Clinical Cytogenetics

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Preface: Cytogenetics Caroline Astbury Sex Chromosomes and Sex Chromosome Abnormalities Xu Li This article focuses on constitutional sex chromosome abnormalities detected by conventional cytogenetics and uorescence in situ hybridization. The author discusses the two general classications of abnormalities: numerical and structural. Also included are descriptions of unique aspects of X and Y chromosomes, technological advances in detection, and future perspectives. Constitutional and Acquired Autosomal Aneuploidy Colleen Jackson-Cook Chromosomal imbalances can result from numerical or structural anomalies. Numerical chromosomal abnormalities are often referred to as aneuploid conditions. This article focuses on the occurrence of constitutional and acquired autosomal aneuploidy in humans. Topics covered include frequency, mosaicism, phenotypic ndings, and etiology. The article concludes with a consideration of anticipated advances that might allow for the development of screening tests and/or lead to improvements in our understanding and management of the role that aneuploidy plays in the aging process and acquisition of age-related and constitutional conditions. Chromosomal Structural Rearrangements: Detection and Elucidation of Mechanisms Using Cytogenomic Technologies Sarah T. South By identifying the imbalance and the genomic architecture associated with the imbalance, the mechanism leading to an imbalance can often be identied. Understanding the mechanism leads to more accurate recurrence risk assessment. Common mechanisms that lead to imbalances are discussed. A combination of technologies is required for the identication of the imbalance and characterization of the genomic architecture. As our technologies improve and increase in resolution, it is likely that our understanding of genomic rearrangement mechanisms will also change; we will continue to be impressed by the dynamic nature of chromosome structure and its relationship to human disease. Fluorescence In Situ Hybridization Karen D. Tsuchiya This chapter presents past and present FISH techniques and specic applications of FISH. Although array technology has revolutionized 525 481 463 xiii

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cytogenetics, FISH remains indispensible. While array technology provides a high resolution screen of the entire genome for gains and losses, it does not allow for visualization of the genomic structure of gains. Thus, FISH continues to be useful as an adjunct to arrays. FISH also continues to be widely used in conjunction with banded chromosome analysis, and as a stand-alone technique for the detection of genomic alterations in neoplastic disorders. The Evolving Picture of Microdeletion/Microduplication Syndromes in the Age of Microarray Analysis: Variable Expressivity and Genomic Complexity Kristen L. Deak, Sarah R. Horn, and Catherine W. Rehder Several new microdeletion and microduplication syndromes have been discovered in a genotype-rst approach. Many of these disorders are caused by nonallelic homologous recombination between blocks of segmental duplication. The authors describe 9 regions for which copy number alteration is proposed to cause an abnormal phenotype. Some of these disorders have been observed in affected individuals and individuals lacking a clearly abnormal phenotype. These deletions and duplications are thought to be contributory, but not always sufcient, to elicit an abnormal outcome. Additional studies are necessary to further evaluate the penetrance and delineate the clinical spectrum associated with many of these newly described disorders. Interpretation of Copy Number Alterations Identied Through Clinical Microarray-Comparative Genomic Hybridization Robert E. Pyatt and Caroline Astbury Many copy number alterations (CNA) currently interpreted as variants of unknown signicance (VUS) will ultimately be determined to be benign; however, their classication requires a more extensive characterization of the human genome than currently exists. There is no denitive set of rules or level of evidence required to dene a CNA as benign. The information needed to accurately assess the pathogenic impact of CNA is beginning to be assembled. Although the lack of understanding of the human genome can make clinical array-comparative genomic hybridization interpretation frustrating, it is precisely why clinical human genetics is an exciting arena in which to work. Clinical Utility of Single Nucleotide Polymorphism Arrays Stuart Schwartz Detection of chromosomal abnormalities has evolved over the past 30 years. Microarray analysis allows for the detection of abnormalities at a level of resolution 100 times greater than chromosomal analysis. In this article, one specic array, a single nucleotide polymorphism array, is reviewed. This array not only allows for increased resolution to detect copy number changes, but the genotyping aspect of the array allows copy neutral detection (for both uniparental disomy and consanguinity). Additionally, use of this array in constitutional postnatal, prenatal, and products of conception studies is reviewed along with the use of the array in oncology studies. 581

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Diagnostic Implications of Excessive Homozygosity Detected by SNP-Based Microarrays: Consanguinity, Uniparental Disomy, and Recessive Single-Gene Mutations Hutton M. Kearney, Joseph B. Kearney, and Laura K. Conlin Single nucleotide polymorphism based microarrays used in diagnostic laboratories for the detection of copy number alterations also provide data allowing for surveillance of the genome for regions of homozygosity. The nding of one (or more) long contiguous stretch of homozygosity (LCSH) in a constitutional (nonneoplastic) diagnostic setting can lead to the diagnosis of uniparental disomy involving an imprinted chromosome or homozygous single gene mutations. The focus of this review is to describe the analytical detection of LCSH, clinical implications of excessive homozygosity, and considerations for follow-up diagnostic testing. Laboratory Aspects of Prenatal Microarray Analysis Allen N. Lamb The recent development and clinical implementation of genomic microarrays has resulted in rapid and signicant changes for postnatal studies in the eld of cytogenetics. This article discusses the benets and issues for the use of microarrays for prenatal genetic diagnosis. It includes sections on specimen processing, prenatal array design, the published prenatal microarray literature, and maternal cell contamination. Acute Lymphoblastic Leukemia Christine J. Harrison Precursor B-ALL (BCP-ALL) is associated with a good outcome in children. Cytogenetics is one of the gold standards for risk stratication for treatment that has contributed to improved survival. Although in T-ALL genetic analysis has not been used to guide therapy, it has contributed signicantly to the understanding of the biology. State-ofthe-art technologies in genomic and high throughput targeted sequencing are revealing novel genetic changes linked to biological and clinical features including outcome. A number of new biomarkers provide the potential for molecular targets for therapy with promise for further improvements in survival and quality of life for ALL sufferers. Genetics of Chronic Lymphocytic Leukemia Andrea Schnaiter, Daniel Mertens, and Stephan Stilgenbauer Morphology and the immunophenotype of chronic lymphocytic leukemia (CLL) are quite homogenous, but CLLs clinical course is not; some patients are stable for years, others experience rapid progression and poor response to chemotherapy. Fluorescence in situ hybridization (FISH) helped determine why these differences occur. Further progress has been made using comparative genomic hybridization and single nucleotide polymorphism (SNP) array analysis. Now the discovery of further dysregulated cellular pathways and potential new therapeutic targets is possible by genome-wide high-throughput next generation sequencing, which will likely also enter clinical diagnostics.

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Acute Myeloid Leukemia: Conventional Cytogenetics, FISH, and Moleculocentric Methodologies Jennifer J.D. Morrissette and Adam Bagg Acute myeloid leukemia (AML) is a complex group of hematologic neoplasms characterized by distinctive morphologic, immunophenotypic, and genetic abnormalities. However, it has become evident that genetic aberrations are central to the genesis of AML and have assumed an increasingly relevant role in the classication of AML. Here we discuss hallmark recurrent translocations that dene specic World Health Organization (WHO) entities and other frequently encountered genetic aberrations that do not (yet) dene specic entities. Additionally, we discuss emerging technologies and their application to the discovery of new abnormalities and to their potential role in the future diagnosis and classication of AML.

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Chronic Myeloid Leukemia: Current Perspectives Yanming Zhang and Janet D. Rowley Chronic myeloid leukemia (CML), characterized by the t(9;22) and BCR/ABL1 fusion, is a disease model for studying the mechanisms of genetic abnormalities in leukemogenesis. The detection of the t(9;22), characterization of the BCR/ABL fusion, and the discovery of imatinib have elegantly reected the success of our research efforts in CML. However, genomic instabilities that lead to the formation of the BCR/ ABL1 fusion are not fully understood. It is important to understand how various genes that are involved in regulating the signaling pathway and epigenetic deregulation cooperate with the BCR/ABL1 fusion in the initiation and progression of CML. Multiple Myeloma: Current Perspectives Marilyn L. Slovak Multiple myeloma (MM) is a malignancy of terminally differentiated plasma cells characterized by complex genetic aberrations and heterogeneous outcomes. Over the past 25 years, cytogenetic analysis has played a key role in the diagnosis and management of MM. This article reviews the conventional cytogenetics, molecular cytogenetics, and genomic diagnostics of MM and highlights a few recent clinical trials that demonstrate the impact of genetic risk stratication on the treatment of this plasma cell malignancy.

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Lymphoma Cytogenetics Bhavana J. Dave, Marilu Nelson, and Warren G. Sanger Lymphomas are a heterogeneous group of neoplasms with distinct morphologic, immunologic, and cytogenetic characteristics. Overlapping morphologic and immunophenotypic features often makes accurate diagnosis difcult. Cytogenetics helps simplify the diagnostic complexities presented in transforming and progressive lymphoid

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malignancies. Genetic studies using technical advances such as uorescence in situ hybridization and the newer approaches of array comparative genomic hybridization and gene expression proling play a critical and often dening role in the diagnosis, progression, prognosis, and therapeutic stratication. This article reviews characteristic cytogenetic abnormalities in specic subtypes of lymphomas at diagnosis, disease progression, and prognosis. Myelodysplastic Syndromes Olatoyosi Odenike, John Anastasi, and Michelle M. Le Beau The myelodysplastic syndromes are a diverse group of clonal stem cell disorders characterized by ineffective hematopoiesis, peripheral cytopenias, and an increased propensity to evolve to acute myeloid leukemia. The molecular pathogenesis of these disorders is poorly understood, but recurring chromosomal abnormalities occur in approximately 50% of cases and are the focus of much investigation. The availability of newer molecular techniques has allowed the identication of additional genetic aberrations, including mutations and epigenetic changes of prognostic and potential therapeutic importance. This review focuses on the key role of cytogenetic analysis in myelodysplastic syndromes in the context of the diagnosis, prognosis, and pathogenesis of these disorders. Solid Tumor Cytogenetics: Current Perspectives Gouri Nanjangud, Ina Amarillo, and P. Nagesh Rao Conventional cytogenetics in conjunction with Fluorescence in Situ Hybridization (FISH) continues to remain an important and integral component in the diagnosis and management of solid tumors. The ability to effectively detect the vast majority of clinically relevant chromosomal aberrations with a rapid-to-acceptable turnaround time makes them the most cost-effective screening/detection tool currently available in modern pathology. In this review, we describe a representative set of solid tumors in which chromosomal analysis and/or FISH plays a signicant role in the routine clinical management of solid tumors. 785 763

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