Complete all-in-one immune repertoire profiling of newborn babies via novel dimer-avoided multiplex PCR (dam-PCR)

Abstract

Abstract There is an increased demand for immune repertoire profiling in both basic research as well as in various clinical settings, such as during vaccine development, lymphocyte tracking in minimal residual disease (MRD), hematopoietic stem cell transplant recovery monitoring, immunotherapy development, and immunological monitoring for prognosis purposes during treatment. Although next generation sequencing of the immune repertoire allows detailed, sequence-specific insight into the adaptive immune response, it usually focuses on only one or two receptor chains. One of the key challenges during immune receptor amplification is the formation of dimers, which can compete with the immune amplicons of interest during library preparation. We therefore developed a novel PCR technique, dimer-avoided multiplex PCR, that allows amplification of both BCRs and TCRs in a single, quantitative multiplex reaction. Our method generates next generation sequencing libraries for all TCR and BCR loci including TCR-beta, TCR-alpha, TCR-delta, TCR-gamma, BCR-IgH, and BCR-IgK and IgL. Here, we report the application of this method to investigate the immune repertoire of cord blood from newborn babies. Our study revealed the vast diversity and abundance of babies’ immune repertoire, the composition of TCR and BCR loci, and the sharing status of unique CDR3s among newborns. This single reaction, cost effective, all-inclusive, and quantitative immune-profiling analysis method shows promise for future applications in both basic research and clinical settings.