Somatic hypermutation targeting is influenced by location within the immunoglobulin V region

► We have presented a quantitative model for the frequency of each sequence surounding mutations in B cells. ► This motif explains most of the variance in the mutation frequency. ► Within this motif, C mutations to T are more frequent than C to G, which are more frequent than C to A. ► Beyond this motif, a position specific effect explains a part of the mutation frequency. The observed mutation pattern in immunoglobulin (Ig) V genes from peripheral B cells is influenced by several mechanisms, including the targeting of AID to specific DNA motifs, negative selection of B cells unable to express Ig receptor, and positive selection of B cells that carry affinity-increasing mutations. These influences, combined with biased codon usage, produce the well-known pattern of increased replacement mutation frequency in the CDR regions, and decreased replacement frequency in the framework regions. Through the analysis of over 12,000 mutated sequences, we show that the specific location in the V gene also significantly influences mutation accumulation. While this position-specific effect is partially explained by selection, it appears independently of the CDR/FWR structure. To further explore the specific targeting of SHM, we propose a statistical formalism describing the mutation probability of a sequence through the multiplication of independent probabilities. Using this model, we show that C → G (or G → C) mutations are almost as frequent as C → T and G → A mutations, in contrast with C → A (or G → T) mutations, which are as any other mutation. The proposed statistical framework allows us to precisely quantify the effect of V gene position, mutation substitution type, and micro-sequence specificity on the observed mutation pattern.