NGS-AI Division, JSR Life Sciences, Epalinges, Switzerland.
MAbs. 2024 Jan-Dec;16(1):2408344. doi: 10.1080/19420862.2024.2408344. Epub 2024 Oct 8.
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 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 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.
抗体已成为主要的生物治疗药物类别，但传统的筛选方法在确定先导候选物方面面临着巨大的时间和资源挑战。将高通量测序与计算方法相结合，标志着抗体发现的重大进展，拓展了抗体的探索空间。在这种情况下，一个重大突破是对展示文库中使用的单链可变片段（scFv）进行全长测序。然而，很少有工具能够完成配对的重链和轻链可变区（VH 和 VL）的注释任务，这是全长 scFv 测序的主要优势。为了解决这个方法学上的差距，我们引入了 Seq2scFv，这是一个专门为分析来自长读测序平台的展示文库而设计的新型开源工具包。Seq2scFv 有助于识别和全面描述 VH 和 VL 区域中的 V(D)J 重组。除了提供注释的 scFv、翻译序列和编号链外，Seq2scFv 还能够推断和描述连接子、用唯一标识符进行序列编码以及量化选择轮次之间的相同序列，从而简化了富集识别。凭借其多功能和独立的功能，我们预计在抗体发现管道中实施 Seq2scFv 工具将有效地加速展示文库的全面表征，并有可能促进高亲和力抗体候选物的鉴定。
