SNPs Array Karyotyping in Non-Hodgkin Lymphoma

Primary mediastinal large B-cell lymphoma is characterized by large-scale copy-neutral loss of heterozygosity

Development of primary mediastinal B-cell lymphoma (PMBL) is driven by cumulative genomic aberrations. We discovered a unique copy-neutral loss of heterozygosity (CN-LOH) landscape of PMBL which distinguishes this tumour from other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma. Using single nucleotide polymorphism array analysis we identified large-scale CN-LOH lesions in 91% (30/33) of diagnostic PMBLs and both investigated PMBL-derived cell lines. Altogether, the cohort showed 157 extra-large (25.3-248.4 Mb) CN-LOH lesions affecting up to 14 chromosomes per case (mean of 4.4) and resulting in a reduction of heterozygosity an average of 9.9% (range 1.3-51%) of the genome. Predominant involvement of terminal chromosomal segments suggests the implication of B-cell specific crossover events in the pathogenesis of PMBL. Notably, CN-LOH stretches non-randomly clustered on 6p (60%), 15 (37.2%) and 17q (40%), and frequently co-occurred with homozygous mutations in the MHC I (6p21), B2M (15q15) and GNA13 (17q23) genes, respectively, as shown by preliminary whole-exome/genome sequencing data. Altogether, our findings implicate CN-LOH as a novel and distinct mutational process contributing to the molecular pathogenesis of PMBL. The aberration acting as 'second hit' in the Knudson hypothesis, ranks as the major mechanism converting to homozygosity the PMBL-related driver genes. Screening of the cohort of 199 B cell leukamia/lymphoma whole-genomes revealed significant differences in the CN-LOH landscape of PMBL and other B-cell malignancies, including the biologically related diffuse large B-cell lymphoma.

Molecular Diagnostics of Non-Hodgkin Lymphoma

Non-Hodgkin lymphoma encompasses a diverse group of B-cell and T-cell neoplasms. Current classification is based on clinical information, histologic assessment, immunophenotypic characteristics, and molecular alterations. A wide range of genetic alterations, including large chromosomal structural rearrangements, aneuploidies, point mutations, and copy number alterations, have been reported across all types of lymphomas. Many of these are now incorporated into the World Health Organization-defined criteria for the diagnostic evaluation of patients with lymphoid proliferations and, therefore, their accurate identification is paramount for diagnosis, subclassification, and selection of treatment. In addition to their value in the diagnostic setting, many alterations that are not routinely evaluated in standard clinical practice may still define specific disease entities as they have important implications in risk stratification, as well as roles in emerging alternate therapies and disease monitoring. Because of the complexity and range of alterations, their accurate and sensitive assessment requires a careful selection of technology. Here, we discuss the most commonly used molecular techniques in current clinical practice and highlight some of the benefits and pitfalls based on the type of alteration.

Genomic Alterations In Primary Cardiac Diffuse Large B Cell Lymphoma: A Case Report And Literature Review

Primary cardiac diffuse large B cell lymphoma (PC-DLBCL) is a rare kind of hematological malignancy, and its clinical and pathologic characteristics, especially in Eastern countries, remain unclear. Moreover, genomic alterations in PC-DLBCL have not been studied previously. We describe a case of a 57-year-old man who presented with exertional dyspnoea due to a heart mass in April 2018 and was diagnosed with PC-DLBCL characterized by immunohistochemical markers of the activated B cell (ABC) subtype and double expression of c-MYC and Bcl-2. Mutations in a total of 11 genes—TBL1XR1, CD79B, IGLL5, ZMYM3, MYD88, TMSB4X, PIM1, BTK, NRXN3, CUX1, and CSMD1—were detected via next-generation sequencing (NGS), while 19 copy number variations (CNVs) such as 1q+, 3p+, 3q+(*2), 5p+, 6p−, 6q−, 7q+, +11, 12q−, 15q−, 17q+, 17p−, +18, 19q+, 19p−, 19q−, X q+, and −Y and 4 copy-neutral loss of heterozygosity (CN-LOH) lesions located at 1q21.1q44, 3p26.3q11.2, 3q13.11q29 and 6p22.2p21.32 were identified by single nucleotide polymorphism (SNP) array karyotyping. Some key gene alterations in lymphoma, such as PRDM1 deletion and Bcl-2 amplification, were identified using SNP array analysis. The patient received 6 courses of chemotherapy (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone, R-CHOP regimen) after surgery and is currently in remission. In summary, the present case was diagnosed as PC-DLBCL, ABC subtype by the Hans algorithm and double expression lymphoma, with co-occurrence of the MYD88^L265P and CD79B mutations (MCD) subtype by genetic alteration analysis. This study presents a unique PC-DLBCL case in which complex genomic alterations were revealed by NGS and SNP array analysis, which has never been reported in the literature, and these findings could provide new insight into the genomic characterization of PC-DLBCL.

SNP Arrays

The papers published in this Special Issue “SNP arrays” (Single Nucleotide Polymorphism Arrays) focus on several perspectives associated with arrays of this type. The range of papers vary from a case report to reviews, thereby targeting wider audiences working in this field. The research focus of SNP arrays is often human cancers but this Issue expands that focus to include areas such as rare conditions, animal breeding and bioinformatics tools. Given the limited scope, the spectrum of papers is nothing short of remarkable and even from a technical point of view these papers will contribute to the field at a general level. Three of the papers published in this Special Issue focus on the use of various SNP array approaches in the analysis of three different cancer types. Two of the papers concentrate on two very different rare conditions, applying the SNP arrays slightly differently. Finally, two other papers evaluate the use of the SNP arrays in the context of genetic analysis of livestock. The findings reported in these papers help to close gaps in the current literature and also to give guidelines for future applications of SNP arrays.