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

Burcu Gurun; Wesley Horton; Dhaarini Murugan; Biqing Zhu; Patrick Leyshock; Sushil Kumar; Katelyn T Byrne; Robert H Vonderheide; Adam A Margolin; Motomi Mori; Paul T Spellman; Lisa M Coussens; Terence P Speed

doi:10.1186/s12864-023-09424-z

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

BMC Genomics. 2023 Jun 26;24(1):349. doi: 10.1186/s12864-023-09424-z.

Authors

Burcu Gurun^{1

2}, Wesley Horton³, Dhaarini Murugan⁴, Biqing Zhu⁵, Patrick Leyshock³, Sushil Kumar⁴, Katelyn T Byrne^{4

6}, Robert H Vonderheide⁶, Adam A Margolin⁷, Motomi Mori⁸, Paul T Spellman⁹, Lisa M Coussens^{10

11}, Terence P Speed^{12

13}

Affiliations

¹ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. [email protected].
² School of Medicine, Oregon Health and Science University, Portland, OR, USA. [email protected].
³ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
⁴ Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
⁵ Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA.
⁶ Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
⁷ NextVivo, Palo Alto, CA, USA.
⁸ Department of Biostatistics, St. Jude's Children's Research Hospital, Memphis, TN, USA.
⁹ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. [email protected].
¹⁰ Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. [email protected].
¹¹ Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. [email protected].
¹² Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. [email protected].
¹³ School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, 3010, Australia. [email protected].

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.

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

MeSH terms

Base Sequence
Chromosome Mapping
High-Throughput Nucleotide Sequencing* / methods
Receptors, Antigen, T-Cell, alpha-beta / genetics
T-Lymphocytes*

Substances

Receptors, Antigen, T-Cell, alpha-beta

Abstract

MeSH terms

Substances

Grants and funding