Cytogenetic Abnormalities Chromosomal, FISH, and Microarray-Based Clinical Reporting and Interpretation of Result

Cytogenetics is the study of the structure and function of chromosomes in relation to phenotypic expression.Chromosomal abnormalities underlie the development of a wide variety of diseases and disorders ranging from Down syndrome to cancer, and are of widespread interest in both basic and clinical research.

Cytogenetic Abnormalities: Chromosomal, FISH, and Microarray-Based Clinical Reporting is a practical guide that describes cytogenetic abnormalities, their clinical implications and how best to report and communicate laboratory findings in research and clinical settings. The text first examines chromosomal, FISH, and microarray-based analyses in constitutional disorders. Using these same methodologies, the book's focus shifts to acquired abnormalities in cancers. Both sections provide illustrative examples of cytogenetic abnormalities and how to communicate these findings in standardized laboratory reports.

Providing both a wealth of cytogenetic information, as well as practical guidance on how best to communicate findings to fellow research and medical professionals, Cytogenetic Abnormalities will be an essential resource for cytogeneticists, laboratory personnel, clinicians, research scientists, and students in the field.

• A guide to interpreting and reporting cytogenetic laboratory results involved in constitutional disorders and cancers
• Guides the reader on implementing the International System for Human Cytogenetic Nomenclature in written reports
• Provides information to allow scientists and medical professionals to fully understand and communicate cytogenetic abnormalities
• Describes a wide array of cytogenetic abnormalities observed in the laboratory
• Divided into user-friendly sections devoted to methodologies and implications of specific diseases

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.

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

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