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