PT  - JOURNAL ARTICLE
AU  - S. Momsen Reincke
AU  - Harald Prüss
AU  - Jakob Kreye
TI  - Brain Antibody Sequence Evaluation (BASE): an easy-to-use software for complete data analysis in single cell immunoglobulin cloning
AID  - 10.1101/836999
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 836999
4099  - http://biorxiv.org/content/early/2019/11/09/836999.short
4100  - http://biorxiv.org/content/early/2019/11/09/836999.full
AB  - Background Repertoire analysis of patient-derived recombinant monoclonal antibodies is an important tool to study the role of B cells in autoimmune diseases of the human brain and beyond. Current protocols for generation of patient-derived recombinant monoclonal antibody libraries are time-consuming and contain repetitive steps, some of which can be assisted with the help of software automation.Results We developed BASE, an easy-to-use software for complete data analysis in single cell immunoglobulin cloning. BASE consists of two modules: aBASE for immunological annotations and cloning primer lookup, and cBASE for plasmid sequence identity confirmation before expression. Comparing automated BASE analysis with manual analysis we confirmed the validity of BASE output: identity between manual and automated aBASE analysis was 100% for all outputs, except for immunoglobulin isotype determination. In this case, aBASE yielded correct results in 96% of cases, whereas 4% of cases required manual confirmation. cBASE automatically concluded expression recommendations in 89.8% of cases, 91.8% of which were identical to manually derived results and none of them were false-positive.Conclusions BASE offers an easy-to-use software solution suitable for complete Ig sequence data analysis and tracking during recombinant mcAB cloning from single cells. Plasmid sequence identity confirmation by cBASE offers functionality not provided by existing software solutions in the field and will help to reduce time-consuming steps of the monoclonal antibody generation workflow.CDRcomplementarity determining regionCSFcerebrospinal fluidIgImmunoglobulinmcABmonoclonal antibodyNGSNext-generation sequencingPCRPolymerase chain reactionSHMSomatic hypermutation