GSSP plots

Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the mutation frequency and substitution bias of SHMs, context-dependent substitution models have been developed at the nucleotide level. However, no context-dependent model has been developed to systematically characterize the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level. In this study, we analyzed functional human antibody repertoires and developed mGSSP (method for Gene-Specific Substitution Profile), a method to construct amino acid substitution profiles from next-generation sequencing-acquired B cell transcripts. These gene-specific substitution profiles (GSSP) are unique to each V gene and highly consistent between donors. By implicitly incorporating context-dependence, GSSPs provide an alternative means for accurate modeling of the SHM process, and provide a means for characterizing features of SHM mutational space, predicting mutational propensities of SHMs, and for better understanding maturation pathways of antibody lineages in a gene-specific context. To date, extensive efforts have been invested to re-elicit naturally occurring broadly neutralizing antibodies against HIV-1 and other pathogens in humans and animal models. Incorporating GSSPs into the modeling of the SHM process may help predict the likelihood of re-eliciting key SHM patterns of interest. These figures show GSSPs for VH, VK, and VL genes with at least 300 lineages present in the pooled sequencing data from three normal donors.