High-throughput sequencing of immunoglobulin repertoires (Ig-seq) enables unprecedented quantitative analysis of adaptive immunity and thereby offers the potential to revolutionize research in immunobiology, vaccine profiling, and monoclonal antibody engineering. It has long been possible to measure humoral (antibody) immunity through conventional serological assays (e.g., ELISA). However, the ability to obtain quantitative information regarding the molecular diversity and distribution of antibody responses has only recently become possible through Ig-seq. However, Ig-seq is compromised by the presence of bias and errors introduced during library preparation and sequencing and thus prevents reliable immunological conclusions from being made. To overcome this, we have developed an integrated experimental-bioinformatic method known as molecular amplification fingerprinting (MAF), which combines single molecule and amplicons labeling with unique molecular identifiers. By applying MAF-based bioinformatic tools we were able to achieve 98-100% error and bias correction in Ig-seq. We then applied this approach of accurate Ig-seq in order to probe the relationship between antibody genotype and phenotype in a large-scale systems vaccinology study in mice. Finally, by applying multivariate and statistical modeling methods, we were able to predict the immune status of mice based simply on Ig-seq measurements. This extensive systems-based analysis demonstrates how Ig-seq provides unprecedented insight on humoral immunity and could be used for the evaluation and design of vaccines and immunotherapeutics.
Sai Reddy is a tenure-track Assistant Professor at ETH Zurich in the Department of Biosystems Science & Engineering (since Feb. 2012). His research group focuses on applying systems and synthetic biology methods to understand and engineer immunity. Prof. Reddy holds B.S. (2003) and M.S. (2004) degrees from Northwestern University (Evanston, IL, USA) in Biomedical Engineering. He completed his Ph.D. thesis at Ecolé Polytechnique Féderale de Lausanne (EPFL, Switzerland) in Bioengineering and Biotechnology in 2008. Prof. Reddy moved to University of Texas, Austin (USA) for his post-doctoral fellowship (2008-2011), where he worked on protein engineering and systems biology.