Rafael Smith


Identifying the antibody specificity repertoire

Antibodies have proven capable of revolutionizing disease diagnostics by serving as biomarkers for disease. Antibodies have a specificity that causes them to bind to very specific epitopes. By comparing the sera of diseased patients against the sera of healthy patients, disease specific antibody peptide interactions can be isolated.  Bacterial Display has thus far shown to be a proven system for disease specific epitope identification. By screening patient’s serums against a peptide library and then magnetically separating antibody-peptide interactions, we can then sequence those separated peptides using NGS technology. After sequencing millions of peptides, a computer algorithm, termed Identifying Motifs Using next generation sequencing Experiments (IMUNE), can be implemented to process and assess the data. First the program converts the base pairs into amino acids, and then the program searches for patterns and combines similar peptide sequences to create motifs. Disease specific motifs are patterns of peptides that are highly enriched in the antibody repertoires of diseased patients and barely present in the repertoires of healthy patients. Longitudinal studies are being done by creating biological replicates of certain patient’s serums and then comparing the specificities to other biological replicates. Bacterial display has great potential for disease specific epitope identification. 

UC Santa Barbara Center for Science and Engineering Partnerships UCSB California NanoSystems Institute UC Santa Barbara’s Parents Fund Campaign for UC Santa Barbara