Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms.

IF 5.6 2区 医学 Q1 MEDICINE, RESEARCH & EXPERIMENTAL
mAbs Pub Date : 2024-01-01 Epub Date: 2024-10-08 DOI:10.1080/19420862.2024.2408344
Marianne Bachmann Salvy, Luca Santuari, Emanuel Schmid-Siegert, Nikolaos Lykoskoufis, Ioannis Xenarios, Bulak Arpat
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引用次数: 0

Abstract

Antibodies have emerged as the leading class of biotherapeutics, yet traditional screening methods face significant time and resource challenges in identifying lead candidates. Integrating high-throughput sequencing with computational approaches marks a pivotal advancement in antibody discovery, expanding the antibody space to explore. In this context, a major breakthrough has been the full-length sequencing of single-chain variable fragments (scFvs) used in in vitro display libraries. However, few tools address the task of annotating the paired heavy and light chain variable domains (VH and VL), which is the primary advantage of full-scFv sequencing. To address this methodological gap, we introduce Seq2scFv, a novel open-source toolkit designed for analyzing in vitro display libraries from long-read sequencing platforms. Seq2scFv facilitates the identification and thorough characterization of V(D)J recombination in both VH and VL regions. In addition to providing annotated scFvs, translated sequences and numbered chains, Seq2scFv enables linker inference and characterization, sequence encoding with unique identifiers and quantification of identical sequences across selection rounds, thereby simplifying enrichment identification. With its versatile and standalone functionality, we anticipate that the implementation of Seq2scFv tools in antibody discovery pipelines will efficiently expedite the full characterization of display libraries and potentially facilitate the identification of high-affinity antibody candidates.

Seq2scFv:用于综合分析长读数测序平台显示文库的工具包。
抗体已成为生物治疗的主要类别,但传统的筛选方法在确定候选先导抗体时面临着时间和资源方面的巨大挑战。将高通量测序与计算方法相结合,标志着抗体发现领域取得了关键性进展,拓展了抗体的探索空间。在这一背景下,体外展示文库中使用的单链可变片段(scFvs)的全长测序取得了重大突破。然而,很少有工具能解决注释成对的重链和轻链可变结构域(VH 和 VL)的任务,而这正是全 scFv 测序的主要优势。为了填补这一方法空白,我们推出了 Seq2scFv,这是一种新型开源工具包,专门用于分析长读数测序平台的体外展示文库。Seq2scFv 有助于识别和彻底鉴定 VH 和 VL 区域的 V(D)J 重组。除了提供带注释的 scFv、翻译序列和编号链外,Seq2scFv 还能进行连接子推断和特征描述、使用唯一标识符进行序列编码以及对各轮选择中的相同序列进行量化,从而简化富集鉴定。我们预计,Seq2scFv 工具在抗体发现管道中的应用将有效加快展示文库的全面表征,并有可能促进高亲和性候选抗体的鉴定。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
mAbs
mAbs 工程技术-仪器仪表
CiteScore
10.70
自引率
11.30%
发文量
77
审稿时长
6-12 weeks
期刊介绍: mAbs is a multi-disciplinary journal dedicated to the art and science of antibody research and development. The journal has a strong scientific and medical focus, but also strives to serve a broader readership. The articles are thus of interest to scientists, clinical researchers, and physicians, as well as the wider mAb community, including our readers involved in technology transfer, legal issues, investment, strategic planning and the regulation of therapeutics.
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