Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies

BMC Genomics

Research Article

Jared Steranka¹  Stephen Desiderio²  Timothy Fuller³  Nicolas Giraldo-Castillo⁴  Eitan Halper-Stromberg⁵  Kathleen H Burns⁶ 

[1] Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA;Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA;Immunology Unit of the Institute for Cell Engineering, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross Building, Room 524, 21205, Baltimore, MD, USA;Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA;Mercer University School of Medicine, Macon, GA, USA;Los Andes University, Bogotá, Colombia;McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA;McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA;Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA;Department of Pathology, Johns Hopkins University, Baltimore, MD, USA;Department of Pathology, Johns Hopkins School of Medicine, 720 Rutland Avenue, Ross Building, Room 524, 21205, Baltimore, MD, USA;

关键词: V(D)J recombination;    Oncogenic translocation;    Lymphoid tumors;    MYC;    BCL-2;    V replacement;   

DOI  :  10.1186/1471-2164-14-565

 received in 2013-01-09, accepted in 2013-08-06,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundLymphocytes achieve diversity in antigen recognition in part by rearranging genomic DNA at loci encoding antibodies and cell surface receptors. The process, termed V(D)J recombination, juxtaposes modular coding sequences for antigen binding. Erroneous recombination events causing chromosomal translocations are recognized causes of lymphoid malignancies. Here we show a hybridization based method for sequence enrichment can be used to efficiently and selectively capture genomic DNA adjacent to V(D)J recombination breakpoints for massively parallel sequencing. The approach obviates the need for PCR amplification of recombined sequences.ResultsUsing tailored informatics analyses to resolve alignment and assembly issues in these repetitive regions, we were able to detect numerous recombination events across a panel of cancer cell lines and primary lymphoid tumors, and an EBV transformed lymphoblast line. With reassembly, breakpoints could be defined to single base pair resolution. The observed events consist of canonical V(D)J or V-J rearrangements, non-canonical rearrangements, and putatively oncogenic reciprocal chromosome translocations. We validated non-canonical and chromosome translocation junctions by PCR and Sanger sequencing. The translocations involved the MYC and BCL-2 loci, and activation of these was consistent with histopathologic features of the respective B-cell tumors. We also show an impressive prevalence of novel erroneous V-V recombination events at sites not incorporated with other downstream coding segments.ConclusionsOur results demonstrate the ability of next generation sequencing to describe human V(D)J recombinase activity and provide a scalable means to chronicle off-target, unexpressed, and non-amplifiable recombinations occurring in the development of lymphoid cancers.

【 授权许可】

Unknown   
© Halper-Stromberg et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.