An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jun 26, 2023
- Source ID
- 10.1186/s12864-023-09424-z
Entities
People
- Adam A. Margolin
- Biqing Zhu
- Burcu Gurun
- Dhaarini Murugan
- Katelyn T. Byrne
- Lisa Coussens
- Motomi Mori
- Patrick Leyshock
- Paul Spellman
- Robert H. Vonderheide
- Sushil Kumar
- Terence P. Speed
- Wesley Horton
Organizations
- American Cancer Society
- National Cancer Institute
- Stand Up to Cancer
- Susan G. Komen for the Cure
- United States Department of Defense