Rapid identification of antibody leads from selection outputs using oxford nanopore technology

Abstract Traditionally, the identification of potential clones of interest from in vitro antibody selections is carried out using random colony picking and Sanger sequencing. In contrast, next-generation sequencing (NGS) provides a comprehensive overview of selection output diversity and dynamics, facilitating lead prioritization and machine learning. Oxford Nanopore Technology (ONT) has emerged as a promising intermediary between Sanger and deeper NGS approaches. ONT offers a lower cost and faster turnaround time relative to Sanger and other NGS platforms. In this paper, we describe our experimental and computational pipeline, RADiANT (Rapid Antibody Discovery Applied to Nanopore Technology), to process and deconvolve unique cloned VHH and scFv sequences from polyclonal yeast-display populations using ONT. For campaigns targeting 10–20 lead candidates, ONT provides deeper sampling than Sanger sequencing and higher reproducibility than Sanger in the recovery of top leads found using PacBio, with up to a 90% cost reduction and a fifteen-fold faster turnaround time.