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Updated: Jun 12, 2026
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VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
Published on: December 28, 2015
GATHeR: graph-based accurate tool for immunoglobulin heavy- and light-chain reconstruction
Seyedmojtaba Seyedraoufi1, Mari Bergstøl Gornitzka1, Andreas Lossius2,3
1Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
Nature Communications
|June 10, 2026
Summary
GATHeR is a new open-source tool that accurately recovers full-length B-cell receptor (BCR) sequences from single-cell RNA sequencing data. It improves BCR analysis, especially in challenging naive and memory B cells.
Area of Science:
- Immunology
- Bioinformatics
- Genomics
Background:
- Recovering full-length B-cell receptor (BCR) sequences from scRNA-seq is challenging, particularly in naive and memory B cells due to sparse immunoglobulin transcripts.
- Current methods struggle with constant-region coverage, limiting resolution of BCR isoforms, subclasses, and alleles.
Purpose of the Study:
- To introduce GATHeR, an open-source tool for assembling, annotating, and extending paired heavy- and light-chain BCR sequences.
- To enable confident subclass and allele assignment and recovery of membrane-bound BCR isoforms.
Main Methods:
- GATHeR assembles and annotates paired BCR sequences.
- It extends assembled sequences into constant regions, supporting Smart-seq2/3 and 10x Genomics libraries.
- The tool enables detection of splice variation, including intron-containing transcripts.
Main Results:
- GATHeR outperforms existing methods, showing significant improvements in naive and memory B cells.
- It allows confident subclass and allele assignment and distinguishes surface BCRs from secreted antibodies.
- Read-level support for splice variation, including intron-containing transcripts, was achieved.
Conclusions:
- GATHeR provides high-fidelity BCR, isoform, and clonal lineage information.
- The tool expands the analytical capabilities of scRNA-seq for B-cell immunology research.
- It offers a robust solution for analyzing BCRs from diverse B cell populations.
