Abstract
Cytogenetic analysis is essential for the diagnosis and prognosis of hematopoietic neoplasms in current clinical practice. Many hematopoietic malignancies are characterized by structural chromosomal abnormalities such as specific translocations, inversions, deletions and/or numerical abnormalities that can be identified by karyotype analysis or fluorescence in situ hybridization (FISH) studies. Single nucleotide polymorphism (SNP) arrays offer high-resolution identification of copy number variants (CNVs) and acquired copy-neutral loss of heterozygosity (LOH)/uniparental disomy (UPD) that are usually not identifiable by conventional cytogenetic analysis and FISH studies. As a result, SNP arrays have been increasingly applied to hematopoietic neoplasms to search for clinically-significant genetic abnormalities. A large numbers of CNVs and UPDs have been identified in a variety of hematopoietic neoplasms. CNVs detected by SNP array in some hematopoietic neoplasms are of prognostic significance. A few specific genes in the affected regions have been implicated in the pathogenesis and may be the targets for specific therapeutic agents in the future. In this review, we summarize the current findings of application of SNP arrays in a variety of hematopoietic malignancies with an emphasis on the clinically significant genetic variants.
Highlights
The progressive accumulation of genetic changes plays an essential role in the tumorigenesis and evolution of human cancers
While Mohamedali’s study failed to show independent prognostic significance of the genetic lesions identified by Single nucleotide polymorphism (SNP) array on multivariate analysis, Tiu showed that the presence of new genetic lesions detected by SNP array was predictive of poor prognosis in myelodysplastic syndrome (MDS) by univariate and multivariate analyses [58]
This study indicates that 17q Uniparental disomy (UPD) with homozygous loss of normal neurofibromatosis 1 (NF1) plays a critical role for the pathogenesis of Juvenile myelomonocytic leukemia (JMML) in NF1 patients
Summary
The progressive accumulation of genetic changes plays an essential role in the tumorigenesis and evolution of human cancers. The characteristic deletions of CDKN2A, PAX5, IKZF1, ETV6, RB1, and EBF1 genes were identified by Safavi et al [35] in adult ALL using SNP array covering 5 million markers and a resolution of 10 kb. Studied 317 cases of pediatric ALL along with 17,958 control cases with an Affymetrix 500K Mapping array, and found two SNPs at chromosome 10q21 (rs10821936 and rs10994982) located in intron 3 of the ARID5B gene to be associated pediatric ALL. As both ARID5B and IKZF1 play important roles in B-lymphocyte growth and differentiation, the possibility of SNPs in these genes predispose the patients to the development of B-ALL is high
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