Year: 2023
Type: article
Abstract: ABSTRACT T cell receptor (TCR) repertoires can be profiled using next generation sequencing (NGS) to monitor dynamical changes in response to disease and other perturbations. Several strategies for profiling TCRs have been recently developed with different benefits and drawbacks. Genomic DNA-based bulk sequencing, however, remains the most cost-effective method to profile TCRs. The major disadvantage of this method is the need for multiplex target amplification with a large set of primer pairs with potentially very different amplification efficiencies. One approach addressing this problem is by iteratively adjusting the concentrations of the primers based on their efficiencies, and then computationally correcting any remaining bias. Yet there are no standard, publicly available protocols to process and analyze raw sequencing data generated by this method. 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 approaches, we show that the concordance between bulk clonality metrics obtained from using the commercial kits and that developed herein is high. Therefore, we suggest the method presented here as an inexpensive and non-commercial alternative for measuring and monitoring adaptive dynamics in TCR clonotype repertoire.
Source: BMC Genomics
Language: English
Topic: T-cell and B-cell Immunology
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,690
Funders: U.S. Department of Defense, American Cancer Society, Susan G. Komen for the Cure, AbbVie, Oregon Health and Science University, Susan G. Komen, Deciphera Pharmaceuticals, Syndax Pharmaceuticals, Roche Innovation Center Zurich, Natera, Plexxikon, National Institutes of Health, Genentech, Stand Up To Cancer, Pharmacyclics, Knight Cancer Institute, Oregon Health and Science University, Foundation Medicine, National Cancer Institute
Awards: G1581679921, G1801729602, G2434301076, G246298631, G2535433541, G2622222925, G3266624898, G4119534169, G4297529078, G5328696325, G5850682332, G6393127489, Regulating the Immune Microenvironment in Breast Cancer, Mechanisms of Immune Privilege in Pancreatic Ductal Adenocarcinoma, Regulation of Inflammation-Associated Epithelial Cancer Development, G7049952571, G7374338445, G9000044262, G9000156400, G935829431
OpenAlex ID: W4382133509