Immunoglobulin (Ig) gene rearrangements and oncogenic translocations are routinely assessed during the characterization of B cell neoplasms and stratification of patients with distinct clinical and biological features, with the assessment done using Sanger sequencing, targeted next-generation sequencing, or fluorescence in situ hybridization (FISH). Currently, a complete Ig characterization cannot be extracted from whole-genome sequencing (WGS) data due to the inherent complexity of the Ig loci. Here, we introduce IgCaller, an algorithm designed to fully characterize Ig gene rearrangements and oncogenic translocations from short-read WGS data. Using a cohort of 404 patients comprising different subtypes of B cell neoplasms, we demonstrate that IgCaller identifies both heavy and light chain rearrangements to provide additional information on their functionality, somatic mutational status, class switch recombination, and oncogenic Ig translocations. Our data thus support IgCaller to be a reliable alternative to Sanger sequencing and FISH for studying the genetic properties of the Ig loci.

免疫球蛋白（Ig）基因重排和致癌性易位是在B细胞肿瘤表征和具有不同临床和生物学特征的患者分层期间常规评估的，评估使用Sanger测序，靶向下一代测序或荧光原位杂交（鱼）。当前，由于Ig基因座的内在复杂性，无法从全基因组测序（WGS）数据中提取完整的Ig特征。在这里，我们介绍IgCaller，该算法旨在从短时读取的WGS数据中全面表征Ig基因重排和致癌性易位。利用404名患者，这些患者包括不同类型的B细胞肿瘤，我们证明IgCaller可以识别重链和轻链重排，以提供有关其功能，体细胞突变状态，类开关重组和致癌性Ig易位的其他信息。因此，我们的数据支持IgCaller成为Sanger测序和FISH的可靠替代品，以研究Ig基因座的遗传特性。