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.
Original language | English (US) |
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Article number | 349 |
Journal | BMC Genomics |
Volume | 24 |
Issue number | 1 |
DOIs | |
State | Published - Dec 2023 |
Keywords
- Amplification bias
- CDR3
- Clonotype counts
- Count normalization
- Multiplex PCR
- Negative binomial
- Normalization
- Synthetic TCR templates
- Synthetic templates
- TCR sequencing
ASJC Scopus subject areas
- Biotechnology
- Genetics