Biology subjects

Looney, T.

Publications and source records attributed to Looney, T..

3 recordsLinked to original sources

bioRxiv2022

Reconstruction of Full-length scFv Libraries with the Extended Range Targeted Sequencing Method

Single chain fragment variable (scFv) phage display libraries of randomly paired VH-VL antibody domains are a powerful and widely adopted tool for the discovery of antibodies of a desired specificity. Characterization of full length VH-VL constructs using synthetic long read assemblies of short read next-generation sequencing data has emerged as a powerful approach to identify antibody candidates with greater speed and sensitivity than classical screening methods. Here we introduce a new version of the synthetic long read approach, which we denote the Extended Range Targeted Sequencing method. We apply the method to demonstrate accurate and high throughput analysis of full-length VH-VL constructs from a commercial scFv combinatorial display library.

genomics↗

bioRxiv2019

TCR convergence in individuals treated with immune checkpoint inhibition for cancer

Tumor antigen-driven selection may expand T cells having T cell receptors (TCRs) of shared antigen specificity but different amino acid or nucleotide sequence in a process known as TCR convergence. Substitution sequencing errors introduced by TCR{beta} (TCRB) repertoire sequencing may create artifacts resembling TCR convergence. Given the anticipated differences in substitution error rates across different next-generation sequencing platforms, the choice of platform could be consequential. To test this, we performed TCRB sequencing on the same peripheral blood mononuclear cells (PBMC) from individuals with cancer receiving anti-CTLA-4 or anti-PD-1 using an Illumina-based approach and an Ion Torrent-based approach. While both approaches found similar TCR diversity, clonality, and clonal overlap, we found that Illumina-based sequencing resulted in higher TCR convergence than with the Ion Torrent approach. Using the latter approach, we found that clonality and convergence independently predicted response and could be combined to improve the accuracy of a logistic regression classifier. These results demonstrate the importance of the sequencing platform in assessing TCRB convergence.

cancer biology↗

bioRxiv2018

Haplotype Analysis of the TRB Locus by TCRB Repertoire Sequencing

Polymorphism within the T cell receptor beta variable gene (TRBV) has been implicated in autoimmune disease and immuneCrelated adverse events (IRAEs) during immunotherapy. Previous efforts to evaluate TRBV polymorphism by whole genome sequencing (WGS) have been hampered by the repetitive nature of the TCRB locus. We present a novel longCamplicon TCRB repertoire sequencing approach to evaluate TRBV polymorphism from peripheral blood, which we use to identify TRBV allele haplotypes in 81 Caucasians.

immunology↗