Journal article

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.

  • Taylor JC NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Martin HC Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Lise S Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Broxholme J Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Cazier JB Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Rimmer A Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Kanapin A Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Lunter G Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Fiddy S Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Allan C Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Aricescu AR Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Attar M Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Babbs C MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Becq J Illumina Cambridge Limited, Saffron Walden, UK.
  • Beeson D Neurosciences Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Bento C Hematology Department, Centro Hospitalar e Universitário de Coimbra, Portugal.
  • Bignell P Molecular Haematology Department, Oxford University Hospitals NHS Trust, Oxford, UK.
  • Blair E Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK.
  • Buckle VJ MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Bull K Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Cais O Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
  • Cario H Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany.
  • Chapel H Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  • Copley RR NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Cornall R Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK.
  • Craft J NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Dahan K Centre de Génétique Humaine, Institut de Génétique et de Pathologie, Gosselies, Belgium.
  • Davenport EE Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Dendrou C MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Devuyst O Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
  • Fenwick AL Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Flint J Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Fugger L MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Gilbert RD University Hospital Southampton NHS Foundation Trust, University of Southampton, Southampton, UK.
  • Goriely A Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Green A Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Greger IH Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
  • Grocock R Illumina Cambridge Limited, Saffron Walden, UK.
  • Gruszczyk AV Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Hastings R Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
  • Hatton E Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Higgs D MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Hill A Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Holmes C Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Howard M NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Hughes L Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Humburg P Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Johnson D Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK.
  • Karpe F Oxford Laboratory for Integrative Physiology, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.
  • Kingsbury Z Illumina Cambridge Limited, Saffron Walden, UK.
  • Kini U Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK.
  • Knight JC Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Krohn J Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Lamble S Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Langman C Kidney Diseases, Feinberg School of Medicine, Northwestern University and the Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.
  • Lonie L Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Luck J Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • McCarthy D Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • McGowan SJ Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • McMullin MF Centre for Cancer Research and Cell Biology, Queen's University, Belfast, UK.
  • Miller KA Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Murray L Illumina Cambridge Limited, Saffron Walden, UK.
  • Németh AH Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
  • Nesbit MA Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.
  • Nutt D Centre for Neuropsychopharmacology, Division of Brain Sciences, Imperial College, London, UK.
  • Ormondroyd E Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
  • Oturai AB Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark.
  • Pagnamenta A NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Patel SY Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  • Percy M Department of Haematology, Belfast City Hospital, Belfast, UK.
  • Petousi N Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  • Piazza P Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Piret SE Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.
  • Polanco-Echeverry G Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Popitsch N NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Powrie F Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
  • Pugh C Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  • Quek L MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Robbins PA Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
  • Robson K MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Russo A Department of Pediatrics, University Hospital, Mainz, Germany.
  • Sahgal N Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • van Schouwenburg PA Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  • Schuh A NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Silverman E Division of Rheumatology, The Hospital for Sick Children, Toronto, Ontario, Canada.
  • Simmons A MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Sørensen PS Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark.
  • Sweeney E Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK.
  • Taylor J NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Thakker RV Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.
  • Tomlinson I NIHR Comprehensive Biomedical Research Centre, Oxford, UK.
  • Trebes A Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Twigg SR Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Uhlig HH Translational Gastroenterology Unit, University of Oxford, Oxford, UK.
  • Vyas P MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Vyse T Division of Genetics, King's College London, Guy's Hospital, London, UK.
  • Wall SA Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK.
  • Watkins H Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
  • Whyte MP Center for Metabolic Bone Disease and Molecular Research, Shriners Hospital for Children, St Louis, Missouri, USA.
  • Witty L Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Wright B Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Yau C Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Buck D Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • Humphray S Illumina Cambridge Limited, Saffron Walden, UK.
  • Ratcliffe PJ Nuffield Department of Medicine, University of Oxford, Oxford, UK.
  • Bell JI Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK.
  • Wilkie AO Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
  • Bentley D Illumina Cambridge Limited, Saffron Walden, UK.
  • Donnelly P Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
  • McVean G Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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  • 2015-05-19
Published in:
  • Nature genetics. - 2015
English To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.
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  • English
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https://folia.unifr.ch/global/documents/271309
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