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    Human molecular genetics. 2016 Mar 23. pii: ddw094. doi: 10.1093/hmg/ddw094
    Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms.
    de la Hoya M1,  Soukarieh O2,  López-Perolio I3,  Vega A4,  Walker LC5,  van Ierland Y6,  Baralle D7,  Santamariña M8,  Lattimore V9,  Wijnen J10,  Whiley P11,  Blanco A12,  Raponi M13,  Hauke J14,  Wappenschmidt B15,  Becker A16,  Hansen TV17,  Behar R18,  Niederacher D19,  Arnold N20,  Dworniczak B21,  Steinemann D22,  Faust U23,  Rubinstein W24,  Hulick PJ25,  Houdayer C26,  Caputo SM27,  Castera L28,  Pesaran T29,  Chao E30,  Brewer C31,  Southey MC32,  van Asperen CJ33,  Singer CF34,  Sullivan J35,  Poplawski N36,  Mai P37,  Peto J38,  Johnson N39,  Burwinkel B40,  Surowy H41,  Bojesen SE,  Flyger H42,  Lindblom A43,  Margolin S44,  Chang-Claude J45,  Rudolph A46,  Radice P47,  Galastri L48,  Olson JE49,  Hallberg E50,  Giles GG51,  Milne RL52,  Andrulis IL53,  Glendon G54,  Hall P55,  Czene K56,  Blows F57,  Shah M58,  Wang Q59,  Dennis J60,  Michailidou K61,  McGuffog L62,  Bolla MK63,  Antoniou AC64,  Easton DF65,  Couch FJ66,  Tavtigian S67,  Vreeswijk M68,  Parsons M69,  Meeks H70,  Martins A71,  Goldgar DE72,  Spurdle AB73
    Author information
    1Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain. amanda.spurdle@qimr.edu.au.
    2Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
    3Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain.
    4Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela, 15706, Spain.
    5Department of Pathology, University of Otago, Christchurch, New Zealand.
    6Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
    7Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
    8CIBERER, Grupo de Medicina Xenómica-USC, Universidade de Santiago de Compostela, Fundacion Galega de Medicina Xenómica (SERGAS), Santiago de Compostela, Spain.
    9Department of Pathology, University of Otago, Christchurch, New Zealand.
    10Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
    11Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
    12Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela, 15706, Spain.
    13Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
    14Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne, Germany.
    15Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne, Germany.
    16Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne, Germany.
    17Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, DK-2100, Denmark.
    18Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain.
    19Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Germany.
    20Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Germany.
    21Institute of Human Genetics, University of Münster, Münster, Germany.
    22Institute of Human Genetics, Hannover Medical School, Hannover, Germany.
    23Institute of Medical Genetics and Applied Genomics, Univeristy Hosptial Tuebingen, Tuebingen, Germany.
    24National Institutes of Health, Bethesda, MD, USA.
    25Center for Medical Genetics, NorthShore University Health System, University of Chicago Pritzker School of Medicine, 1000 Central Street, Suite 620, Evanston, IL, USA.
    26Service de Génétique, Department de Biologie des Tumeurs, Institut Curie and INSERM U830, centre de recherche de l'Institut Curie, Paris, and Universite Paris Descartes, Sorbonne Paris Cite, Paris, France.
    27Service de Génétique, Department de Biologie des Tumeurs, Institut Curie, Paris, France.
    28Centre Francois Baclesse, Laboratoire de Biologie et de Genetique du Cancer, 14076, Caen, France.
    29Ambry Genetics, 15 Argonaut, Aliso Viejo, CA 92656, USA.
    30Ambry Genetics, 15 Argonaut, Aliso Viejo, CA 92656, USA.
    31Department of Clinical Genetics, Royal Devon and Exeter Hospital, Exeter, UK.
    32Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Vic, 3010, Australia.
    33Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
    34Dept of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria.
    35Genetic Health Service NZ, South Island Hub, Christchurch Hospital, New Zealand.
    36Adult Genetics Unit, South Australian Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, 72 King William Road, North Adelaide, SA 5067, Australia. University Department of Paediatrics, University of Adelaide, North Terrace, Adelaide, SA 5000, Australia.
    37Clinical Genetics Branch, DCEG, NCI, NIH, 9609 Medical Center Drive, Room 6E-454, Bethesda, MD, USA.
    38London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
    39Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK. Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK.
    40Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, 69120, Germany. Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg, 69120, Germany.
    41Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, 69120, Germany. Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg, 69120, Germany.
    42Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark.
    43Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, SE-171 77, Sweden.
    44Department of Oncology Pathology, Karolinska Institutet, Sweden.
    45Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany. University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
    46Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany.
    47Unit of "Molecular bases of genetic risk and genetic testing", Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
    48Associazione Volontari Italiani Sangue (AVIS) comunale di Milano, Milano, Italy.
    49Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA.
    50Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA.
    51Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Vic, 3010, Australia. Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Vic, 3004, Australia.
    52Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Vic, 3010, Australia. Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Vic, 3004, Australia.
    53Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada. Department of Molecular Genetics, University of Toronto, Canada.
    54Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.
    55Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, SE-171 77, Sweden.
    56Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, SE-171 77, Sweden.
    57Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK.
    58Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK.
    59Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
    60Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
    61Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK. Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Cyprus.
    62Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK.
    63Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
    64Strangeways Research Laboratory, Worts Causeway, Cambridge CB1 8RN, UK.
    65Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK. Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
    66Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA. Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
    67Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine.
    68Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
    69Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
    70Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine.
    71Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
    72Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
    73Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia. mhoya@hotmail.com.
    Abstract

    A recent analysis using family history weighting and co-observation classification modeling indicated thatBRCA1c.594-2A>C (IVS9-2A>C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenicBRCA1variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A>C. The combined odds for causality considering case-control, segregation, and breast tumor pathology information was 3.23x10(-8) Our data indicate that c.594-2A>C is always inciswith c.641A>G.The spliceogenic effect of c.[594-2A>C;641A>G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A>C; 641A>G] caused exon 10 skipping, albeit not due to c.594-2A>C impairing the acceptor site but rather by c.641A>G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with aper allele BRCA1expression profile comprised of ≈70-80% truncating transcripts, and ≈20-30% of in-frame Δ9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm thatBRCA1c.[594-2A>C;641A>G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant inBRCA1exons 9 or 10, or any otherBRCA1allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.


    © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

    Publikations ID: 27008870
    Quelle: öffnen
     
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