ASAP - A Webserver for Immunoglobulin-Sequencing Analysis Pipeline.

Area of Science:

• Immunology
• Bioinformatics
• Computational Biology

Background:

• Antibody repertoire data is crucial for immunology research.
• Next-generation sequencing (NGS) offers quantitative insights into antibody composition.
• Analyzing NGS antibody sequence data presents significant computational challenges.

Purpose of the Study:

• To develop a user-friendly webserver for analyzing antibody variable region sequences from NGS data.
• To address computational hurdles in error handling, hypermutation analysis, and clonal expansion.
• To facilitate robust and reproducible immune repertoire analysis for researchers.

Main Methods:

• Development of the ASAP (A webserver for Immunoglobulin-Seq Analysis Pipeline) webserver.
• Input processing of paired-end NGS datasets with or without unique molecular identifiers.
• Sequence read filtering, annotation using germline data, and various computational analyses (e.g., somatic hypermutation, CDR3 length, V(D)J assignment).
• Joint analysis of replicates to identify reliable sequences and clonal expansion analysis.
• Generation of variable region databases for proteomic analysis.

Main Results:

• ASAP provides a comprehensive pipeline for filtering, annotating, and analyzing antibody NGS data.
• The webserver enables detailed analysis of somatic hypermutation, CDR3 lengths, V(D)J usage, and clonal expansion.
• ASAP facilitates the comparison of replicates to distinguish biological signals from technical noise.
• The tool supports proteomic analysis by generating databases for LC-MS/MS interpretation.

Conclusions:

• ASAP is a user-friendly, free, and open-access webserver that simplifies complex antibody repertoire analysis.
• The pipeline enhances the reproducibility and robustness of immunological studies.
• ASAP empowers both basic and applied researchers, including non-experts, to leverage immune repertoire data for B cell development, vaccine design, and antibody engineering.