T cell receptor repertoires can be profiled using next generation sequencing (NGS) to measure and monitor adaptive dynamical changes in response to disease and other perturbations. Genomic DNA-based bulk sequencing is cost-effective but necessitates multiplex target amplification using multiple primer pairs with highly variable amplification efficiencies. Here, we utilize an equimolar primer mixture and propose a single statistical normalization step that efficiently corrects for amplification bias post sequencing. Using samples analyzed by both our open protocol and a commercial solution, we show high concordance between bulk clonality metrics. This approach is an inexpensive and open-source alternative to commercial solutions.
CITATION STYLE
Gurun, B., Horton, W., Murugan, D., Zhu, B., Leyshock, P., Kumar, S., … Speed, T. P. (2023). An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences. BMC Genomics, 24(1). https://doi.org/10.1186/s12864-023-09424-z
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