Using the alphabetr package to determine paired T cell receptor sequences
useR!2017: Using the alphabetr package to determine...
The immune system has the monumental challenge of being capable of respond- ing to any pathogen or foreign substance invading the body while ignoring self and innocuous molecules. T cells—which play a central role in directing immune responses, regulating other immune cells, and remembering past infections— accomplish this feat by maintaining a diverse repertoire of T cell receptors (TCR). A typical T cell expresses one unique TCR, and the TCR is made up of two chains—the TCRα and TCRβ chains—that both determine the set of molecules that the T cell can respond to. Since T cells play such a central role in many immune responses, identifying the TCR pairs of T cells involved in infec- tious diseases, cancers, and autoimmune diseases can have profound insights for designing vaccines and immunotherapies. I introduce a novel approach to ob- taining paired TCR sequences with the alphabetr package, which implements algorithms that identify TCR pairs in an efficient, high-throughput fashion for antigen-specific T cell populations (Lee et al. 2017).