PMID- 32636395
OWN - NLM
STAT- MEDLINE
DCOM- 20200908
LR  - 20210707
IS  - 2041-1723 (Electronic)
IS  - 2041-1723 (Linking)
VI  - 11
IP  - 1
DP  - 2020 Jul 7
TI  - IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic 
      translocations from whole-genome sequencing in lymphoid neoplasms.
PG  - 3390
LID - 10.1038/s41467-020-17095-7 [doi]
LID - 3390
AB  - 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.
FAU - Nadeu, Ferran
AU  - Nadeu F
AUID- ORCID: 0000-0003-2910-9440
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain. nadeu@clinic.cat.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain. 
      nadeu@clinic.cat.
FAU - Mas-de-Les-Valls, Rut
AU  - Mas-de-Les-Valls R
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
FAU - Navarro, Alba
AU  - Navarro A
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
FAU - Royo, Romina
AU  - Royo R
AD  - Barcelona Supercomputing Center (BSC), Barcelona, Spain.
FAU - Martin, Silvia
AU  - Martin S
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
FAU - Villamor, Neus
AU  - Villamor N
AUID- ORCID: 0000-0001-6538-4111
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
AD  - Hospital Clinic of Barcelona, Barcelona, Spain.
FAU - Suarez-Cisneros, Helena
AU  - Suarez-Cisneros H
AD  - Unitat de Genomica, IDIBAPS, Barcelona, Spain.
FAU - Mares, Roso
AU  - Mares R
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
FAU - Lu, Junyan
AU  - Lu J
AD  - European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
FAU - Enjuanes, Anna
AU  - Enjuanes A
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Unitat de Genomica, IDIBAPS, Barcelona, Spain.
FAU - Rivas-Delgado, Alfredo
AU  - Rivas-Delgado A
AUID- ORCID: 0000-0003-0385-3415
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Hospital Clinic of Barcelona, Barcelona, Spain.
FAU - Aymerich, Marta
AU  - Aymerich M
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
AD  - Hospital Clinic of Barcelona, Barcelona, Spain.
FAU - Baumann, Tycho
AU  - Baumann T
AD  - Hospital Clinic of Barcelona, Barcelona, Spain.
FAU - Colomer, Dolors
AU  - Colomer D
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
AD  - Hospital Clinic of Barcelona, Barcelona, Spain.
AD  - Universitat de Barcelona, Barcelona, Spain.
FAU - Delgado, Julio
AU  - Delgado J
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
AD  - Hospital Clinic of Barcelona, Barcelona, Spain.
FAU - Morin, Ryan D
AU  - Morin RD
AUID- ORCID: 0000-0003-2932-7800
AD  - Department of Molecular Biology and Biochemistry, Simon Fraser University, 
      Burnaby, BC, Canada.
AD  - Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 
      Vancouver, BC, Canada.
FAU - Zenz, Thorsten
AU  - Zenz T
AUID- ORCID: 0000-0001-7890-9845
AD  - Department of Medical Oncology and Hematology, University Hospital and University 
      of Zurich, Zurich, Switzerland.
FAU - Puente, Xose S
AU  - Puente XS
AUID- ORCID: 0000-0001-9525-1483
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
AD  - Departamento de Bioquimica y Biologia Molecular, Instituto Universitario de 
      Oncologia, Universidad de Oviedo, Oviedo, Spain.
FAU - Campbell, Peter J
AU  - Campbell PJ
AUID- ORCID: 0000-0002-3921-0510
AD  - Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK.
FAU - Bea, Silvia
AU  - Bea S
AUID- ORCID: 0000-0001-7192-2385
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
AD  - Universitat de Barcelona, Barcelona, Spain.
FAU - Maura, Francesco
AU  - Maura F
AUID- ORCID: 0000-0002-5017-1620
AD  - Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK.
AD  - Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 
      New York, NY, USA.
FAU - Campo, Elias
AU  - Campo E
AUID- ORCID: 0000-0001-9850-9793
AD  - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, 
      Spain.
AD  - Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Madrid, Spain.
AD  - Hospital Clinic of Barcelona, Barcelona, Spain.
AD  - Universitat de Barcelona, Barcelona, Spain.
LA  - eng
GR  - P01 CA229100/CA/NCI NIH HHS/United States
GR  - P30 CA008748/CA/NCI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20200707
PL  - England
TA  - Nat Commun
JT  - Nature communications
JID - 101528555
SB  - IM
MH  - Algorithms
MH  - Cohort Studies
MH  - *Genes, Immunoglobulin
MH  - Genome, Human
MH  - Hematologic Neoplasms/genetics/immunology
MH  - High-Throughput Nucleotide Sequencing
MH  - Humans
MH  - Immunoglobulin Class Switching
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Lymphoma, B-Cell/genetics/immunology
MH  - *Oncogenes
MH  - Software
MH  - *Translocation, Genetic
MH  - Whole Genome Sequencing
PMC - PMC7341758
COIS- The authors declare no competing interests.
EDAT- 2020/07/09 06:00
MHDA- 2020/09/09 06:00
PMCR- 2020/07/07
CRDT- 2020/07/09 06:00
PHST- 2019/11/13 00:00 [received]
PHST- 2020/06/11 00:00 [accepted]
PHST- 2020/07/09 06:00 [entrez]
PHST- 2020/07/09 06:00 [pubmed]
PHST- 2020/09/09 06:00 [medline]
PHST- 2020/07/07 00:00 [pmc-release]
AID - 10.1038/s41467-020-17095-7 [pii]
AID - 17095 [pii]
AID - 10.1038/s41467-020-17095-7 [doi]
PST - epublish
SO  - Nat Commun. 2020 Jul 7;11(1):3390. doi: 10.1038/s41467-020-17095-7.