SNP Array in Hematopoietic Neoplasms: A Review

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.

MicroRNA-499 rs3746444 polymorphism in Egyptian children with biliary atresia

“…Many studies have claimed a key role for miR-499 in modulating the immune response, cell proliferation, apoptosis, inflammation, and immune response. Exploring gene targets of miR-499a identified inflammatory-related gene targets, including interleukin (IL)-13 and IL-23, IL6, IL-2 and IL-17 [ 12 ].…”

Predicted the P2RX7 rs3751143 polymorphism is associated with cancer risk: a meta-analysis and systematic review

“…SNPs in the P2X7R gene have been described to influence the function of this receptor, including loss or gain of function [ 38–41 ]. Song et al summarised the SNP arrays with regard to hematopoietic malignancies in general [ 42 ]. For instance, three P2X7R SNPs with amino acid changes, rs3751143 (1513A>C, Glu496Ala), rs2230911 (1096 C>G, Thr357Ser), and rs7958311 (835G>A, Arg270His), have been shown to result in a loss of receptor function in both channel and pore function [ 39 , 40 ].…”

Structural Variants as a Basis for Targeted Therapies in Hematological Malignancies

“…In recent years, both techniques have been developed further to be more sensitive, to be applicable more broadly and to be more high-throughput (41, 42). Furthermore, SNP arrays are a form of DNA arrays in which you can identify single nucleotide exchanges as well as alterations from the diploidy of cells (44). Another method in routine diagnostics is FISH (43).…”