Antibody repertoire analytics: the development of a visualization toolkit and its application to high-throughput Ig-seq data

表达抗体(Abs)的NGS被称为Ig-seq，越来越多地用于解决基本的免疫学问题，如：对病原体、疫苗和治疗性抗体的免疫反应有何不同？健康的抗体曲目和免疫功能障碍的曲目有什么不同？一个典型的Ig-seq数据集由来自多个样本的数百万个部分mRNA Ab序列组成，每个样本来自单个个体和时间点。有一些方法可以分析这些数据的各个方面，包括注释单个抗体以及它们之间的关系的工具(例如www.imgt.org)。这个项目的目的是开发一个可视化分析Ig-seq的工具包，使生物学家能够快速探索他们的数据，产生新的假说，并做出新的发现。重点将是支持整个抗体谱系分析，并表征与疫苗设计和治疗性抗体发现相关的基本特性(谱系多样性、谱系内部和之间的抗体趋同，以及谱系进化的动力学)。例如，在筛选治疗性抗体之前，使用两种策略来产生抗体多样性：动物免疫和噬菌体展示。在这两种情况下，衡量多样性并引发多样性的正确方式都鲜为人知。在这里，工具包可以发挥重要作用，更好地理解动物谱系的进化，以应对挑战(最终导致更好的免疫策略)，并帮助识别(并最终填补)现有抗体噬菌体文库中的空白。这个项目的学生将从事两个相辅相成的活动：工具开发和免疫学研究。工具包开发带来了几个挑战。为了方便丰富的分析，该工具包将结合不同模式的视觉表示(如网络、密度图)和多个相似性度量(如遗传距离、CDR3序列同一性)，并提供用于比较曲目的基本操作。后者特别具有挑战性，因为每个样本都捕获了一小部分谱系多样性，因此共享序列的数量是对真实的体内重叠的较差估计；样本质量各不相同，但解决这一问题的最佳归一化策略尚不清楚。该工具包还需要处理不同类型(例如成对的重链和未配对的重链/轻链)和不同格式(例如IMGT和Kabat编号方案)的大型谱系数据集。学生将在PHD的早期阶段与UCB一起进行免疫学研究，帮助设计改进噬菌体展示文库构建的实验，并有助于解释来自免疫动物的实验数据。在Birkbeck，学生将分析现有疫苗设计合作产生的抗体谱系，并对公共Ig-seq数据集进行荟萃分析，包括专注于人类免疫模型的跨物种分析。该项目正好属于BBSRC的战略优先事项“数据驱动生物学”。拟议的动物抗体分析曲目旨在帮助科学家在知情的情况下选择他们在免疫学研究中使用的动物(与“3R”优先事项相关)；并将对不同年龄的健康人的样本进行荟萃分析(与“整个生命过程中的健康老龄化”相关)。

NGS of expressed antibodies (Abs), known as Ig-seq, is increasingly used to address fundamental immunological questions, such as: How do immune responses to pathogens, vaccines and therapeutic Abs differ? And what are the differences between healthy Ab repertoires and those associated with immune dysfunction? A typical Ig-seq dataset consists of millions of partial mRNA Ab sequences derived from multiple samples, each from a single individual and timepoint. There are methods for analysing aspects of this data, including tools for annotating individual Abs and the relationships between them (e.g. www.imgt.org). However, tools that support interactive engagement with Ig-seq datasets do not exist.The aim of this project is to develop a toolkit for visually analysing Ig-seq, enabling biologists to rapidly explore their data, generate novel hypotheses and make new discoveries. The priority will be to support whole Ab repertoire analytics and to characterize fundamental properties (repertoire diversity, Ab convergence within and between repertoires, and the dynamics of repertoire evolution) relevant to vaccine design and therapeutic Ab discovery. For example, two strategies are used to generate Ab diversity prior to screening for therapeutic Abs: animal immunization, and phage display. In both cases, the right ways to measure diversity, and to elicit it, are poorly understood. Here the toolkit can play a vital role, engendering a better understanding of animal repertoire evolution in response to challenge (ultimately leading to better immunization strategies), and helping to identify (and ultimately fill) gaps in existing Ab phage libraries.The student on this project will engage in two complementary activities: tool development and immunology research. Toolkit development poses several challenges. To facilitate rich analyses, the toolkit will incorporate different modes of visual representations (e.g. networks, density plots) with multiple similarity metrics (e.g. genetic distance, CDR3 sequence identity) and provide essential operations for comparing repertoires. The latter is particularly challenging because each sample captures a small proportion of repertoire diversity, hence the number of shared sequences is a poor estimate of the true, in vivo overlap; and sample quality varies, but the optimal normalization strategy for addressing this is unclear. The toolkit will also need to handle large repertoire datasets of different types (e.g. paired vs. unpaired heavy/light chains) and in different formats (e.g. IMGT vs. Kabat numbering schemes).The student will undertake immunology research with UCB from an early stage of the PhD, helping to design experiments that improve phage display library construction and contributing to the interpretation of experimental data from immunized animals. At Birkbeck the student will analyse Ab repertoires arising from an existing vaccine design collaboration, and undertake meta-analyses of public Ig-seq datasets, including cross-species analyses focusing on models of human immunity.This project falls squarely within the BBSRC strategic priority of "data driven biology". The proposed analyses of animal Ab repertoires are designed to help scientists make informed choices about the animals they use in immunology research (relevant to the "3Rs" priority); and meta-analyses of samples from healthy individuals of various ages will be undertaken (relevant to "healthy ageing across the lifecourse").