https://ror.org/048a87296 Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
https://ror.org/048a87296 SciLifeLab, Uppsala University, Uppsala, Sweden.
Life Sci Alliance. 2024 May 22;7(8). doi: 10.26508/lsa.202302481. Print 2024 Aug.
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, the cell line offers a practical model for the study of pediatric B-ALL. In recent years, short- and long-read DNA and RNA sequencing have emerged as a complement to karyotyping techniques in the resolution of structural variants in an oncological context. Here, we explore the integration of long-read PacBio and Oxford Nanopore whole-genome sequencing, IsoSeq RNA sequencing, and short-read Illumina sequencing to create a detailed genomic and transcriptomic characterization of the REH cell line. Whole-genome sequencing clarified the molecular traits of disrupted ALL-associated genes including , , , , and , as well as the glucocorticoid receptor Meanwhile, transcriptome sequencing identified seven fusion genes within the genomic breakpoints. Together, our extensive whole-genome investigation makes high-quality open-source data available to the leukemia genomics community.
B 细胞急性淋巴细胞白血病 (ALL) 细胞系 REH 具有 t(12;21) 易位，其特征是一系列大规模染色体重排导致的复杂核型。该细胞系取自一名 15 岁复发的患者，为研究儿科 B-ALL 提供了一个实用的模型。近年来，短读长和长读长 DNA 和 RNA 测序已成为核型分析技术的补充，可在肿瘤学背景下解析结构变异。在这里，我们探索了长读长 PacBio 和 Oxford Nanopore 全基因组测序、IsoSeq RNA 测序和短读长 Illumina 测序的整合，以对 REH 细胞系进行详细的基因组和转录组特征分析。全基因组测序阐明了被破坏的 ALL 相关基因的分子特征，包括 、 、 、 、 和 ，以及糖皮质激素受体 。同时，转录组测序在基因组断裂点识别出了七个融合基因。总的来说，我们广泛的全基因组研究为白血病基因组学社区提供了高质量的开源数据。
