title: Qualifying high-throughput immune repertoire sequencing.
abstract: Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform.
authors.affiliation: Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: norbert.niklas@o.roteskreuz.at.
authors.forename: Norbert
authors.initials: N
authors.lastname: Niklas
authors.affiliation: Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: johannes.proell@o.roteskreuz.at.
authors.forename: Johannes
authors.initials: J
authors.lastname: Pröll
authors.affiliation: Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: johannes.weinberger@o.roteskreuz.at.
authors.forename: Johannes
authors.initials: J
authors.lastname: Weinberger
authors.affiliation: Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: agnes.zopf@o.roteskreuz.at.
authors.forename: Agnes
authors.initials: A
authors.lastname: Zopf
authors.affiliation: Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: karin.wiesinger@o.roteskreuz.at.
authors.forename: Karin
authors.initials: K
authors.lastname: Wiesinger
authors.affiliation: University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria. Electronic address: konstantin.krismer@students.fh-hagenberg.at.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Krismer
authors.affiliation: Division of Hematology/Oncology, Elisabethinen Hospital Linz, Fadingerstraße 1, 4020 Linz, Austria. Electronic address: peter@bettelheim.eu.
authors.forename: Peter
authors.initials: P
authors.lastname: Bettelheim
authors.affiliation: Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria. Electronic address: christian.gabriel@o.roteskreuz.at.
authors.forename: Christian
authors.initials: C
authors.lastname: Gabriel
mesh_terms: D001483:Base Sequence; D016022:Case-Control Studies; D002999:Clone Cells; D015894:Genome, Human; D018095:Germ-Line Mutation; D059014:High-Throughput Nucleotide Sequencing / Q000592:standards*; D006801:Humans; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000235:genetics* / Q000276:immunology / Q000473:pathology; D008969:Molecular Sequence Data; D010802:Phylogeny; D011947:Receptors, Antigen, B-Cell / Q000145:classification / Q000235:genetics* / Q000276:immunology; D011948:Receptors, Antigen, T-Cell / Q000145:classification / Q000235:genetics* / Q000276:immunology; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
chemical_list: D011947:Receptors, Antigen, B-Cell; D011948:Receptors, Antigen, T-Cell
keywords: Big data visualization; Clonotyping; Diversity generation; Immune repertoire; Immunoglobulin heavy chain; Next-generation sequencing; Somatic hypermutation; T cell receptor β; VDJ recombination