Assigning and visualizing germline genes in antibody repertoires.

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.

S.K.L.P. and B.M. were supported in part by the U.S. National Institutes of Health (AI110181, AI90970, AI100665, DA34978, GM93939, HL108460, GM110749, LM7092, MH97520, MH83552), the UCSD Center for AIDS Research (Developmental Grant, AI36214, Bioinformatics and Information Technologies Core), the International AIDS Vaccine Initiative (through AI90970), the UC Laboratory Fees Research Program (grant no. 12-LR-236617). G.J.S. was supported in part the U.S. National Institute of Health (AI90118, AI68063, AI40305, and NIAID HHS N272201400019C), and a grant from the Lupus Research Institute. A.S.M.M.H. was supported by an Islamic Development Bank Scholarship, and S.D.W.F. was supported in part by the UK MRC Methodology Research Programme (grant no. MR/J013862/1).

This is the final published version. It first appeared at http://rstb.royalsocietypublishing.org/content/370/1676/20140240.