title: Assigning and visualizing germline genes in antibody repertoires.
abstract: Identifying the germline genes involved in immunoglobulin rearrangements is an essential first step in the analysis of antibody repertoires. Based on our prior work in analysing diverse recombinant viruses, we present IgSCUEAL (Immunoglobulin Subtype Classification Using Evolutionary ALgorithms), a phylogenetic approach to assign V and J regions of immunoglobulin sequences to their corresponding germline alleles, with D regions assigned using a simple pairwise alignment algorithm. We also develop an interactive web application for viewing the results, allowing the user to explore the frequency distribution of sequence assignments and CDR3 region length statistics, which is useful for summarizing repertoires, as well as a detailed viewer of rearrangements and region alignments for individual query sequences. We demonstrate the accuracy and utility of our method compared with sequence similarity-based approaches and other non-phylogenetic model-based approaches, using both simulated data and a set of evaluation datasets of human immunoglobulin heavy chain sequences. IgSCUEAL demonstrates the highest accuracy of V and J assignment amongst existing approaches, even when the reassorted sequence is highly mutated, and can successfully cluster sequences on the basis of shared V/J germline alleles.
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK.
authors.forename: Simon D W
authors.identifier: http://orcid.org/0000-0002-5207-9879
authors.initials: SD
authors.lastname: Frost
authors.affiliation: Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Murrell
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK.
authors.forename: A S Md Mukarram
authors.initials: AS
authors.lastname: Hossain
authors.affiliation: Department of Medicine, New York University School of Medicine, New York, NY 10016, USA Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Gregg J
authors.initials: GJ
authors.lastname: Silverman
authors.affiliation: Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA spond@ucsd.edu.
authors.forename: Sergei L Kosakovsky
authors.initials: SL
authors.lastname: Pond
mesh_terms: D000465:Algorithms; D000916:Antibody Diversity / Q000235:genetics*; D003198:Computer Simulation; D030541:Databases, Genetic; D015322:Gene Rearrangement, B-Lymphocyte; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D008957:Models, Genetic; D018448:Models, Immunological; D010802:Phylogeny; D016415:Sequence Alignment / Q000706:statistics & numerical data; D060152:V(D)J Recombination
chemical_list: D007143:Immunoglobulin Heavy Chains
keywords: IgSCUEAL; V(D)J rearrangements; classification; immunoglobulin; phylogenetic models; visualization