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

BACKGROUND: Lymphocytes 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 chromos...

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Autores principales: Halper-Stromberg, Eitan, Steranka, Jared, Giraldo-Castillo, Nicolas, Fuller, Timothy, Desiderio, Stephen, Burns, Kathleen H
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846541/
https://www.ncbi.nlm.nih.gov/pubmed/23957733
http://dx.doi.org/10.1186/1471-2164-14-565
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author Halper-Stromberg, Eitan
Steranka, Jared
Giraldo-Castillo, Nicolas
Fuller, Timothy
Desiderio, Stephen
Burns, Kathleen H
author_facet Halper-Stromberg, Eitan
Steranka, Jared
Giraldo-Castillo, Nicolas
Fuller, Timothy
Desiderio, Stephen
Burns, Kathleen H
author_sort Halper-Stromberg, Eitan
collection PubMed
description BACKGROUND: Lymphocytes 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. RESULTS: Using 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. CONCLUSIONS: Our 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.
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spelling pubmed-38465412013-12-03 Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies Halper-Stromberg, Eitan Steranka, Jared Giraldo-Castillo, Nicolas Fuller, Timothy Desiderio, Stephen Burns, Kathleen H BMC Genomics Research Article BACKGROUND: Lymphocytes 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. RESULTS: Using 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. CONCLUSIONS: Our 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. BioMed Central 2013-08-19 /pmc/articles/PMC3846541/ /pubmed/23957733 http://dx.doi.org/10.1186/1471-2164-14-565 Text en Copyright © 2013 Halper-Stromberg et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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.
spellingShingle Research Article
Halper-Stromberg, Eitan
Steranka, Jared
Giraldo-Castillo, Nicolas
Fuller, Timothy
Desiderio, Stephen
Burns, Kathleen H
Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies
title Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies
title_full Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies
title_fullStr Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies
title_full_unstemmed Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies
title_short Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies
title_sort fine mapping of v(d)j recombinase mediated rearrangements in human lymphoid malignancies
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846541/
https://www.ncbi.nlm.nih.gov/pubmed/23957733
http://dx.doi.org/10.1186/1471-2164-14-565
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