title: VDJSeq-Solver: in silico V(D)J recombination detection tool.
abstract: In this paper we present VDJSeq-Solver, a methodology and tool to identify clonal lymphocyte populations from paired-end RNA Sequencing reads derived from the sequencing of mRNA neoplastic cells. The tool detects the main clone that characterises the tissue of interest by recognizing the most abundant V(D)J rearrangement among the existing ones in the sample under study. The exact sequence of the clone identified is capable of accounting for the modifications introduced by the enzymatic processes. The proposed tool overcomes limitations of currently available lymphocyte rearrangements recognition methods, working on a single sequence at a time, that are not applicable to high-throughput sequencing data. In this work, VDJSeq-Solver has been applied to correctly detect the main clone and identify its sequence on five Mantle Cell Lymphoma samples; then the tool has been tested on twelve Diffuse Large B-Cell Lymphoma samples. In order to comply with the privacy, ethics and intellectual property policies of the University Hospital and the University of Verona, data is available upon request to supporto.utenti@ateneo.univr.it after signing a mandatory Materials Transfer Agreement. VDJSeq-Solver JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/VDJSeq-Solver/.
authors: Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy.
authors: Giulia
authors: G
authors: Paciello
authors: Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy.
authors: Andrea
authors: A
authors: Acquaviva
authors: Department of Pathology and Diagnostics, University of Verona, Verona, Italy; Department of Pathology, Children Hospital Boston, Harvard Medical School, Boston, USA.
authors: Chiara
authors: C
authors: Pighi
authors: Department of Biotechnology, University of Verona, Verona, Italy.
authors: Alberto
authors: A
authors: Ferrarini
authors: Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy.
authors: Enrico
authors: E
authors: Macii
authors: Department of Pathology and Diagnostics, University of Verona, Verona, Italy.
authors: Alberto
authors: A
authors: Zamo'
authors: Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy.
authors: Elisa
authors: E
authors: Ficarra
mesh_terms: D000465:Algorithms; D002999:Clone Cells; D003198:Computer Simulation; D005803:Genes, Immunoglobulin; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D016403:Lymphoma, Large B-Cell, Diffuse / Q000175:diagnosis* / Q000235:genetics; D020522:Lymphoma, Mantle-Cell / Q000175:diagnosis* / Q000235:genetics; D016133:Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software; D060152:V(D)J Recombination / Q000235:genetics*