{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001004090"],"sample_count":["1"],"description":["EGA dataset EGAD00001004090"],"repository":["EGA"],"title":["WGS of cell line MMML-seq / MALY-DE tumor_4167452"],"pubmed_abstract":["The <i>WHO Classification of Tumours of Haematopoietic and Lymphoid Tissue</i> notes instances of Burkitt lymphoma/leukemia (BL) with IG-<i>MYC</i> rearrangement displaying a B-cell precursor immunophenotype (termed herein \"preBLL\"). To characterize the molecular pathogenesis of preBLL, we investigated 13 preBLL cases (including 1 cell line), of which 12 were analyzable using genome, exome, and targeted sequencing, imbalance mapping, and DNA methylation profiling. In 5 patients with reads across the IG-<i>MYC</i> breakpoint junctions, we found evidence that the translocation derived from an aberrant VDJ recombination, as is typical for IG translocations arising in B-cell precursors. Genomic changes like biallelic IGH translocations or VDJ rearrangements combined with translocation into the VDJ region on the second allele, potentially preventing expression of a productive immunoglobulin, were detected in 6 of 13 cases. We did not detect mutations in genes frequently altered in BL, but instead found activating <i>NRAS</i> and/or <i>KRAS</i> mutations in 7 of 12 preBLLs. Gains on 1q, recurrent in BL and preB lymphoblastic leukemia/lymphoma (pB-ALL/LBL), were detected in 7 of 12 preBLLs. DNA methylation profiling showed preBLL to cluster with precursor B cells and pB-ALL/LBL, but apart from BL. We conclude that preBLL genetically and epigenetically resembles pB-ALL/LBL rather than BL. Therefore, we propose that preBLL be considered as a pB-ALL/LBL with recurrent genetic abnormalities."],"pubmed_title":["IG-<i>MYC</i> <sup>+</sup> neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas."],"pubmed_authors":["Wagener Rabea R, López Cristina C, Kleinheinz Kortine K, Bausinger Julia J, Aukema Sietse M SM, Nagel Inga I, Toprak Umut H UH, Seufert Julian J, Altmüller Janine J, Thiele Holger H, Schneider Christof C, Kolarova Julia J, Park Jeongbin J, Hübschmann Daniel D, Murga Penas Eva M EM, Drexler Hans G HG, Attarbaschi Andishe A, Hovland Randi R, Kjeldsen Eigil E, Kneba Michael M, Kontny Udo U, de Leval Laurence L, Nürnberg Peter P, Oschlies Ilske I, Oscier David D, Schlegelberger Brigitte B, Stilgenbauer Stephan S, Wössmann Wilhelm W, Schlesner Matthias M, Burkhardt Birgit B, Klapper Wolfram W, Jaffe Elaine S ES, Küppers Ralf R, Siebert Reiner R"],"additional_accession":[]},"is_claimable":false,"name":"233fa72b-87ef-4a9b-b96d-dfb6ca9543bd - samples","description":"This dataset contains the aligned whole genome sequencing data of cell line 380.\nThis cell was established from the peripheral blood of a 15-year-old boy with acute lymphoblastic leukemia at relapse, showing an immature phenotype and carrying an IGH-MYC (t(8;14)) as well as an IGH-BCL2 (t(14;18)) chromosomal translocation. The sequencing was performed on an Illumina X-ten sequencer.","dates":{"updated":"2018-10-17 16:35:41"},"accession":"EGAD00001004090","cross_references":{"TAXONOMY":["9606"],"pubmed":["30282799"],"EGA":["EGAC00001000010","EGAS00001002968"]}}