IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms Journal Article
| Authors: | Nadeu, F.; Mas-de-les-Valls, R.; Navarro, A.; Royo, R.; Martín, S.; Villamor, N.; Suárez-Cisneros, H.; Mares, R.; Lu, J.; Enjuanes, A.; Rivas-Delgado, A.; Aymerich, M.; Baumann, T.; Colomer, D.; Delgado, J.; Morin, R. D.; Zenz, T.; Puente, X. S.; Campbell, P. J.; Beà, S.; Maura, F.; Campo, E. |
| Article Title: | IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms |
| Abstract: | 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. © 2020, The Author(s). |
| Keywords: | gene sequence; gene translocation; overall survival; sequence analysis; single nucleotide polymorphism; polymerase chain reaction; gene; gene expression; tumor volume; protein; gene frequency; in situ hybridization; oncogene; fluorescence in situ hybridization; gene rearrangement; sequence alignment; lymphoma; immunophenotyping; genome; bioinformatics; comparative genomic hybridization; dna extraction; reconstruction; translocation; copy number variation; nucleic acid base substitution; prenatal diagnosis; metagenomics; sanger sequencing; human; article; stereotypy; whole exome sequencing |
| Journal Title: | Nature Communications |
| Volume: | 11 |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2020-07-07 |
| Start Page: | 3390 |
| Language: | English |
| DOI: | 10.1038/s41467-020-17095-7 |
| PUBMED: | 32636395 |
| PROVIDER: | scopus |
| PMCID: | PMC7341758 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 3 August 2020 -- Source: Scopus |
