IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms

Ferran Nadeu (), Rut Mas- de-les-Valls, Alba Navarro, Romina Royo, Silvia Martín, Neus Villamor, Helena Suárez-Cisneros, Rosó Mares, Junyan Lu, Anna Enjuanes, Alfredo Rivas-Delgado, Marta Aymerich, Tycho Baumann, Dolors Colomer, Julio Delgado, Ryan D. Morin, Thorsten Zenz, Xose S. Puente, Peter J. Campbell, Sílvia Beà, Francesco Maura and Elías Campo
Additional contact information
Ferran Nadeu: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Rut Mas- de-les-Valls: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Alba Navarro: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Romina Royo: Barcelona Supercomputing Center (BSC)
Silvia Martín: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Neus Villamor: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Helena Suárez-Cisneros: IDIBAPS
Rosó Mares: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Junyan Lu: European Molecular Biology Laboratory (EMBL)
Anna Enjuanes: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Alfredo Rivas-Delgado: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Marta Aymerich: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Tycho Baumann: Hospital Clínic of Barcelona
Dolors Colomer: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Julio Delgado: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Ryan D. Morin: Simon Fraser University
Thorsten Zenz: University Hospital and University of Zürich
Xose S. Puente: Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)
Peter J. Campbell: Wellcome Sanger Institute, Hinxton
Sílvia Beà: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
Francesco Maura: Wellcome Sanger Institute, Hinxton
Elías Campo: Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-17095-7

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