Synthetic Standards Combined With Error and Bias Correction Improve the Accuracy and Quantitative Resolution of Antibody Repertoire Sequencing in Human Naïve and Memory B Cells

Open access
Date
2018-06-20Type
- Journal Article
Citations
Cited 18 times in
Web of Science
Cited 18 times in
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ETH Bibliography
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Abstract
High-throughput sequencing of immunoglobulin (Ig) repertoires (Ig-seq) is a powerful method for quantitatively interrogating B cell receptor sequence diversity. When applied to human repertoires, Ig-seq provides insight into fundamental immunological questions, and can be implemented in diagnostic and drug discovery projects. However, a major challenge in Ig-seq is ensuring accuracy, as library preparation protocols and sequencing platforms can introduce substantial errors and bias that compromise immunological interpretation. Here, we have established an approach for performing highly accurate human Ig-seq by combining synthetic standards with a comprehensive error and bias correction pipeline. First, we designed a set of 85 synthetic antibody heavy-chain standards (in vitro transcribed RNA) to assess correction workflow fidelity. Next, we adapted a library preparation protocol that incorporates unique molecular identifiers (UIDs) for error and bias correction which, when applied to the synthetic standards, resulted in highly accurate data. Finally, we performed Ig-seq on purified human circulating B cell subsets (naïve and memory), combined with a cellular replicate sampling strategy. This strategy enabled robust and reliable estimation of key repertoire features such as clonotype diversity, germline segment, and isotype subclass usage, and somatic hypermutation. We anticipate that our standards and error and bias correction pipeline will become a valuable tool for researchers to validate and improve accuracy in human Ig-seq studies, thus leading to potentially new insights and applications in human antibody repertoire profiling. Show more
Permanent link
https://doi.org/10.3929/ethz-b-000272798Publication status
publishedExternal links
Journal / series
Frontiers in ImmunologyVolume
Pages / Article No.
Publisher
Frontiers Research FoundationSubject
Antibody repertoire; next-generation sequencing; unique molecular identifiers; B cells; bioinformatics; Systems immunologyOrganisational unit
03952 - Reddy, Sai / Reddy, Sai
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Show all metadata
Citations
Cited 18 times in
Web of Science
Cited 18 times in
Scopus
ETH Bibliography
yes
Altmetrics