An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences
- Author(s)
- Gurun, B; Horton, W; Murugan, D; Zhu, B; Leyshock, P; Kumar, S; Byrne, KT; Vonderheide, RH; Margolin, AA; Mori, M; Spellman, PT; Coussens, LM; Speed, TP;
- Details
- Publication Year 2023-06-26,Volume 24,Issue #1,Page 349
- Journal Title
- BMC Genomics
- Abstract
- 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.
- Publisher
- BMC
- Keywords
- Amplification bias; Cdr3; Clonotype counts; Count normalization; Multiplex PCR; Negative binomial; Normalization; Synthetic TCR templates; Synthetic templates; TCR sequencing
- Research Division(s)
- Bioinformatics
- PubMed ID
- 37365517
- Publisher's Version
- https://doi.org/10.1186/s12864-023-09424-z
- Open Access at Publisher's Site
https://doi.org/10.1186/s12864-023-09424-z- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2023-06-30 02:16:06
Last Modified: 2023-06-30 02:38:52