The analysis of clonal expansions in normal and autoimmune B cell repertoires

U Hershberg, ET Luning Prak - … Transactions of the …, 2015 - royalsocietypublishing.org
U Hershberg, ET Luning Prak
Philosophical Transactions of the Royal Society B …, 2015royalsocietypublishing.org
Clones are the fundamental building blocks of immune repertoires. The number of different
clones relates to the diversity of the repertoire, whereas their size and sequence diversity
are linked to selective pressures. Selective pressures act both between clones and within
different sequence variants of a clone. Understanding how clonal selection shapes the
immune repertoire is one of the most basic questions in all of immunology. But how are
individual clones defined? Here we discuss different approaches for defining clones, starting …
Clones are the fundamental building blocks of immune repertoires. The number of different clones relates to the diversity of the repertoire, whereas their size and sequence diversity are linked to selective pressures. Selective pressures act both between clones and within different sequence variants of a clone. Understanding how clonal selection shapes the immune repertoire is one of the most basic questions in all of immunology. But how are individual clones defined? Here we discuss different approaches for defining clones, starting with how antibodies are diversified during different stages of B cell development. Next, we discuss how clones are defined using different experimental methods. We focus on high-throughput sequencing datasets, and the computational challenges and opportunities that these data have for mining the antibody repertoire landscape. We discuss methods that visualize sequence variants within the same clone and allow us to consider collections of shared mutations to determine which sequences share a common ancestry. Finally, we comment on features of frequently encountered expanded B cell clones that may be of particular interest in the setting of autoimmunity and other chronic conditions.
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