IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms
| Autor: | Junyan Lu, Rosó Mares, Thorsten Zenz, Anna Enjuanes, Ryan D. Morin, Alfredo Rivas-Delgado, Julio Delgado, Rut Mas-de-les-Valls, Peter J. Campbell, Neus Villamor, Tycho Baumann, Ferran Nadeu, Helena Suárez-Cisneros, Dolors Colomer, Alba Navarro, Elias Campo, Romina Royo, Marta Aymerich, Francesco Maura, Xose S. Puente, Silvia Martín, Sílvia Beà |
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| Přispěvatelé: | Barcelona Supercomputing Center, University of Zurich, Nadeu, Ferran |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
General Physics and Astronomy Genome Translocation Genetic Cohort Studies 0302 clinical medicine Cancer genomics lcsh:Science In Situ Hybridization Fluorescence Genòmica -- Informàtica Sanger sequencing Multidisciplinary medicine.diagnostic_test Genes Immunoglobulin High-Throughput Nucleotide Sequencing Genomics Immunoglobulin genes 3100 General Physics and Astronomy 030220 oncology & carcinogenesis Hematologic Neoplasms symbols Immunoglobulin Gene Rearrangement Algorithms Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC] Lymphoma B-Cell Science 610 Medicine & health 1600 General Chemistry Computational biology Biology Immunoglobulin light chain General Biochemistry Genetics and Molecular Biology Article 03 medical and health sciences symbols.namesake 1300 General Biochemistry Genetics and Molecular Biology IgCaller Ig gene rearrangements medicine Immunogenetics Humans Gene Whole genome sequencing Haematological cancer Whole Genome Sequencing Genome Human General Chemistry Oncogenes Immunoglobulin Class Switching Genòmica 030104 developmental biology Cancer--Genetic aspects Immunoglobulin class switching 10032 Clinic for Oncology and Hematology lcsh:Q Software Fluorescence in situ hybridization |
| Zdroj: | Nature Communications Scopus Nature Communications, Vol 11, Iss 1, Pp 1-11 (2020) RUO: Repositorio Institucional de la Universidad de Oviedo Universidad de Oviedo (UNIOVI) UPCommons. Portal del coneixement obert de la UPC Universitat Politècnica de Catalunya (UPC) RUO. Repositorio Institucional de la Universidad de Oviedo instname |
| Popis: | 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. Immunoglobulin (Ig) rearrangement and translocation information are usually obtained by targeted sequencing of the respective loci. Here, the authors present the IgCaller algorithm, which extracts Ig heavy and light chain genetic properties from short-read whole-genome sequencing results to provide a feasible alternative to direct sequencing. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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