An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.

Autor:	Gurun, Burcu, Horton, Wesley, Murugan, Dhaarini, Zhu, Biqing, Leyshock, Patrick, Kumar, Sushil, Byrne, Katelyn T., Vonderheide, Robert H., Margolin, Adam A., Mori, Motomi, Spellman, Paul T., Coussens, Lisa M., Speed, Terence P.
Předmět:	NUCLEOTIDE sequencing T cell receptors T cells
Zdroj:	BMC Genomics; 6/26/2023, Vol. 24 Issue 1, p1-13, 13p
Abstrakt:	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. [ABSTRACT FROM AUTHOR]
Databáze:	Complementary Index
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