IgLibQC: quality control pipeline for the construction of antibody libraries

Le résumé fourni par la source

During the past two decades, a large number of antibody libraries have been constructed to meet the needs of drug discovery and diagnostic processes. The advent of next-generation sequencing (NGS) technology has enabled scientists to rigorously assess library size, quality, diversity and robustness at different stages of the construction process. The currently available bioinformatic tools mainly focus on the analysis of clonotypes of T cell receptors. We propose a new software pipeline, igLibQC, designed to facilitate a high-throughput analysis of NGS reads of the variable (V) domain of an antibody chain. The igLibQC pipeline includes all the essential analysis steps from merging paired-end reads, annotating V-(D)-J rearrangement, estimating the abundance levels of germline genes and families, visualising the alignment quality of germline genes (including the filtering of low quality sequences), predicting frame shifts and identifying functional clones, and finally calculating spectratypes and clonotypes to estimate the diversity of the library. Importantly, igLibQC also contains functionality to facilitate the selection of the best combination of restriction enzymes for the construction of library vectors. We illustrate the pipeline capabilities by applying it to a naïve IgM repertoire extracted from peripheral blood lymphocyte (PBL) of pooled human donors. The results show that the abundance of germline genes is inline with the natural distribution that is reported in the literature. The integrity of frameworks, complementarity-determining regions and secretion signals has been examined through comprehensive motif analysis. Overall, the results confirm that the repertoire is not pathological and can be used for library construction.

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