title: Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.
abstract: Immunoglobulins (Ig) are produced by B lymphocytes as secreted antibodies or as part of the B-cell receptor. There is tremendous diversity of potential Ig transcripts (>1 × 10(12)) as a result of hundreds of germ-line gene segments, random nucleotide incorporation during joining of gene segments into a complete transcript, and the process of somatic hypermutation at individual nucleotides. This recombination and mutation process takes place in the maturing B cell and is responsible for the diversity of potential epitope recognition. Cancers arising from mature B cells are characterized by clonal production of Ig heavy (IGH@) and light chain transcripts, although whether the sequence has undergone somatic hypermutation is dependent on the maturation stage at which the neoplastic clone arose. Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults and arises from a mature B cell with either mutated or unmutated IGH@ transcripts, the latter having worse prognosis and the assessment of which is routinely performed in the clinic. Currently, IGHV mutation status is assessed by Sanger sequencing and comparing the transcript to known germ-line genes. In this paper, we demonstrate that complete IGH@ V-D-J sequences can be computed from unselected RNA-seq reads with results equal or superior to the clinical procedure: in the only discordant case, the clinical transcript was out-of-frame. Therefore, a single RNA-seq assay can simultaneously yield gene expression profile, SNP and mutation information, as well as IGHV mutation status, and may one day be performed as a general test to capture multidimensional clinically relevant data in CLL.
authors: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210;
authors: James S
authors: JS
authors: Blachly
authors: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210;
authors: Amy S
authors: AS
authors: Ruppert
authors: Department of Pathology, The Ohio State University, Columbus, OH 43210;
authors: Weiqiang
authors: W
authors: Zhao
authors: Department of Pathology, The Ohio State University, Columbus, OH 43210;
authors: Susan
authors: S
authors: Long
authors: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210;
authors: Joseph
authors: J
authors: Flynn
authors: Hematologic Malignancies Research Program, Sarah Cannon Research Institute, Nashville, TN 37203;
authors: Ian
authors: I
authors: Flinn
authors: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210;
authors: Jeffrey
authors: J
authors: Jones
authors: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210;
authors: Kami
authors: K
authors: Maddocks
authors: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210;
authors: Leslie
authors: L
authors: Andritsos
authors: Moores Cancer Center, University of California at San Diego, La Jolla, CA 92092-0820;
authors: Emanuela M
authors: EM
authors: Ghia
authors: Moores Cancer Center, University of California at San Diego, La Jolla, CA 92092-0820;
authors: Laura Z
authors: LZ
authors: Rassenti
authors: Moores Cancer Center, University of California at San Diego, La Jolla, CA 92092-0820;
authors: Thomas J
authors: TJ
authors: Kipps
authors: Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210; and Albert.delaChapelle@osumc.edu john.byrd@osumc.edu.
authors: Albert
authors: A
authors: de la Chapelle
authors: Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210; College of Pharmacy, The Ohio State University, Columbus, OH 43210 Albert.delaChapelle@osumc.edu john.byrd@osumc.edu.
authors: John C
authors: JC
authors: Byrd
mesh_terms: D000483:Alleles; D001483:Base Sequence; D022801:Complementarity Determining Regions / Q000737:chemistry / Q000235:genetics; D016678:Genome; D006801:Humans; D007135:Immunoglobulin Variable Region / Q000235:genetics; D007136:Immunoglobulins / Q000737:chemistry*; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000276:immunology*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011379:Prognosis; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D027041:Somatic Hypermutation, Immunoglobulin; D059467:Transcriptome; D045567:VDJ Recombinases / Q000235:genetics
chemical_list: D022801:Complementarity Determining Regions; D007135:Immunoglobulin Variable Region; D007136:Immunoglobulins; D045567:VDJ Recombinases
keywords: B cells; CLL; RNA sequencing; immunoglobulin; somatic hypermutation