Algorithms for Reconstructing B Cell Lineages in the Presence of Context-Dependent Somatic Hypermutation

We introduce a method for approximating posterior probabilities of phylogenetic trees and reconstructing ancestral sequences under models of sequence evolution with site-dependence, where standard phylogenetic likelihood computations (pruning) fail. Our approach uses a combined data-augmentation and importance sampling scheme. A key advantage of our approach is the ability to leverage existing highly optimized phylogenetic software. We apply our approach to the reconstruction of B cell receptor affinity maturation lineages from high-throughput repertoire sequencing data and evaluate the impact of incorporating site-dependence on the reconstruction accuracy of both trees and ancestral sequences. We show that accounting for context-dependence during inference always improves the estimates of both ancestral sequences and lineage trees on simulated datasets. We also examine the impact of incorporating priors based on VDJ recombination models, and find that they significantly improve ancestral sequence reconstruction in germline-encoded regions, but increase errors in non-templated nucleotides. We propose a modified, piecewise prior to address this demonstrate that it improves empirical reconstruction accuracy. We apply our approach to the analysis of the HIV broadly neutralizing antibodies DH270 and CH235 which are important targets of current vaccine design efforts.