Today, a lot of proteomic research is aimed at discovering disease specific proteins. This requires theavailability of high-throughput, ultra-sensitive protein detection methods. Compartmentalized immunosequencing(cI-Seq) is a proximity-independent immuno-polymerase chain reaction (IPCR) based proteindetection method. Antigen recognition in cI-Seq is mediated by antibody pairs in which one of theantibodies is conjugated to a DNA-probe. The affinity recognition events occur in emulsion droplets inwhich the DNA-probes will be amplified through emulsion PCR (emPCR) and thereafter analyzed usingMassively Parallel Sequencing (MPS). The amplifiable nature of the DNA-probes improves the sensitivityof the detection, while the use of emulsion droplets and MPS increases the multiplex capacity andthroughput. Ultimately, cI-Seq enables analysis and detection even of lowly abundant proteins therebyincreasing the probability of discovering novel disease specific proteins. In this project, conjugation of DNA probes to antibodies was performed through two different approaches;Covalent Conjugation and Conjugation using Biotin and NeutrAvidin. Both of these approaches showedadvantageous and disadvantageous features. However, neither of them succeeded in producing stableconjugates in an efficient and reproducible manner. After conjugation, the DNA-conjugated antibodieswere used in immune complex formation. However, the immune complexes either failed to form or wereformed in an inefficient manner.

Lyme borreliosis, more commonly referred to as Lyme disease, is the fastest growing zoonotic disease in North America with approximately 30,000 confirmed cases and 300,000 estimated infections per year. In nature, the causative agent of Lyme disease, the bacterium Borrelia burgdorferi, cycles between Ixodes sp. ticks and small mammals. Humans become infected with Lyme disease after being bitten by an infected tick. The primary indicator of a Borrelia burgdorferi infection is a bull’s eye rash typically followed by flu-like symptoms with treatment consisting of a 2-4 week course of antibiotics. If not treated, later stages of the disease can result in arthritis, cardiovascular and neurological symptoms. Diagnosis of Lyme disease is challenging and currently requires a complex laboratory diagnostic using indirect detection of host-generated antibodies by a two-tiered approach consisting of an enzyme linked immunosorbent assay (ELISA) followed by IgM and IgG immunoblots. Although two-tier testing has provided an adequate approach for Lyme disease diagnosis, it has weaknesses including subjective analysis, complex protocols and lack of reagent standardization. Immuno-PCR (iPCR) is a method that combines ELISA-based detection specificity with the sensitivity of PCR signal amplification and has demonstrated increased sensitivity for many applications such as detection of disease biomarkers but has yet to be applied for diagnosis of Lyme disease. Herein, using iPCR and recombinant B. burgdorferi antigens, an assay for both the direct and the indirect detection of Lyme disease was developed iv and demonstrated improved sensitivity for detection of B. burgdorferi antibodies using a murine model. Moreover, we present evidence using human Lyme disease patient serum samples that iPCR using both multiple antigens and a unique single hybrid antigen is capable of achieving increased sensitivity and specificity compared to existing methodology. These data represent the first demonstration of iPCR for Lyme disease diagnosis and support the replacement of two-tier testing with a more simplified and objective approach.