The study of recurrent chromosomal defects has yielded profound insights into the biology of chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL) that have translated into improved prognostic precision and changes in management. These advances have relied on interphase fluorescent in situ hybridization (FISH) to examine non-dividing CLL cells. A landmark report of FISH analysis of CLL cells with eight probes published in 2000 established a clinically applicable hierarchical prognostic risk stratification method [Citation1]. However, FISH analysis of CLL cells provides a limited view of the genetic defects in CLL. A more comprehensive and higher resolution method of detecting genomic defects in CLL cells is likely to provide additional insights into the biology of CLL, improve prognostic precision, and guide more precisely targeted therapy.
Genome wide analysis with array-based comparative genomic hybridization (aCGH) and single nucleotide polymorphism (aSNP) assays provide an exciting new approach to detection of novel genetic defects in CLL [Citation2–5]. aCGH and aSNP analyses can detect defects in CLL cells that are not included in current FISH probe sets, and can also detect lesions that are below the level of resolution of FISH analysis. However, currently available aCGH and aSNP cytogenetic assays can usually only detect defects that are present in at least 20–30% of the tested cells compared to 5–10% for FISH analysis [Citation2,Citation6], and array analysis cannot readily identify subclones or clonal evolution. In addition, the cost and technical complexity of aCGH and aSNP assays currently limit their utility in clinical laboratories. However, these array-based assays are very useful discovery tools in detecting novel genomic defects in CLL, measuring the heterogeneity of these defects, and determining if defects occur in multiple genes which are functionally related.
In this issue of the Journal, Jarasova et al. report the results of an CGH study analyzing gain of genetic material by duplication of the short arm of chromosome 2 (2p+) in a subset of patients with CLL [Citation7]. Their low density aCGH shows acquisition of a common approximately 64 Mb region of 2p (p13–p25) in all cases studied. This large region of 2p includes the loci for NMYC, REL, and ALK, genes which the authors consider to be of particular interest in the etiology of CLL. However, they provide no new data on the expression of these genes in the affected CLL cells to support their hypothesis. The study also provides a detailed description of the karyotypic abnormalities involving 2p detected in these patients. As expected for a population of patients with CLL with intermediate to advanced clinical stage disease, most of the patients with 2p+ have other additional markers of poor risk disease. This study thus contributes to our knowledge of 2p+ in CLL by providing a more detailed genetic map of the additional chromosomal material in these cells and suggesting genes of interest for future study.
The study by Jarasova et al. does not provide conclusive data supporting their recommendation of routine testing for 2p+ using a FISH probe for NMYC in patients with CLL. The NMYC probe could fail to detect some patients with CLL with 2p+. In three published array cytogenetics studies, a subset of CLL patients with 2p+ exhibited small (3–3.5 Mb) copy number gains that variously implicate REL, BCL11A, and NMYC as targets of the copy number change [Citation2–4] and in one of these studies NMYC was not an informative target locus in some patients with 2p+ [Citation2]. In addition, 2p+ has not yet been proven to be an independent prognostic factor in CLL. As array cytogenetics continues to identify multiple potentially important regions of gain and loss of genetic material, each of these genomic defects will need to be investigated in prospective studies of large populations of representative patients with CLL using multivariate analysis to determine their independent prognostic value. Only those probes for defects of validated independent prognostic value should be added to the clinical FISH assay for CLL.
Future evaluation of genetic defects in CLL is likely to include multiple complementary technologies. However, in the short term, FISH analysis will remain the primary testing modality in clinical practice and its clinical utility could be enhanced by several technical improvements. Genomic analysis could be broadened by the addition of FISH probes of proven independent prognostic value. The ability of FISH (and array cytogenetic analysis) to detect small populations of CLL cells with a genetic defect could be increased by analysis of purified B cells which could also improve the accuracy of serial monitoring of the percentage of CLL cells with a specific genetic defect. These data could be useful in monitoring patients with CLL for clonal evolution and expansion [Citation8]. As aCGH and aSNP analyses become more reliable, sensitive and affordable they could supersede FISH analysis for genomic defects in CLL. Array-based genome wide analysis of genetic defects in CLL cells combined with targeted therapy could then result in improved management of patients with CLL.
Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the article.
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