Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires
Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires
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DOI：
10.4049/jimmunol.1800708
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发表时间：
2018-10-15
影响因子：
4.4
通讯作者：
Krawczyk, Konrad
中科院分区：
文献类型：
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作者：
Kovaltsuk, Aleksandr;Leem, Jinwoo;Krawczyk, Konrad
Abs 是免疫系统蛋白质，可识别并消除有害分子。它们的序列多样性和结合多功能性使抗体成为生物制药的主要类别。最近，使用 Ig 基因库的新一代测序 (Ig-seq) 来查询其巨大的自然多样性已成为可能。然而，Ig-seq 输出目前在存储库中分散，并且往往以原始核苷酸读数的形式呈现，这意味着需要付出巨大的努力才能重复使用数据进行分析。为了解决这个问题，我们收集了 55 项研究的 Ig-seq 输出，涵盖不同免疫状态、生物体（主要是人类和小鼠）和个体的超过 5 亿 Ab 序列。我们对这些序列进行了排序、清理、注释、翻译和编号，并通过我们的观察抗体空间 (OAS) 资源（网址为 http://antibodymap.org）提供数据。 OAS 内的数据将定期更新为新发布的 Ig-seq 数据集。我们相信 OAS 将促进免疫库的数据挖掘，以增进对免疫系统的了解并开发更好的生物治疗药物。
Abs are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made Abs the primary class of biopharmaceuticals. Recently, it has become possible to query their immense natural diversity using next-generation sequencing of Ig gene repertoires (Ig-seq). However, Ig-seq outputs are currently fragmented across repositories and tend to be presented as raw nucleotide reads, which means nontrivial effort is required to reuse the data for analysis. To address this issue, we have collected Ig-seq outputs from 55 studies, covering more than half a billion Ab sequences across diverse immune states, organisms (primarily human and mouse), and individuals. We have sorted, cleaned, annotated, translated, and numbered these sequences and make the data available via our Observed Antibody Space (OAS) resource at http://antibodymap.org. The data within OAS will be regularly updated with newly released Ig-seq datasets. We believe OAS will facilitate data mining of immune repertoires for improved understanding of the immune system and development of better biotherapeutics.