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

BMC Genomics

Research Article

Robert H. Vonderheide¹  Terence P. Speed²  Biqing Zhu³  Motomi Mori⁴  Sushil Kumar⁵  Dhaarini Murugan⁵  Katelyn T. Byrne⁶  Paul T. Spellman⁷  Wesley Horton⁷  Patrick Leyshock⁷  Lisa M. Coussens⁸  Burcu Gurun⁹  Adam A. Margolin^1,10 

[1] Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 3052, Parkville, VIC, Australia;School of Mathematics and Statistics, University of Melbourne, 3010, Parkville, VIC, Australia;Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA;Department of Biostatistics, St. Jude’s Children’s Research Hospital, Memphis, TN, USA;Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA;Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA;Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA;Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA;Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA;Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA;Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA;School of Medicine, Oregon Health and Science University, Portland, OR, USA;NextVivo, Palo Alto, CA, USA;

关键词: Multiplex PCR;    Amplification bias;    Clonotype counts;    TCR sequencing;    Normalization;    Negative binomial;    Count normalization;    Synthetic templates;    Synthetic TCR templates;    CDR3;   

DOI  :  10.1186/s12864-023-09424-z

 received in 2022-10-10, accepted in 2023-05-31,  发布年份 2023

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© The Author(s) 2023

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