysis (CMA) 243 16 Bacterial artificial chromosome, oligoarray and single nucleotide polymorphism array methodologies for analysis 245 16.1 Introduction 245 16.2 Clinical utility of chromosomal microarray analysis 250 16.3 Guidelines for classification states 251 16.4 ISCN rules and reporting of normal results 252 16.5 Comments, disclaimers and recommendations 253 17 Microarray abnormal results 257 17.1 Reporting of abnormal results 257 17.2 Loss or gain of a single chromosome 258 17.3 Loss or gain of a whole chromosome complement 262 17.4 Microdeletions 263 17.5 Microduplications 265 17.6 Derivative chromosomes 267 17.7 Variants of unknown significance 269 17.8 Uniparental disomy/loss of heterozygosity/regions of homozygosity 269 17.9 Mosaicism 271 17.10 Common comments in abnormal reports 273 17.11 Microarrays with concurrent FISH studies and/or chromosome studies 274 17.12 Microarrays with concurrent parental studies 274 17.13 Preimplantation genetic diagnosis testing 275 17.14 Non-invasive prenatal testing 276 18 Pathogenic chromosomal microarray copy number changes by chromosome order 285 18.1 Chromosome 1 285 18.2 Chromosome 2 287 18.3 Chromosome 3 289 18.4 Chromosome 4 290 18.5 Chromosome 5 291 18.6 Chromosome 7 292 18.7 Chromosome 8 293 18.8 Chromosome 14 294 18.9 Chromosome 15 294 18.10 Chromosome 16 296 18.11 Chromosome 17 298 18.12 Chromosome 19 301 18.13 Chromosome 22 302 18.14 Chromosome X 306 19 Integrated reports with cytogenetics, FISH and microarrays 315 19.1 Reporting of a deletion 315 19.2 Reporting of a supernumerary chromosome 316 19.3 Reporting of an unbalanced translocation - deletion/duplication 318 19.4 Reporting of multiple abnormal cell lines 322 Part 2: Acquired Abnormalities in Hematological and Tumor Malignancies 325 Section 1: Chromosome Analysis 327 20 Introduction 329 20.1 Description of World Health Organization classification for hematological malignancies 332 20.2 Description of different tumor types with significant cytogenetic abnormalities 332 20.3 Set-up and analysis of specific cultures for optimal results 333 20.4 Nomenclature rules for normal and simple abnormal results 336 20.5 Common report comments for hematological malignancies 338 21 Results with constitutional or other non-neoplastic abnormalities 347 21.1 Possible constitutional abnormalities observed 347 21.2 Age-related abnormalities 349 21.3 Non-clonal aberrations 351 21.4 No growth and poor growth 354 22 Cytogenetic abnormalities in myeloid disorders 357 22.1 Introduction to myeloid disorders 357 22.2 Individual myeloid abnormalities by chromosome order 360 23 Cytogenetic abnormalities in lymphoid disorders 395 23.1 Introduction to lymphoid disorders 395 23.2 Hyperdiploidy and hypodiploidy 396 23.3 Individual lymphoid abnormalities by chromosome order 398 24 Common biphenotypic abnormalities and secondary changes 423 24.1 Translocation (4;11)(q21;q23) 423 24.2 Del(9q) 424 24.3 Translocation (11;19)(q23;p13.3) 424 24.4 Del(12)(p11.2p13) 425 24.5 Trisomy 15 425 24.6 i(17q) 426 25 Reporting complex abnormalities and multiple cell lines 429 25.1 Stemline and sideline abnormalities 430 25.2 Unrelated abnormal clones 434 25.3 Composite karyotypes 435 25.4 Double minute chromosomes 436 25.5 Modal ploidy numbers 438 25.6 Multiple abnormal cell lines indicative of clonal evolution 440 26 Breakage disorders 445 26.1 Ataxia telangiectasia 445 26.2 Bloom syndrome 446 26.3 Fanconi anemia 447 26.4 Nijmegen syndrome 448 27 Cytogenetic abnormalities in solid tumors 451 27.1 Clear cell sarcoma 451 27.2 Chondrosarcoma 452 27.3 Ewing sarcoma 453 27.4 Liposarcoma 453 27.5 Neuroblastoma 454 27.6 Rhabdomyosarcoma 455 27.7 Synovial sarcoma 456 27.8 Wilms tumor 456 Section 2: Fluorescence In Situ Hybridization (FISH) Analysis 459 28 Introduction to FISH analysis for hematological disorders and solid tumors 461 28.1 General results 462 28.2 Bone marrow transplantation results 468 29 Recurrent FISH abnormalities in myeloid disorders 471 29.1 Individual abnormalities in myeloid disorders by chromosome order 471 29.2 Biphenotypic and therapy-related abnormalities 491 29.3 Panels of probes 492 30 Recurrent FISH abnormalities in lymphoid disorders 499 30.1 Individual abnormalities in lymphoid disorders by chromosome order 499 30.2 Panels of probes 520 31 Integrated reports with cytogenetics and FISH in hematological malignancies 531 31.1 Translocation (9;22) with BCR/ABL1 FISH analysis 531 31.2 Monosomy 7 with a marker chromosome and chromosome 7 FISH analysis 532 31.3 Complex abnormalities with the MDS FISH panel 532 31.4 Complex abnormalities with ALL FISH panel 533 31.5 Complex abnormalities with MM FISH panel 535 31.6 Complex abnormalities with AML FISH panel 536 31.7 Complex abnormalities with AML FISH panel in therapy-related disease 537 32 Recurrent FISH abnormalities in solid tumors using paraffin-embedded tissue 541 32.1 Ewing sarcoma 544 32.2 Liposarcoma 545 32.3 Neuroblastoma 546 32.4 Non-small cell lung cancer 547 32.5 Oligodendroglioma 552 32.6 Rhabdomyosarcoma 554 32.7 Synovial sarcoma 554 33 Breast cancer - HER2 FISH analysis 559 33.1 Common report comments 560 33.2 Example HER2 reports 561 33.3 Genetic heterogeneity 563 34 Bladder cancer FISH analysis 569 34.1 Common report comments 570 34.2 Example reports 570 Section 3: Chromosomal Microarray Analysis (CMA) 577 35 Chromosomal microarray analysis for hematological disorders 579 35.1 Introduction 579 35.2 Categories of abnormalities 580 35.3 Complex abnormalities throughout the genome, chromothripsis and homozygosity 581 35.4 Normal results and disclaimers 582 35.5 Example abnormal results in hematological malignancies 583 36 Chromosomal microarrays for tumors 595 36.1 Introduction and disclaimers 595 36.2 Breast cancer 596 36.3 Lung cancer 604 36.4 Colon cancer 606 36.5 Prostate cancer 607 36.6 Unspecified tumor present 607 37 Integrated reports with chromosomes, FISH and microarrays 611 37.1 Homozygous deletion of 9p21 identified by FISH and CMA 611 37.2 Identifying marker chromosomes by chromosome analysis, FISH and CMA 612 37.3 Unbalanced translocation identification by chromosomes, FISH and CMA 614 Appendix 1: Example assay-specific reagent (ASR) FISH validation plan for constitutional disorders and hematological malignancies on fresh tissue 617 Glossary 623 Index 641

About the Author

Susan Mahler Zneimer Ph.D., FACMGG is a clinical cytogeneticist and is the Scientific Director and CEO of MOSYS Consulting and Adjunct Professor at Moorpark College in Moorpark, California.

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