Evidence-based review of genomic aberrations in diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS): Report from the cancer genomics consortium lymphoma working group.

Diffuse large B cell lymphoma, not otherwise specified (DLBCL, NOS) is the most common type of non-Hodgkin lymphoma (NHL). The 2016 World Health Organization (WHO) classification defined DLBCL, NOS and its subtypes based on clinical findings, morphology, immunophenotype, and genetics. However, even within the WHO subtypes, it is clear that additional clinical and genetic heterogeneity exists. Significant efforts have been focused on utilizing advanced genomic technologies to further subclassify DLBCL, NOS into clinically relevant subtypes. These efforts have led to the implementation of novel algorithms to support optimal risk-oriented therapy and improvement in the overall survival of DLBCL patients. We gathered an international group of experts to review the current literature on DLBCL, NOS, with respect to genomic aberrations and the role they may play in the diagnosis, prognosis and therapeutic decisions. We comprehensively surveyed clinical laboratory directors/professionals about their genetic testing practices for DLBCL, NOS. The survey results indicated that a variety of diagnostic approaches were being utilized and that there was an overwhelming interest in further standardization of routine genetic testing along with the incorporation of new genetic testing modalities to help guide a precision medicine approach. Additionally, we present a comprehensive literature summary on the most clinically relevant genomic aberrations in DLBCL, NOS. Based upon the survey results and literature review, we propose a standardized, tiered testing approach which will help laboratories optimize genomic testing in order to provide the maximum information to guide patient care.

Assessing genome-wide copy number aberrations and copy-neutral loss-of-heterozygosity as best practice: An evidence-based review from the Cancer Genomics Consortium working group for plasma cell disorders.

BACKGROUND: Plasma cell neoplasms (PCNs) encompass a spectrum of disorders including monoclonal gammopathy of undetermined significance, smoldering myeloma, plasma cell myeloma, and plasma cell leukemia. Molecular subtypes have been defined by recurrent cytogenetic abnormalities and somatic mutations that are prognostic and predictive. Karyotype and fluorescence in situ hybridization (FISH) have historically been used to guide management; however, new technologies and markers raise the need to reassess current testing algorithms. METHODS: We convened a panel of representatives from international clinical laboratories to capture current state-of-the-art testing from published reports and to put forward recommendations for cytogenomic testing of plasma cell neoplasms. We reviewed 65 papers applying FISH, chromosomal microarray (CMA), next-generation sequencing, and gene expression profiling for plasma cell neoplasm diagnosis and prognosis. We also performed a survey of our peers to capture current laboratory practice employed outside our working group. RESULTS: Plasma cell enrichment is widely used prior to FISH testing, most commonly by magnetic bead selection. A variety of strategies for direct, short- and long-term cell culture are employed to ensure clonal representation for karyotyping. Testing of clinically-informative 1p/1q, del(13q) and del(17p) are common using karyotype, FISH and, increasingly, CMA testing. FISH for a variety of clinically-informative balanced IGH rearrangements is prevalent. Literature review found that CMA analysis can detect abnormalities in 85-100% of patients with PCNs; more specifically, in 5-53% (median 14%) of cases otherwise normal by FISH and cytogenetics. CMA results in plasma cell neoplasms are usually complex, with alteration counts ranging from 1 to 74 (median 10-20), primarily affecting loci not covered by FISH testing. Emerging biomarkers include structural alterations of MYC as well as somatic mutations of KRAS, NRAS, BRAF, and TP53. Together, these may be measured in a comprehensive manner by a combination of newer technologies including CMA and next-generation sequencing (NGS). Our survey suggests most laboratories have, or are soon to have, clinical CMA platforms, with a desire to move to NGS assays in the future. CONCLUSION: We present an overview of current practices in plasma cell neoplasm testing as well as an algorithm for integrated FISH and CMA testing to guide treatment of this disease.

Medical conditions and risk of adult myeloid leukemia.

PURPOSE: Although a few previous studies have reported positive associations between adult myeloid leukemia and a history of certain medical conditions, the etiology of most cases remains largely unknown. Our purpose was to examine associations between certain medical conditions and adult myeloid leukemia. METHODS: Using logistic regression, we evaluated associations between 16 self-reported medical conditions and myeloid leukemia in a case-control study of 670 cases [including 420 acute myeloid leukemia (AML) and 186 chronic myelogenous leukemia (CML)] and 701 population-based controls. RESULTS: We observed significant positive associations between AML and ulcerative colitis (odds ratio (OR) = 3.8; 95 % confidence interval (CI), 1.1-13) and between CML and peptic ulcer (OR = 2.0; 95% CI, 1.1-3.8). A personal cancer history increased both AML (OR = 2.6; 95% CI, 1.7-3.9) and CML (OR = 3.5; 95% CI, 2.0-5.8) risk even after excluding individuals who reported prior radiation and/or chemotherapy treatment. CONCLUSION: Certain inflammatory medical conditions and a personal history of cancer, independent from therapy, are associated with an increased risk of myeloid leukemia.

High polymorphism in the trisomic portion of a gastric cancer cell line.

BACKGROUND: Genetic instability is a hallmark of malignancy, and microsatellite instability is a widely appreciated mechanism of generating genetic changes. We have recently observed four markers clustered on chromosome 20 that showed the effects of microsatellite instability in the gastric adenocarcinoma cell line SNU-1. Each affected marker had alleles of three different sizes. The aim of this study was to investigate the origin for this high-density polymorphism on a single chromosome. METHODS: The high polymorphism located on chromosome 20 was confirmed using 37 additional markers. To further evaluate this finding, 15 clones of the cell line were generated and then assayed with the triallelic markers. RESULTS: All told, almost a third of the markers on chromosome 20 had triallelic patterns, but only 0.3% of the markers not on chromosome 20 showed this result. The number of clones showing allelic variation was an average of 50% greater for chromosome 20 markers than for markers elsewhere. A karyotype analysis showed that the progenitor cell line of SNU-1 was trisomic for chromosome 20, and the high polymorphism on that chromosome is almost certainly due to the trisomy. CONCLUSIONS: Not only are there more chromosome copies and therefore more gene copies subject to mutation in cells containing trisomy, but also more mutations may be passed on to the progeny. This elevated polymorphism increases the repertoire of genetic changes that could affect cellular growth, and may independently increase genomic instability.

ERBB2 amplifications in esophageal adenocarcinoma.

BACKGROUND: ERBB2 (v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, Her-2-neu) gene amplification and overexpression has been reported in several types of cancer. The purpose of this study was to (1) determine the frequency of ERBB2 amplification (in comparison to other proto-oncogenes) in tumors from patients with esophageal adenocarcinoma, (2) characterize structural details of an ERBB2 amplicon in the esophageal adenocarcinoma cell line OE19 (contains a 100-fold ERBB2 amplification), and (3) test whether growth of the OE19 cell line is sensitive to the ERBB2 inhibitor trastuzumab (Herceptin; Genetech, Inc, San Francisco, CA). METHODS: First, we determined the frequency, by Southern blotting techniques, of amplification of ERBB2 and 13 other proto-oncogenes in a panel of 25 esophageal adenocarcinoma tumors. Then, in a second panel of 10 tumor specimens, expression levels of the ERBB2 gene and of several other genes that flank ERBB2 on chromosome 17 were determined by microarray analysis. Next we characterized the ERBB2 amplicon in the esophageal adenocarcinoma cell line OE19 using cytogenetic methods and a Rec-A protein assisted restriction endonuclease mapping technique. Finally, an in vitro growth inhibition assay was used to measure the sensitivity of OE19 and OE33 cells to treatment with trastuzumab (humanized antibody to ERBB2). RESULTS: ERBB2 was the most frequently amplified proto-oncogene among 25 esophageal adenocarcinoma tumors tested (greater than 10-fold amplification in 3 of 25 (12%) tumors tested). The OE19 cell line contains a 100-fold amplification of the ERBB2 gene, and highly expresses its messenger ribonucleic acid. Transcripts from genes that flank ERBB2 including GRB7, a protein linked to metastasis in esophageal cancer, also showed high levels of expression. In OE19 cells, the ERBB2 amplicon was localized to a homogeneously staining region of chromosome 14. Southern blots from the Rec-A protein assisted restriction endonuclease cleavage mapping experiments in OE19 showed a strong band of 210 kilobases in size, demonstrating that the main amplicon was a tandem repeat. In the in vitro growth inhibition assay, trastuzumab inhibited the OE19 and OE33 cells growth by 49% and 20%, respectively, at a saturating concentration of 20 microg/mL. CONCLUSIONS: ERBB2 is the most frequently amplified proto-oncogene in esophageal adenocarcinoma among the genes that we tested. In the OE19 esophageal adenocarcinoma cell line, the ERBB2 amplicon is translocated onto chromosome 14, is amplified 100-fold at the deoxyribonucleic acid level, and is highly overexpressed at the messenger ribonucleic acid level. Finally, the growth of this cell line was inhibited by incubation with trastuzumab. These results demonstrate that a substantial number of esophageal adenocarcinomas have amplified copies of the ERBB2 gene, and that they may be responsive to ERBB2 targeted therapies such as trastuzumab.

Duplication of the distal long arm of chromosome 15: report of three new patients and review of the literature.

Patients with trisomies or duplications of distal 15q have rarely been reported in the literature. Previous authors [Zollino et al., 1999: Am J Med Genet 87:391-394] have described a distal 15q trisomy syndrome, including the unusual features of prenatal overgrowth, tall stature, macrocephaly, and craniosynostosis. We report three new patients with a duplication of 15q24-q26.3; features common to the two surviving patients include ptosis, small size, and developmental delay. None of these patients had craniosynostosis or overgrowth. We propose that the previously described distal 15q trisomy syndrome [Zollino et al., 1999: Am J Med Genet 87:391-394] may result from specific disruption of a gene linked to 15q25, rather than partial trisomy for the region.