title: Comprehensive annotation of splice junctions supports pervasive alternative splicing at the BRCA1 locus: a report from the ENIGMA consortium.
abstract: Loss-of-function germline mutations in BRCA1 (MIM #113705) confer markedly increased risk of breast and ovarian cancer. The full-length transcript codifies for a protein involved in DNA repair pathways and cell-cycle checkpoints. Several BRCA1 splicing isoforms have been described in public domain databases, but the physiological role (if any) of BRCA1 alternative splicing remains to be established. An accurate description of 'naturally occurring' alternative splicing at this locus is a prerequisite to understand its biological significance. However, a systematic analysis of alternative splicing at the BRCA1 locus is yet to be conducted. Here, the Evidence-Based Network for the Interpretation of Germ-Line Mutant Alleles consortium combines RT-PCR, exon scanning, cloning, sequencing and relative semi-quantification to describe naturally occurring BRCA1 alternative splicing with unprecedented resolution. The study has been conducted in blood-related RNA sources, commonly used for clinical splicing assays, as well as in one healthy breast tissue. We have characterized a total of 63 BRCA1 alternative splicing events, including 35 novel findings. A minimum of 10 splicing events (Δ1Aq, Δ5, Δ5q, Δ8p, Δ9, Δ(9,10), Δ9_11, Δ11q, Δ13p and Δ14p) represent a substantial fraction of the full-length expression level (ranging from 5 to 100%). Remarkably, our data indicate that BRCA1 alternative splicing is similar in blood and breast, a finding supporting the clinical relevance of blood-based in vitro splicing assays. Overall, our data suggest an alternative splicing model in which most non-mutually exclusive alternative splicing events are randomly combined into individual mRNA molecules to produce hundreds of different BRCA1 isoforms.
authors.affiliation: Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
authors.forename: Mara
authors.initials: M
authors.lastname: Colombo
authors.affiliation: Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.
authors.forename: Marinus J
authors.initials: MJ
authors.lastname: Blok
authors.affiliation: Molecular Cancer Epidemiology Laboratory, Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
authors.forename: Phillip
authors.initials: P
authors.lastname: Whiley
authors.affiliation: Grupo de Medicina Xenómica-USC, Universidad de Santiago de Compostela, CIBERER, IDIS, Santiago de Compostela, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Santamariña
authors.affiliation: Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and.
authors.forename: Sara
authors.initials: S
authors.lastname: Gutiérrez-Enríquez
authors.affiliation: Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain.
authors.forename: Atocha
authors.initials: A
authors.lastname: Romero
authors.affiliation: Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain.
authors.forename: Pilar
authors.initials: P
authors.lastname: Garre
authors.affiliation: Center of Familial Breast and Ovarian Cancer, University Hospital Cologne, Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Becker
authors.affiliation: Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
authors.forename: Lindsay Denise
authors.initials: LD
authors.lastname: Smith
authors.affiliation: Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
authors.forename: Giovanna
authors.initials: G
authors.lastname: De Vecchi
authors.affiliation: Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.
authors.forename: Rita D
authors.initials: RD
authors.lastname: Brandão
authors.affiliation: Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.
authors.forename: Demis
authors.initials: D
authors.lastname: Tserpelis
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
authors.forename: Melissa
authors.initials: M
authors.lastname: Brown
authors.affiliation: Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Blanco
authors.affiliation: Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Oncogenetics Group, Vall d'Hebron Research Institute (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain.
authors.forename: Sandra
authors.initials: S
authors.lastname: Bonache
authors.affiliation: Genetic Diagnosis Unit, Hereditary Cancer Program, Institut Català d'Oncologia, Barcelona, Spain.
authors.forename: Mireia
authors.initials: M
authors.lastname: Menéndez
authors.affiliation: Service de Génétique and INSERM U830, Institut Curie and Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
authors.forename: Claude
authors.initials: C
authors.lastname: Houdayer
authors.affiliation: Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
authors.forename: Claudia
authors.initials: C
authors.lastname: Foglia
authors.affiliation: Department of Medicine, The University of Chicago Medical Center, Chicago, IL, USA.
authors.forename: James D
authors.initials: JD
authors.lastname: Fackenthal
authors.affiliation: Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
authors.forename: Diana
authors.initials: D
authors.lastname: Baralle
authors.affiliation: Center of Familial Breast and Ovarian Cancer, University Hospital Cologne, Cologne, Germany, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
authors.forename: Barbara
authors.initials: B
authors.lastname: Wappenschmidt
authors.affiliation: Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain, Servicio de Oncología Médica, Hospital Clínico San Carlos, Madrid, Spain.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Díaz-Rubio
authors.affiliation: Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain.
authors.forename: Trinidad
authors.initials: T
authors.lastname: Caldés
authors.affiliation: Department of Pathology, University of Otago, Christchurch, New Zealand.
authors.forename: Logan
authors.initials: L
authors.lastname: Walker
authors.affiliation: Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Oncogenetics Group, Vall d'Hebron Research Institute (VHIR), Universitat Autonoma de Barcelona, Barcelona, Spain, Oncogenetics Group, University Hospital of Vall d'Hebron, Barcelona, Spain.
authors.forename: Orland
authors.initials: O
authors.lastname: Díez
authors.affiliation: Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain.
authors.forename: Ana
authors.initials: A
authors.lastname: Vega
authors.affiliation: Molecular Cancer Epidemiology Laboratory, Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
authors.forename: Amanda B
authors.initials: AB
authors.lastname: Spurdle
authors.affiliation: Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Radice
authors.affiliation: Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain, mhoya@hotmail.com mdhoya@hotmail.com.
authors.forename: Miguel
authors.initials: M
authors.lastname: De La Hoya
mesh_terms: D017398:Alternative Splicing; D019313:BRCA1 Protein / Q000097:blood* / Q000235:genetics*; D001940:Breast / Q000378:metabolism*; D005260:Female; D006801:Humans; D020033:Protein Isoforms / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA
chemical_list: D019313:BRCA1 Protein; D020033:Protein Isoforms; D012333:RNA, Messenger