Whole genome scanning as a cytogenetic tool in hematologic malignancies

Abstract

Over the years, methods of cytogenetic analysis evolved and became part of routine laboratory testing, providing valuable diagnostic and prognostic information in hematologic disorders. Karyotypic aberrations contribute to the understanding of the molecular pathogenesis of disease and thereby to rational application of therapeutic modalities. Most of the progress in this field stems from the application of metaphase cytogenetics (MC), but recently, novel molecular technologies have been introduced that complement MC and overcome many of the limitations of traditional cytogenetics, including a need for cell culture. Whole genome scanning using comparative genomic hybridization and single nucleotide polymorphism arrays (CGH-A; SNP-A) can be used for analysis of somatic or clonal unbalanced chromosomal defects. In SNP-A, the combination of copy number detection and genotyping enables diagnosis of copy-neutral loss of heterozygosity, a lesion that cannot be detected using MC but may have important pathogenetic implications. Overall, whole genome scanning arrays, despite the drawback of an inability to detect balanced translocations, allow for discovery of chromosomal defects in a higher proportion of patients with hematologic malignancies. Newly detected chromosomal aberrations, including somatic uniparental disomy, may lead to more precise prognostic schemes in many diseases. Routine cytogenetics diagnostics and its limitationsCytogenetic analysis has provided fundamental insights into the molecular pathogenesis of a variety of hematologic disorders. The discovery of the Philadelphia chromosome and other chromosomal aberrations paved the way for the characterization of molecular lesions that lead to phenotypic characteristics of a number of hematologic malignancies. Metaphase cytogenetics (MC) has proven an extremely valuable diagnostic tool, providing definite diagnoses, for example, in the case of balanced pathognomonic translocations in chronic myeloid leukemia (CML), acute promyelocytic leukemia (APL), or core binding factor acute myelogenous leukemias (AMLs). 1,2 Chromosomal aberrations support the cytomorphologic diagnosis and provide prognostic information, for example, in myelodysplastic syndromes (MDSs), [3][4][5] AML with unbalanced translocations, 6-10 multiple myeloma (MM), 11,12 and chronic lymphocytic leukemia (CLL). 13,14 Irrespective of their location, size, and corresponding phenotype, chromosomal defects also represent suitable markers of clonality suggestive of clonal dominance by the malignant clone or, in rare circumstances, of oligoclonality due to a profound depletion of stem cell reserves 15 (Figure 1). Such a scenario explains the occasional occurrence of chromosomal abnormalities in otherwise typical aplastic anemia (AA; M. Wlodarski, L. Gondek, C. L. O'Keefe, R. Tiu, A. Haddad, A. Risitano, J.P.M., manuscript submitted May 2008). Technical advantages and limitations of MCRoutine MC allows for detection of large clonal populations (Ͼ 10% of dividing cells), indicating the presence of sign...

Novel homo- and hemizygous mutations in EZH2 in myeloid malignancies

“…1 Discovery of UPD9p paved the way for identification of the JAK2V617F mutation in MPN. Since then, through application of SNP-A, several new mutations have been identified in the homozygous configuration in the malignant cells of patients with hematological malignancies.…”

“…1 Mapping of such microdeletions was instrumental in the ultimate identification of TET2 and CBL mutations, which were found to be present in the hemizygous configuration in the regions affected by microdeletions. 3 Often, portions of chromosomes affected by loss of heterozygosity (LOH) due to both UPD and deletions overlap Letters to the Editor (4q24 and 11q23, for example).…”

“…The requirement for immunoglobulin production means that the myeloma plasma cell is reliant upon the unfolded protein response (UPR) and molecular chaperones for survival. 1 Heat shock protein (Hsp) 90 is a molecular chaperone that has an important role in the pathophysiology of myeloma and represents a relevant therapeutic target. 2,3 It fulfils two essential roles in plasma cells: firstly it is a major pro-survival chaperone, which associates with and stabilizes an extensive range of signal transducers important to plasma cell survival and proliferation (insulin-like growth factor-1, vascular endothelial growth factor, RAF and p42/44 mitogenactivated protein kinase), cell cycle regulation (AKT and nuclear factor-kB), migration (phosphoinositide 3-kinase) and antiapoptotic (nuclear factor-kB) pathways.…”

Prognosis of Myelodysplastic Syndromes

“…31 Data from several groups have indicated that SNP-A can be used to detect genetic alterations in MDS and can be of prognostic value. [31][32][33] Apart from the technological and analytical issues with this type of assay, it has become apparent that it is important to control for germ line alterations using the patient's own normal tissue as a control. 34 The use of SNP-A has allowed the identification of areas of uniparenteral dysomy (UPD).…”

Gene expression profiling in MDS and AML: potential and future avenues

“…77 With regard to 'omics' other than transcriptomics, genomewide array CGH and/or single nucleotide polymorphism analyses have revealed a large number of leukemia-specific copy number alterations (CNAs) as well as acquired homozygosity in the form of segmental uniparental disomy (UPD). 78 Parallel analysis of GEP and array CGH/single nucleotide polymorphism-defined CNAs has facilitated delineation of candidate genes in the respective genomic regions, as for example, demonstrated in AML with complex aberrations. 79 In contrast to ALL, the analysis of CNAs in AML has yielded only a small number of CNAs in most genomes of adult and pediatric AML patients, and the spectrum of AML-associated CNAs seems to be mainly non-recurrent.…”