cAb-Rep

INTRODUCTION

cAb-Rep is a database of curated antibody repertoires. It currently includes 306 B cell repertoires collected from 121 human individuals, including healthy, vaccinated, and autoimmune disease donors. The database has a total of 267.9 and 72.9 million curated full-length V(D)J heavy and light chain transcripts respectively, which were generated using illumina sequencing technology in previous studies. We removed redundancy and sequencing errors in the raw datasets, and annotated each transcript including gene origin, antibody isotype, mutations, post-translational modification, and other characteristics.

The diversity of B cell receptors, generated by V(D)J recombination and somatic hypermutation, provides a basis for recognizing numerous pathogens. To accelerate investigations of B cell response and antibody diversity, we provide tools to search cAb-Rep to estimate the frequency of antibody transcripts with user-defined features and patterns of somatic hypermutation. We hope that the cAb-Rep database and computational tools are useful for investigating features of B cell repertoires, understanding mechanisms of affinity maturation, and identifying potential barriers in eliciting broadly neutralizing antibodies in vaccine design.

Estimate prevalence of antibody with signature of interest?:

                        

    

              

                                                              

Estimate rarity of somatic hypermutation?:

         

    I. Input a sequence and estimate the rarity of the substitution:
             Select a fasta file:

    II. Input amino acids and find the substitution rarity at a V gene postion (Kabat scheme):
                 

                                                          

Gene-specific frequency of glycosylation?:

    

    Please input a V gene postion (Kabat scheme):
        

                                                          

Citation:

Gene-specific subsitution profile:
Zizhang Sheng, Chaim A. Schramm, Rui Kong, NISC Comparative Sequencing Program, James C. Mullikin, John R. Mascola, Peter D. Kwong, and Lawrence Shapiro. Gene-specific substitution profiles describe the types and frequencies of amino acid changes during antibody somatic hypermutation. Front. Immunol. 8:537. doi: 10.3389/mmu.2017.00537 (2017).

cAb-Rep database:
Yicheng Guo, Kevin Chen, Peter D. Kwong, Lawrence Shaprio, and Zizhang Sheng. cAb-Rep: a database of curated antibody repertoires for exploring B cell response and predicting antibody prevalence. Front. Immunol. doi: 10.3389/fimmu.2019.02365 (2019).