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Estimating Diversity in the Naïve B Cell Repertoire

Estimating Diversity in the Naïve B Cell Repertoire

B cells produce antibodies which recognize and neutralize foreign pathogens as part of the adaptive immune system. B cell receptors are generated by a stochastic process involving random recombination of V(D)J gene segments and random addition of non-templated nucleotides at junction sites. Recent work has shown that individuals can share similar and sometimes even identical rearrangements referred to as public clonotypes. Vaccine design strategies that target B cell lineages that initiate from public clonotypes may be an effective way to reproducibly guide B cell responses within a vaccinated population. Accurate models of V(D)J recombination are required to calculate the probability of individuals sharing the same or similar B cell receptor sequences. This summer internship will involve harnessing large B cell repertoire next generation sequencing datasets to estimate the parameters of a V(D)J recombination model and then applying that model to the analysis of public clonotypes as well as estimating the distance between public and private clonotypes of interest. The work pursued in this project will inform on-going vaccine design efforts for influenza and HIV