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Abstract
High-throughput sequencing has ushered in a diversity of approaches for identifying genetic variants and understanding genome structure and function. When applied to individuals with rare genetic diseases, these approaches have greatly accelerated gene discovery and patient diagnosis. Over the past decade, exome sequencing has emerged as a comprehensive and cost-effective approach to identify pathogenic variants in the protein-coding regions of the genome. However, for individuals in whom exome-sequencing fails to identify a pathogenic variant, we discuss recent advances that are helping to reduce the diagnostic gap.
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Affiliation(s)
- Laure Frésard
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, School of Medicine, Stanford, California 94305, USA
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Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, Flicek P. Registered access: authorizing data access. Eur J Hum Genet 2018; 26:1721-1731. [PMID: 30069064 PMCID: PMC6244209 DOI: 10.1038/s41431-018-0219-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/08/2018] [Accepted: 06/20/2018] [Indexed: 12/14/2022] Open
Abstract
The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada.
- Montreal Neurological Institute, Faculty of Medicine, McGill University, Montreal, QC, Canada.
| | - Mikael Linden
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ilkka Lappalainen
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Jordi Rambla De Argila
- Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | | | - David Lloyd
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- The Global Alliance for Genomics and Health, MaRS Centre, West Tower, 661 University Avenue, Suite 510, Toronto, M5G 0A3, ON, Canada
| | - J Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Julia Foreman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tim Cutts
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mahsa Shabani
- Center for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | | | | | | | - Xiaoqian Jiang
- Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA
| | - Shuang Wang
- Department of Biomedical Informatics, UC San Diego, La Jolla, CA, USA
| | - Daniel Perrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Tiffany Boughtwood
- Australian Genomics Health Alliance, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | | | - Anthony J Brookes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | | | | | | | - Serena Scollen
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Samir Das
- McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Alan C Evans
- McGill Centre for Integrative Neurosciences, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, London, UK
| | - Steven E Brenner
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, USA
| | - Tommi Nyrönen
- CSC - IT Center for Science, Espoo, Finland
- ELIXIR Compute Platform, ELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Gunnar Rätsch
- Department of Computer Science, Biomedical Informatics, ETH Zurich, Zurich, Switzerland
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham & Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Michael Baudis
- University of Zurich & Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Stephen T Sherry
- National Centre for Biotechnology Information, US National Library of Medicine, Bethesda, MD, USA
| | - Kazuto Kato
- Department of Biomedical Ethics and Public Policy, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Dixie Baker
- Martin, Blanck & Associates, Alexandria, VA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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Splinter K, Adams DR, Bacino CA, Bellen HJ, Bernstein JA, Cheatle-Jarvela AM, Eng CM, Esteves C, Gahl WA, Hamid R, Jacob HJ, Kikani B, Koeller DM, Kohane IS, Lee BH, Loscalzo J, Luo X, McCray AT, Metz TO, Mulvihill JJ, Nelson SF, Palmer CGS, Phillips JA, Pick L, Postlethwait JH, Reuter C, Shashi V, Sweetser DA, Tifft CJ, Walley NM, Wangler MF, Westerfield M, Wheeler MT, Wise AL, Worthey EA, Yamamoto S, Ashley EA. Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease. N Engl J Med 2018; 379:2131-2139. [PMID: 30304647 PMCID: PMC6481166 DOI: 10.1056/nejmoa1714458] [Citation(s) in RCA: 244] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Many patients remain without a diagnosis despite extensive medical evaluation. The Undiagnosed Diseases Network (UDN) was established to apply a multidisciplinary model in the evaluation of the most challenging cases and to identify the biologic characteristics of newly discovered diseases. The UDN, which is funded by the National Institutes of Health, was formed in 2014 as a network of seven clinical sites, two sequencing cores, and a coordinating center. Later, a central biorepository, a metabolomics core, and a model organisms screening center were added. METHODS We evaluated patients who were referred to the UDN over a period of 20 months. The patients were required to have an undiagnosed condition despite thorough evaluation by a health care provider. We determined the rate of diagnosis among patients who subsequently had a complete evaluation, and we observed the effect of diagnosis on medical care. RESULTS A total of 1519 patients (53% female) were referred to the UDN, of whom 601 (40%) were accepted for evaluation. Of the accepted patients, 192 (32%) had previously undergone exome sequencing. Symptoms were neurologic in 40% of the applicants, musculoskeletal in 10%, immunologic in 7%, gastrointestinal in 7%, and rheumatologic in 6%. Of the 382 patients who had a complete evaluation, 132 received a diagnosis, yielding a rate of diagnosis of 35%. A total of 15 diagnoses (11%) were made by clinical review alone, and 98 (74%) were made by exome or genome sequencing. Of the diagnoses, 21% led to recommendations regarding changes in therapy, 37% led to changes in diagnostic testing, and 36% led to variant-specific genetic counseling. We defined 31 new syndromes. CONCLUSIONS The UDN established a diagnosis in 132 of the 382 patients who had a complete evaluation, yielding a rate of diagnosis of 35%. (Funded by the National Institutes of Health Common Fund.).
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Affiliation(s)
- Kimberly Splinter
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - David R Adams
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Carlos A Bacino
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Hugo J Bellen
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Jonathan A Bernstein
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Alys M Cheatle-Jarvela
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Christine M Eng
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Cecilia Esteves
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - William A Gahl
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Rizwan Hamid
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Howard J Jacob
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Bijal Kikani
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - David M Koeller
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Isaac S Kohane
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Brendan H Lee
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Joseph Loscalzo
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Xi Luo
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Alexa T McCray
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Thomas O Metz
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - John J Mulvihill
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Stanley F Nelson
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Christina G S Palmer
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - John A Phillips
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Leslie Pick
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - John H Postlethwait
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Chloe Reuter
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Vandana Shashi
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - David A Sweetser
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Cynthia J Tifft
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Nicole M Walley
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Michael F Wangler
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Monte Westerfield
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Matthew T Wheeler
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Anastasia L Wise
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Elizabeth A Worthey
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Shinya Yamamoto
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
| | - Euan A Ashley
- From Harvard Medical School (K.S., C.E., I.S.K., J.L., A.T.M., D.A.S.), Brigham and Women's Hospital (J.L.), and Massachusetts General Hospital (D.A.S.) - all in Boston; the National Institutes of Health Clinical Center (D.R.A., W.A.G., J.J.M., C.J.T.) and the National Human Genome Research Institute (A.L.W.), Bethesda, and the University of Maryland, College Park (A.M.C.-J., B.K., L.P.) - all in Maryland; Baylor College of Medicine, Houston (C.A.B., H.J.B., C.M.E., B.H.L., X.L., M.F.W., S.Y.); Stanford University, Stanford (J.A.B., C.R., M.T.W., E.A.A.), and the University of California, Los Angeles, Los Angeles (S.F.N., C.G.S.P.) - both in California; Vanderbilt University, Nashville (R.H., J.A.P.); HudsonAlpha Institute for Biotechnology, Huntsville, AL (H.J.J., E.A.W.); Oregon Health and Science University, Portland (D.M.K.); the Pacific Northwest National Laboratory, Richland, WA (T.O.M.); the University of Oregon, Eugene (J.H.P., M.W.); and Duke University, Durham, NC (V.S., N.M.W.)
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54
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Affiliation(s)
- David R Adams
- From the Office of the Clinical Director, National Human Genome Research Institute, and the Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD (D.R.A.); and the Department of Molecular and Human Genetics, Baylor College of Medicine, and Baylor Genetics - both in Houston (C.M.E.)
| | - Christine M Eng
- From the Office of the Clinical Director, National Human Genome Research Institute, and the Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD (D.R.A.); and the Department of Molecular and Human Genetics, Baylor College of Medicine, and Baylor Genetics - both in Houston (C.M.E.)
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55
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Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102072. [PMID: 30248891 PMCID: PMC6210164 DOI: 10.3390/ijerph15102072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022]
Abstract
The time required to reach a correct diagnosis is a key concern for rare disease (RD) patients. Diagnostic delay can be intolerably long, often described as an “odyssey” and, for some, a diagnosis may remain frustratingly elusive. The International Rare Disease Research Consortium proposed, as ultimate goal for 2017–2027, to enable all people with a suspected RD to be diagnosed within one year of presentation, if the disorder is known. Subsequently, unsolved cases would enter a globally coordinated diagnostic and research pipeline. In-depth analysis of the genotype through next generation sequencing, together with a standardized in-depth phenotype description and sophisticated high-throughput approaches, have been applied as diagnostic tools to increase the chance of a timely and accurate diagnosis. The success of this approach is evident in the Orphanet database. From 2010 to March 2017 over 600 new RDs and roughly 3600 linked genes have been described and identified. However, combination of -omics and phenotype data, as well as international sharing of this information, has raised ethical concerns. Values to be assessed include not only patient autonomy but also family implications, beneficence, non-maleficence, justice, solidarity and reciprocity, which must be respected and promoted and, at the same time, balanced among each other. In this work we suggest that, to maximize patients’ involvement in the search for a diagnosis and identification of new causative genes, undiagnosed patients should have the possibility to: (1) actively participate in the description of their phenotype; (2) choose the level of visibility of their profile in matchmaking databases; (3) express their preferences regarding return of new findings, in particular which level of Variant of Unknown Significance (VUS) significance should be considered relevant to them. The quality of the relationship between individual patients and physicians, and between the patient community and the scientific community, is critically important for optimizing the use of available data and enabling international collaboration in order to provide a diagnosis, and the attached support, to unsolved cases. The contribution of patients to collecting and coding data comprehensively is critical for efficient use of data downstream of data collection.
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56
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Fujiwara T, Yamamoto Y, Kim JD, Buske O, Takagi T. PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases. Am J Hum Genet 2018; 103:389-399. [PMID: 30173820 DOI: 10.1016/j.ajhg.2018.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/01/2018] [Indexed: 01/29/2023] Open
Abstract
Recently, to speed up the differential-diagnosis process based on symptoms and signs observed from an affected individual in the diagnosis of rare diseases, researchers have developed and implemented phenotype-driven differential-diagnosis systems. The performance of those systems relies on the quantity and quality of underlying databases of disease-phenotype associations (DPAs). Although such databases are often developed by manual curation, they inherently suffer from limited coverage. To address this problem, we propose a text-mining approach to increase the coverage of DPA databases and consequently improve the performance of differential-diagnosis systems. Our analysis showed that a text-mining approach using one million case reports obtained from PubMed could increase the coverage of manually curated DPAs in Orphanet by 125.6%. We also present PubCaseFinder (see Web Resources), a new phenotype-driven differential-diagnosis system in a freely available web application. By utilizing automatically extracted DPAs from case reports in addition to manually curated DPAs, PubCaseFinder improves the performance of automated differential diagnosis. Moreover, PubCaseFinder helps clinicians search for relevant case reports by using phenotype-based comparisons and confirm the results with detailed contextual information.
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SpainUDP: The Spanish Undiagnosed Rare Diseases Program. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15081746. [PMID: 30110963 PMCID: PMC6121381 DOI: 10.3390/ijerph15081746] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 11/24/2022]
Abstract
One of the IRDiRC goals for 2017–2027 is to achieve definitive diagnosis for rare undiagnosed diseases within one year, as delay in diagnosis remains one of the pending issues in the rare diseases field. The Spanish Undiagnosed Rare Diseases Program (SpainUDP) was created in response to this challenging scenario to cover patients’ needs and after seeing the success of the Undiagnosed Diseases Program (UDP) in the USA. SpainUDP offers a multidisciplinary approach to those patients who have long sought a diagnosis without any success. During the first phase of the protocol, undiagnosed cases are sent to SpainUDP by individual patients or families, patient organizations or hospitals. After careful analysis of phenotype, data from sequencing experiments (WES) is processed with a standard pipeline and detailed standardized phenotypic information (mapped to the Human Phenotype Ontology, HPO) is connected to genetic data. In addition, the participation of SpainUDP in international initiatives such as the European projects RD-Connect and Solve RD, the Undiagnosed Diseases Network International (UDNI), and the MatchMaker Exchange (MME) platform, allows the establishment of a global data sharing strategy across multiple projects submitting data to these international initiatives. From the official beginning of the program (at the end of 2015) until early 2018, 147 cases were accepted in SpainUDP. During this time, 37 cases (25%) dropped out the program due to several reasons. The remaining 110 cases are distributed as follows: phenotypic and genotypic (WES) characterization was finished in 30 cases, of which 20 (67%) were diagnosed; 21 cases are pending on variants’ validation by Sanger sequencing; in 25 cases, WES is ongoing and 34 cases are being studied for deep phenotypic characterization. In conclusion, SpainUDP aims to achieve a diagnosis following two recommendations of the IRDiRC: the patients’ diagnosis in as short a time as possible and the promotion of data sharing (especially genomic) at the international level.
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58
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Abstract
Diagnosing rare diseases can be challenging for clinicians. This article gives an overview on novel approaches, which enable automated phenotype-driven analyses of differential diagnoses for rare diseases as well as genomic variation data of affected individuals. The focus lies on reliable methods for collating clinical phenotypic data and new algorithms for precise and robust assessment of the similarity between phenotypic profiles. The Human Phenotype Ontology project (HPO; www.human-phenotype-ontology.org ) provides an ontology for collating symptoms and clinical phenotypic abnormalities. Using ontologies makes it possible to capture these data in a precise and comprehensive fashion as well as to apply reliable and robust automated analyses. Tools, such as the Phenomizer, enable the algorithmic calculation of similarity values amongst patients or between patients and disease descriptions. Such digital tools represent a solid foundation for differential diagnostic applications. Many rare diseases have a strong genetic component but the analysis of the coding DNA variants in rare disease patients is an enormously complex procedure, which often impedes successful molecular diagnostics. In this situation a combined analysis of the patients HPO-coded phenotypic features and the genomic characteristics of the variants can be of substantial help. In this case the HPO project and the associated algorithms are helpful: it is therefore an important component for phenotype-driven translational research and prioritization of disease-relavant genomic variations.
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Affiliation(s)
- S Köhler
- Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, 10178, Berlin, Deutschland.
- Einstein Center Digital Future, Wilhelmstr. 67, 10117, Berlin, Deutschland.
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Deutschland.
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Deep Phenotyping on Electronic Health Records Facilitates Genetic Diagnosis by Clinical Exomes. Am J Hum Genet 2018; 103:58-73. [PMID: 29961570 DOI: 10.1016/j.ajhg.2018.05.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/24/2018] [Indexed: 01/17/2023] Open
Abstract
Integration of detailed phenotype information with genetic data is well established to facilitate accurate diagnosis of hereditary disorders. As a rich source of phenotype information, electronic health records (EHRs) promise to empower diagnostic variant interpretation. However, how to accurately and efficiently extract phenotypes from heterogeneous EHR narratives remains a challenge. Here, we present EHR-Phenolyzer, a high-throughput EHR framework for extracting and analyzing phenotypes. EHR-Phenolyzer extracts and normalizes Human Phenotype Ontology (HPO) concepts from EHR narratives and then prioritizes genes with causal variants on the basis of the HPO-coded phenotype manifestations. We assessed EHR-Phenolyzer on 28 pediatric individuals with confirmed diagnoses of monogenic diseases and found that the genes with causal variants were ranked among the top 100 genes selected by EHR-Phenolyzer for 16/28 individuals (p < 2.2 × 10-16), supporting the value of phenotype-driven gene prioritization in diagnostic sequence interpretation. To assess the generalizability, we replicated this finding on an independent EHR dataset of ten individuals with a positive diagnosis from a different institution. We then assessed the broader utility by examining two additional EHR datasets, including 31 individuals who were suspected of having a Mendelian disease and underwent different types of genetic testing and 20 individuals with positive diagnoses of specific Mendelian etiologies of chronic kidney disease from exome sequencing. Finally, through several retrospective case studies, we demonstrated how combined analyses of genotype data and deep phenotype data from EHRs can expedite genetic diagnoses. In summary, EHR-Phenolyzer leverages EHR narratives to automate phenotype-driven analysis of clinical exomes or genomes, facilitating the broader implementation of genomic medicine.
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60
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Maiella S, Olry A, Hanauer M, Lanneau V, Lourghi H, Donadille B, Rodwell C, Köhler S, Seelow D, Jupp S, Parkinson H, Groza T, Brudno M, Robinson PN, Rath A. Harmonising phenomics information for a better interoperability in the rare disease field. Eur J Med Genet 2018; 61:706-714. [PMID: 29425702 DOI: 10.1016/j.ejmg.2018.01.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/30/2017] [Accepted: 01/27/2018] [Indexed: 01/30/2023]
Abstract
HIPBI-RD (Harmonising phenomics information for a better interoperability in the rare disease field) is a three-year project which started in 2016 funded via the E-Rare 3 ERA-NET program. This project builds on three resources largely adopted by the rare disease (RD) community: Orphanet, its ontology ORDO (the Orphanet Rare Disease Ontology), HPO (the Human Phenotype Ontology) as well as PhenoTips software for the capture and sharing of structured phenotypic data for RD patients. Our project is further supported by resources developed by the European Bioinformatics Institute and the Garvan Institute. HIPBI-RD aims to provide the community with an integrated, RD-specific bioinformatics ecosystem that will harmonise the way phenomics information is stored in databases and patient files worldwide, and thereby contribute to interoperability. This ecosystem will consist of a suite of tools and ontologies, optimized to work together, and made available through commonly used software repositories. The project workplan follows three main objectives: The HIPBI-RD ecosystem will contribute to the interpretation of variants identified through exome and full genome sequencing by harmonising the way phenotypic information is collected, thus improving diagnostics and delineation of RD. The ultimate goal of HIPBI-RD is to provide a resource that will contribute to bridging genome-scale biology and a disease-centered view on human pathobiology. Achievements in Year 1.
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Affiliation(s)
- Sylvie Maiella
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Annie Olry
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Marc Hanauer
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Valérie Lanneau
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Halima Lourghi
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Bruno Donadille
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Charlotte Rodwell
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France
| | - Sebastian Köhler
- NeuroCure Cluster of Excellence, Charité Universitätsklinikum, Charitéplatz 1, 10117 Berlin, Germany
| | - Dominik Seelow
- NeuroCure Cluster of Excellence, Charité Universitätsklinikum, Charitéplatz 1, 10117 Berlin, Germany
| | - Simon Jupp
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tudor Groza
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, NSW, Australia
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto M5S 1A1, Canada
| | - Peter N Robinson
- Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ana Rath
- INSERM, US14 - Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
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61
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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62
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Clinical validity of phenotype-driven analysis software PhenoVar as a diagnostic aid for clinical geneticists in the interpretation of whole-exome sequencing data. Genet Med 2018; 20:942-949. [PMID: 29388948 DOI: 10.1038/gim.2017.239] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/20/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE We sought to determine the diagnostic yield of whole-exome sequencing (WES) combined with phenotype-driven analysis of variants in patients with suspected genetic disorders. METHODS WES was performed on a cohort of 51 patients presenting dysmorphisms with or without neurodevelopmental disorders of undetermined etiology. For each patient, a clinical geneticist reviewed the phenotypes and used the phenotype-driven analysis software PhenoVar (http://phenovar.med.usherbrooke.ca/) to analyze WES variants. The prioritized list of potential diagnoses returned was reviewed by the clinical geneticist, who selected candidate variants to be confirmed by segregation analysis. Conventional analysis of the individual variants was performed in parallel. The resulting candidate variants were subsequently reviewed by the same geneticist, to identify any additional potential diagnoses. RESULTS A molecular diagnosis was identified in 35% of the patients using the conventional analysis, and 17 of these 18 diagnoses were independently identified using PhenoVar. The only diagnosis initially missed by PhenoVar was rescued when the optional "minimal phenotypic cutoff" filter was omitted. PhenoVar reduced by half the number of potential diagnoses per patient compared with the conventional analysis. CONCLUSION Phenotype-driven software prioritizes WES variants, provides an efficient diagnostic aid to clinical geneticists and laboratories, and should be incorporated in clinical practice.
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63
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Dudding-Byth T, Baxter A, Holliday EG, Hackett A, O'Donnell S, White SM, Attia J, Brunner H, de Vries B, Koolen D, Kleefstra T, Ratwatte S, Riveros C, Brain S, Lovell BC. Computer face-matching technology using two-dimensional photographs accurately matches the facial gestalt of unrelated individuals with the same syndromic form of intellectual disability. BMC Biotechnol 2017; 17:90. [PMID: 29258477 PMCID: PMC5735520 DOI: 10.1186/s12896-017-0410-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 12/07/2017] [Indexed: 12/23/2022] Open
Abstract
Background Massively parallel genetic sequencing allows rapid testing of known intellectual disability (ID) genes. However, the discovery of novel syndromic ID genes requires molecular confirmation in at least a second or a cluster of individuals with an overlapping phenotype or similar facial gestalt. Using computer face-matching technology we report an automated approach to matching the faces of non-identical individuals with the same genetic syndrome within a database of 3681 images [1600 images of one of 10 genetic syndrome subgroups together with 2081 control images]. Using the leave-one-out method, two research questions were specified:Using two-dimensional (2D) photographs of individuals with one of 10 genetic syndromes within a database of images, did the technology correctly identify more than expected by chance: i) a top match? ii) at least one match within the top five matches? or iii) at least one in the top 10 with an individual from the same syndrome subgroup? Was there concordance between correct technology-based matches and whether two out of three clinical geneticists would have considered the diagnosis based on the image alone?
Results The computer face-matching technology correctly identifies a top match, at least one correct match in the top five and at least one in the top 10 more than expected by chance (P < 0.00001). There was low agreement between the technology and clinicians, with higher accuracy of the technology when results were discordant (P < 0.01) for all syndromes except Kabuki syndrome. Conclusions Although the accuracy of the computer face-matching technology was tested on images of individuals with known syndromic forms of intellectual disability, the results of this pilot study illustrate the potential utility of face-matching technology within deep phenotyping platforms to facilitate the interpretation of DNA sequencing data for individuals who remain undiagnosed despite testing the known developmental disorder genes. Electronic supplementary material The online version of this article (10.1186/s12896-017-0410-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tracy Dudding-Byth
- Hunter Genetics, Hunter New England Health Service, Newcastle, NSW, Australia. .,GrowUpWell, Priority of Research Excellence, The University of Newcastle, Newcastle, NSW, Australia. .,Hunter Medical Research Institute, Newcastle, NSW, Australia. .,New South Wales Genetics of Learning Disability (GOLD) service, Hunter New England Health Service, Newcastle, NSW, 2298, Australia.
| | - Anne Baxter
- Hunter Genetics, Hunter New England Health Service, Newcastle, NSW, Australia
| | - Elizabeth G Holliday
- Hunter Medical Research Institute, Newcastle, NSW, Australia.,The University of Newcastle, Newcastle, NSW, Australia
| | - Anna Hackett
- Hunter Genetics, Hunter New England Health Service, Newcastle, NSW, Australia.,The University of Newcastle, Newcastle, NSW, Australia.,New South Wales Genetics of Learning Disability (GOLD) service, Hunter New England Health Service, Newcastle, NSW, 2298, Australia
| | - Sheridan O'Donnell
- Hunter Genetics, Hunter New England Health Service, Newcastle, NSW, Australia
| | - Susan M White
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - John Attia
- Hunter Medical Research Institute, Newcastle, NSW, Australia.,The University of Newcastle, Newcastle, NSW, Australia
| | - Han Brunner
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bert de Vries
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Koolen
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Seshika Ratwatte
- The University of Newcastle, Newcastle, NSW, Australia.,The Department of Medicine, John Hunter Hospital, Newcastle, NSW, Australia
| | - Carlos Riveros
- Hunter Medical Research Institute, Newcastle, NSW, Australia
| | | | - Brian C Lovell
- Imagus Technology, Brisbane, QLD, Australia.,School of ITEE, The University of Queensland, Brisbane, QLD, Australia
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64
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Hartley T, Wagner JD, Warman-Chardon J, Tétreault M, Brady L, Baker S, Tarnopolsky M, Bourque PR, Parboosingh JS, Smith C, McInnes B, Innes AM, Bernier F, Curry CJ, Yoon G, Horvath GA, Bareke E, Gillespie M, Majewski J, Bulman DE, Dyment DA, Boycott KM. Whole-exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families. Clin Genet 2017; 93:301-309. [PMID: 28708278 DOI: 10.1111/cge.13101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 01/02/2023]
Abstract
The inherited peripheral neuropathies (IPNs) are characterized by marked clinical and genetic heterogeneity and include relatively frequent presentations such as Charcot-Marie-Tooth disease and hereditary motor neuropathy, as well as more rare conditions where peripheral neuropathy is associated with additional features. There are over 250 genes known to cause IPN-related disorders but it is estimated that in approximately 50% of affected individuals a molecular diagnosis is not achieved. In this study, we examine the diagnostic utility of whole-exome sequencing (WES) in a cohort of 50 families with 1 or more affected individuals with a molecularly undiagnosed IPN with or without additional features. Pathogenic or likely pathogenic variants in genes known to cause IPN were identified in 24% (12/50) of the families. A further 22% (11/50) of families carried sequence variants in IPN genes in which the significance remains unclear. An additional 12% (6/50) of families had variants in novel IPN candidate genes, 3 of which have been published thus far as novel discoveries (KIF1A, TBCK, and MCM3AP). This study highlights the use of WES in the molecular diagnostic approach of highly heterogeneous disorders, such as IPNs, places it in context of other published neuropathy cohorts, while further highlighting associated benefits for discovery.
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Affiliation(s)
- T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J D Wagner
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J Warman-Chardon
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - M Tétreault
- Department of Human Genetics, McGill University, Montréal, Canada
| | - L Brady
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - S Baker
- Department of Medicine, McMaster University Medical Centre, Hamilton, Canada
| | - M Tarnopolsky
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - P R Bourque
- Department of Medicine, University of Ottawa, Ottawa, Canada
| | - J S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - C Smith
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B McInnes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - A M Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - F Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - C J Curry
- Department of Pediatrics, University of California, San Francisco, California
| | - G Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G A Horvath
- Division of Biochemical Diseases, Department of Pediatrics, B.C. Children's Hospital, University of British Columbia, Vancouver, Canada
| | - E Bareke
- Department of Human Genetics, McGill University, Montréal, Canada
| | - M Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | | | - J Majewski
- Department of Human Genetics, McGill University, Montréal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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65
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Pogue RE, Cavalcanti DP, Shanker S, Andrade RV, Aguiar LR, de Carvalho JL, Costa FF. Rare genetic diseases: update on diagnosis, treatment and online resources. Drug Discov Today 2017; 23:187-195. [PMID: 29129805 DOI: 10.1016/j.drudis.2017.11.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/28/2017] [Accepted: 11/02/2017] [Indexed: 12/23/2022]
Abstract
Rare genetic diseases collectively impact a significant portion of the world's population. For many diseases there is limited information available, and clinicians can find difficulty in differentiating between clinically similar conditions. This leads to problems in genetic counseling and patient treatment. The biomedical market is affected because pharmaceutical and biotechnology industries do not see advantages in addressing rare disease treatments, or because the cost of the treatments is too high. By contrast, technological advances including DNA sequencing and analysis, together with computer-aided tools and online resources, are allowing a more thorough understanding of rare disorders. Here, we discuss how the collection of various types of information together with the use of new technologies is facilitating diagnosis and, consequently, treatment of rare diseases.
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Affiliation(s)
- Robert E Pogue
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil.
| | | | - Shreya Shanker
- Illinois Mathematics and Science Academy (IMSA), IL, USA
| | - Rosangela V Andrade
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil
| | - Lana R Aguiar
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil
| | - Juliana L de Carvalho
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil; OneSkin Technologies, San Francisco, CA, USA
| | - Fabrício F Costa
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Distrito Federal, Brazil; MATTER, Chicago, IL, USA; The Founder Institute, San Francisco, CA, USA.
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66
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Rare Diseases: Drug Discovery and Informatics Resource. Interdiscip Sci 2017; 10:195-204. [PMID: 29094320 DOI: 10.1007/s12539-017-0270-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 10/19/2017] [Accepted: 10/23/2017] [Indexed: 12/13/2022]
Abstract
A rare disease refers to any disease with very low prevalence individually. Although the impacted population is small for a single disease, more than 6000 rare diseases affect millions of people across the world. Due to the small market size, high cost and possibly low return on investment, only in recent years, the research and development of rare disease drugs have gradually risen globally, in several domains including gene therapy, enzyme replacement therapy, and drug repositioning. Due to the complex etiology and heterogeneous symptoms, there is a large gap between basic research and patient unmet needs for rare disease drug discovery. As computational biology increasingly arises researchers' awareness, the informatics database on rare disease have grown rapidly in the recent years, including drug targets, genetic variant and mutation, phenotype and ontology and patient registries. Along with the advances of informatics database and networks, new computational models will help accelerate the target identification and lead optimization process for rare disease pre-clinical drug development.
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67
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Sobreira NLM, Arachchi H, Buske OJ, Chong JX, Hutton B, Foreman J, Schiettecatte F, Groza T, Jacobsen JOB, Haendel MA, Boycott KM, Hamosh A, Rehm HL. Matchmaker Exchange. ACTA ACUST UNITED AC 2017; 95:9.31.1-9.31.15. [PMID: 29044468 DOI: 10.1002/cphg.50] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In well over half of the individuals with rare disease who undergo clinical or research next-generation sequencing, the responsible gene cannot be determined. Some reasons for this relatively low yield include unappreciated phenotypic heterogeneity; locus heterogeneity; somatic and germline mosaicism; variants of uncertain functional significance; technically inaccessible areas of the genome; incorrect mode of inheritance investigated; and inadequate communication between clinicians and basic scientists with knowledge of particular genes, proteins, or biological systems. To facilitate such communication and improve the search for patients or model organisms with similar phenotypes and variants in specific candidate genes, we have developed the Matchmaker Exchange (MME). MME was created to establish a federated network connecting databases of genomic and phenotypic data using a common application programming interface (API). To date, seven databases can exchange data using the API (GeneMatcher, PhenomeCentral, DECIPHER, MyGene2, matchbox, Australian Genomics Health Alliance Patient Archive, and Monarch Initiative; the latter included for model organism matching). This article guides usage of the MME for rare disease gene discovery. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nara L M Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | - Orion J Buske
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Julia Foreman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | | | - Tudor Groza
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine (IGM), Clinical Director, IGM. Scientific Director, OMIM. Johns Hopkins University. Baltimore, Maryland
| | - Heidi L Rehm
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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68
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Worthey EA. Analysis and Annotation of Whole-Genome or Whole-Exome Sequencing Derived Variants for Clinical Diagnosis. ACTA ACUST UNITED AC 2017; 95:9.24.1-9.24.28. [PMID: 29044471 DOI: 10.1002/cphg.49] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Over the last 10 years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing or analysis (given access to appropriate tools), but rather clinical interpretation. Interpretation of genetic findings in a complex and ever changing clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires application of appropriate interpretation tools, as well as development and application of appropriate methodologies and standard procedures. This unit provides an overview of these items. Specific challenges related to implementation of genome-wide sequencing in a clinical setting are discussed. © 2017 by John Wiley & Sons, Inc.
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69
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Wangler MF, Yamamoto S, Chao HT, Posey JE, Westerfield M, Postlethwait J, Hieter P, Boycott KM, Campeau PM, Bellen HJ. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research. Genetics 2017; 207:9-27. [PMID: 28874452 PMCID: PMC5586389 DOI: 10.1534/genetics.117.203067] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022] Open
Abstract
Efforts to identify the genetic underpinnings of rare undiagnosed diseases increasingly involve the use of next-generation sequencing and comparative genomic hybridization methods. These efforts are limited by a lack of knowledge regarding gene function, and an inability to predict the impact of genetic variation on the encoded protein function. Diagnostic challenges posed by undiagnosed diseases have solutions in model organism research, which provides a wealth of detailed biological information. Model organism geneticists are by necessity experts in particular genes, gene families, specific organs, and biological functions. Here, we review the current state of research into undiagnosed diseases, highlighting large efforts in North America and internationally, including the Undiagnosed Diseases Network (UDN) (Supplemental Material, File S1) and UDN International (UDNI), the Centers for Mendelian Genomics (CMG), and the Canadian Rare Diseases Models and Mechanisms Network (RDMM). We discuss how merging human genetics with model organism research guides experimental studies to solve these medical mysteries, gain new insights into disease pathogenesis, and uncover new therapeutic strategies.
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Affiliation(s)
- Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Hsiao-Tuan Chao
- Department of Pediatrics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
| | - Monte Westerfield
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4C, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario K1H 8L1, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Quebec H3T 1C5, Canada
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine (BCM), Houston, Texas 77030
- Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, Texas 77030
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70
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Dyke SOM, Knoppers BM, Hamosh A, Firth HV, Hurles M, Brudno M, Boycott KM, Philippakis AA, Rehm HL. "Matching" consent to purpose: The example of the Matchmaker Exchange. Hum Mutat 2017; 38:1281-1285. [PMID: 28699299 DOI: 10.1002/humu.23278] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 01/11/2023]
Abstract
The Matchmaker Exchange (MME) connects rare disease clinicians and researchers to facilitate the sharing of data from undiagnosed patients for the purpose of novel gene discovery. Such sharing raises the odds that two or more similar patients with candidate genes in common may be found, thereby allowing their condition to be more readily studied and understood. Consent considerations for data sharing in MME included both the ethical and legal differences between clinical and research settings and the level of privacy risk involved in sharing varying amounts of rare disease patient data to enable patient matches. In this commentary, we discuss these consent considerations and the resulting MME Consent Policy as they may be relevant to other international data sharing initiatives.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ontario, Canada
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts
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71
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WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features. Am J Hum Genet 2017; 101:139-148. [PMID: 28686853 DOI: 10.1016/j.ajhg.2017.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/30/2017] [Indexed: 11/21/2022] Open
Abstract
We report 15 individuals with de novo pathogenic variants in WDR26. Eleven of the individuals carry loss-of-function mutations, and four harbor missense substitutions. These 15 individuals comprise ten females and five males, and all have intellectual disability with delayed speech, a history of febrile and/or non-febrile seizures, and a wide-based, spastic, and/or stiff-legged gait. These subjects share a set of common facial features that include a prominent maxilla and upper lip that readily reveal the upper gingiva, widely spaced teeth, and a broad nasal tip. Together, these features comprise a recognizable facial phenotype. We compared these features with those of chromosome 1q41q42 microdeletion syndrome, which typically contains WDR26, and noted that clinical features are consistent between the two subsets, suggesting that haploinsufficiency of WDR26 contributes to the pathology of 1q41q42 microdeletion syndrome. Consistent with this, WDR26 loss-of-function single-nucleotide mutations identified in these subjects lead to nonsense-mediated decay with subsequent reduction of RNA expression and protein levels. We derived a structural model of WDR26 and note that missense variants identified in these individuals localize to highly conserved residues of this WD-40-repeat-containing protein. Given that WDR26 mutations have been identified in ∼1 in 2,000 of subjects in our clinical cohorts and that WDR26 might be poorly annotated in exome variant-interpretation pipelines, we would anticipate that this disorder could be more common than currently appreciated.
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72
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Gall T, Valkanas E, Bello C, Markello T, Adams C, Bone WP, Brandt AJ, Brazill JM, Carmichael L, Davids M, Davis J, Diaz-Perez Z, Draper D, Elson J, Flynn ED, Godfrey R, Groden C, Hsieh CK, Fischer R, Golas GA, Guzman J, Huang Y, Kane MS, Lee E, Li C, Links AE, Maduro V, Malicdan MCV, Malik FS, Nehrebecky M, Park J, Pemberton P, Schaffer K, Simeonov D, Sincan M, Smedley D, Valivullah Z, Wahl C, Washington N, Wolfe LA, Xu K, Zhu Y, Gahl WA, Tifft CJ, Toro C, Adams DR, He M, Robinson PN, Haendel MA, Zhai RG, Boerkoel CF. Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience. Front Med (Lausanne) 2017; 4:62. [PMID: 28603714 PMCID: PMC5445140 DOI: 10.3389/fmed.2017.00062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/03/2017] [Indexed: 12/13/2022] Open
Abstract
Traditionally, the use of genomic information for personalized medical decisions relies on prior discovery and validation of genotype-phenotype associations. This approach constrains care for patients presenting with undescribed problems. The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) hypothesized that defining disease as maladaptation to an ecological niche allows delineation of a logical framework to diagnose and evaluate such patients. Herein, we present the philosophical bases, methodologies, and processes implemented by the NIH UDP. The NIH UDP incorporated use of the Human Phenotype Ontology, developed a genomic alignment strategy cognizant of parental genotypes, pursued agnostic biochemical analyses, implemented functional validation, and established virtual villages of global experts. This systematic approach provided a foundation for the diagnostic or non-diagnostic answers provided to patients and serves as a paradigm for scalable translational research.
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Affiliation(s)
- Timothy Gall
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elise Valkanas
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Christofer Bello
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Thomas Markello
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - William P. Bone
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Alexander J. Brandt
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Jennifer M. Brazill
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | | | - Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Joie Davis
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Zoraida Diaz-Perez
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - David Draper
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Elise D. Flynn
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Rena Godfrey
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Catherine Groden
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | | | - Roxanne Fischer
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Gretchen A. Golas
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Jessica Guzman
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Yan Huang
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Megan S. Kane
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Elizabeth Lee
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Chong Li
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Amanda E. Links
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - May Christine V. Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Fayeza S. Malik
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Michele Nehrebecky
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Joun Park
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Paul Pemberton
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Katherine Schaffer
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Dimitre Simeonov
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Murat Sincan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Damian Smedley
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Zaheer Valivullah
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Colleen Wahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Nicole Washington
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Lynne A. Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Karen Xu
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - Yi Zhu
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - William A. Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Cynthia J. Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Camillo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
| | - David R. Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Miao He
- Palmieri Metabolic Disease Laboratory, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pathology and Laboratory of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Peter N. Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, United States
| | - R. Grace Zhai
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, FL, United States
| | - Cornelius F. Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, United States
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73
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Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet 2017; 100:695-705. [PMID: 28475856 PMCID: PMC5420351 DOI: 10.1016/j.ajhg.2017.04.003] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.
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Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada.
| | - Ana Rath
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Research Center, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Gareth Baynam
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto M5S 1A1, Canada
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine and University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Johan T den Dunnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Xavier Estivill
- Experimental Division, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar; Genetics Unit, Dexeus Woman's Health, 08028 Barcelona, Spain
| | - Jack Goldblatt
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Catherine Gonthier
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Ivo Gut
- Centre Nacional d'Anàlisi Genòmica, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21286, USA
| | - Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sophie Höhn
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Petra Kaufmann
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Jeffrey P Krischer
- University of South Florida Health Informatics Institute, Tampa, FL 33620, USA
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, 150 06 Prague 5, Czech Republic
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Annie Olry
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | | | - Justin Paschall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité Universitätsmdizin Berlin, 13353 Berlin, Germany; Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, China
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv 4002, Bulgaria
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome 299-00161, Italy
| | - Divya Unni
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Megan R Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Feng Zhang
- WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China; WuXi NextCODE, Cambridge, MA 02142, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, 6229 GT Maastricht, the Netherlands
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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74
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Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R. Semantic prioritization of novel causative genomic variants. PLoS Comput Biol 2017; 13:e1005500. [PMID: 28414800 PMCID: PMC5411092 DOI: 10.1371/journal.pcbi.1005500] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/01/2017] [Accepted: 04/04/2017] [Indexed: 12/14/2022] Open
Abstract
Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants. We address the problem of how to distinguish which of the many thousands of DNA sequence variants carried by an individual with a rare disease is responsible for the disease phenotypes. This can help clinicians arrive at a diagnosis, but also can be instrumental in improving our understanding of the pathobiology of the disease. Many methods are currently available to help with the problem of determining causative variant, using information about evolutionary conservation and prediction of the functional consequences of the sequence variant. We have developed a novel algorithm (PVP) which augments existing strategies by using the similarity of the patients phenotype to known phenotype-genotype data in human and model organism databases to further rank potential candidate genes. In a retrospective study, we apply PVP to the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism, and find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.
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Affiliation(s)
- Imane Boudellioua
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Rozaimi B. Mahamad Razali
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Maxat Kulmanov
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Yasmeen Hashish
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Eva Goncalves-Serra
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Nadia Schoenmakers
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust—Medical Research Council, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Georgios V. Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
- Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (GVG); (PNS); (RH)
| | - Paul N. Schofield
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (GVG); (PNS); (RH)
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
- * E-mail: (GVG); (PNS); (RH)
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75
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Köhler S, Robinson PN. [Diagnostics in human genetics : Integration of phenotypic and genomic data]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2017; 60:542-549. [PMID: 28293716 DOI: 10.1007/s00103-017-2538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The development of reliable methods for annotation of clinical phenotypes and algorithms to calculate similarity values for clinical phenotype profiles will be a major challenge for genomic personalized medicine, since combined analysis of phenotypic features and genetic variants can increase diagnostic yield, especially with exome or genome sequencing. The Human Phenotype Ontology project (HPO; www.human-phenotype-ontology.org ) provides an ontology for capturing phenotypic abnormalities in human disease in a precise and comprehensive fashion. The HPO not only enables reliable integration of disease-relevant information from numerous databases, but it also allows for similarity between patients or between patients and disease descriptions to be calculated algorithmically. The HPO thereby represents a solid foundation for differential diagnostic applications as well as for translational research and prioritization of novel disease genes in exome or genome sequencing projects.
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Affiliation(s)
- Sebastian Köhler
- NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland.
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, 06032, Farmington, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, USA
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76
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Kernohan KD, Dyment DA, Pupavac M, Cramer Z, McBride A, Bernard G, Straub I, Tetreault M, Hartley T, Huang L, Sell E, Majewski J, Rosenblatt DS, Shoubridge E, Mhanni A, Myers T, Proud V, Vergano S, Spangler B, Farrow E, Kussman J, Safina N, Saunders C, Boycott KM, Thiffault I. Matchmaking facilitates the diagnosis of an autosomal-recessive mitochondrial disease caused by biallelic mutation of the tRNA isopentenyltransferase (TRIT1
) gene. Hum Mutat 2017; 38:511-516. [DOI: 10.1002/humu.23196] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Kristin D. Kernohan
- Children's Hospital of Eastern Ontario Research Institute; Ottawa Ontario Canada
| | - David A. Dyment
- Children's Hospital of Eastern Ontario Research Institute; Ottawa Ontario Canada
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - Mihaela Pupavac
- Department of Human Genetics; McGill University; Montréal Québec Canada
| | - Zvi Cramer
- Department of Human Genetics; McGill University; Montréal Québec Canada
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute; Ottawa Ontario Canada
| | - Genevieve Bernard
- Department of Human Genetics; McGill University; Montréal Québec Canada
| | - Isabella Straub
- Department of Human Genetics; McGill University; Montréal Québec Canada
| | - Martine Tetreault
- McGill University and Genome Quebec Innovation Centre; Montreal Quebec Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute; Ottawa Ontario Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute; Ottawa Ontario Canada
| | - Erick Sell
- Division of Neurology; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - Jacek Majewski
- Department of Human Genetics; McGill University; Montréal Québec Canada
- McGill University and Genome Quebec Innovation Centre; Montreal Quebec Canada
| | | | - Eric Shoubridge
- Department of Human Genetics; McGill University; Montréal Québec Canada
| | - Aziz Mhanni
- Section of Genetics and Metabolism; Children's Hospital and the Department of Pediatrics and Child Health; University of Manitoba; Winnipeg Manitoba Canada
| | - Tara Myers
- Department of Pediatrics; Children's Mercy Hospitals; Kansas City Missouri
| | - Virginia Proud
- Division of Medical Genetics and Metabolism; Children's Hospital of the King's Daughters; Norfolk Virginia
| | - Samanta Vergano
- Division of Medical Genetics and Metabolism; Children's Hospital of the King's Daughters; Norfolk Virginia
| | - Brooke Spangler
- Division of Medical Genetics and Metabolism; Children's Hospital of the King's Daughters; Norfolk Virginia
| | - Emily Farrow
- Center for Pediatric Genomic Medicine; Children's Mercy Hospital; Kansas City Missouri
- University of Missouri-Kansas City School of Medicine; Kansas City Missouri
| | - Jennifer Kussman
- Department of Pediatrics; Children's Mercy Hospitals; Kansas City Missouri
| | - Nicole Safina
- Department of Pediatrics; Children's Mercy Hospitals; Kansas City Missouri
| | - Carol Saunders
- Center for Pediatric Genomic Medicine; Children's Mercy Hospital; Kansas City Missouri
- University of Missouri-Kansas City School of Medicine; Kansas City Missouri
| | - Kym M. Boycott
- Children's Hospital of Eastern Ontario Research Institute; Ottawa Ontario Canada
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine; Children's Mercy Hospital; Kansas City Missouri
- University of Missouri-Kansas City School of Medicine; Kansas City Missouri
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77
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Ramoni RB, Mulvihill JJ, Adams DR, Allard P, Ashley EA, Bernstein JA, Gahl WA, Hamid R, Loscalzo J, McCray AT, Shashi V, Tifft CJ, Wise AL, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernick D, Bernstein JA, Bican A, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brownstein CA, Brush M, Burke EA, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eastwood R, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Iglesias B, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Martin C, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Robertson AK, Rodan LH, Rosenfeld JA, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tifft CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. The Undiagnosed Diseases Network: Accelerating Discovery about Health and Disease. Am J Hum Genet 2017; 100:185-192. [PMID: 28157539 PMCID: PMC5294757 DOI: 10.1016/j.ajhg.2017.01.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/30/2016] [Indexed: 01/07/2023] Open
Abstract
Diagnosis at the edges of our knowledge calls upon clinicians to be data driven, cross-disciplinary, and collaborative in unprecedented ways. Exact disease recognition, an element of the concept of precision in medicine, requires new infrastructure that spans geography, institutional boundaries, and the divide between clinical care and research. The National Institutes of Health (NIH) Common Fund supports the Undiagnosed Diseases Network (UDN) as an exemplar of this model of precise diagnosis. Its goals are to forge a strategy to accelerate the diagnosis of rare or previously unrecognized diseases, to improve recommendations for clinical management, and to advance research, especially into disease mechanisms. The network will achieve these objectives by evaluating patients with undiagnosed diseases, fostering a breadth of expert collaborations, determining best practices for translating the strategy into medical centers nationwide, and sharing findings, data, specimens, and approaches with the scientific and medical communities. Building the UDN has already brought insights to human and medical geneticists. The initial focus has been on data sharing, establishing common protocols for institutional review boards and data sharing, creating protocols for referring and evaluating patients, and providing DNA sequencing, metabolomic analysis, and functional studies in model organisms. By extending this precision diagnostic model nationally, we strive to meld clinical and research objectives, improve patient outcomes, and contribute to medical science.
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78
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Oud MM, Tuijnenburg P, Hempel M, van Vlies N, Ren Z, Ferdinandusse S, Jansen MH, Santer R, Johannsen J, Bacchelli C, Alders M, Li R, Davies R, Dupuis L, Cale CM, Wanders RJA, Pals ST, Ocaka L, James C, Müller I, Lehmberg K, Strom T, Engels H, Williams HJ, Beales P, Roepman R, Dias P, Brunner HG, Cobben JM, Hall C, Hartley T, Le Quesne Stabej P, Mendoza-Londono R, Davies EG, de Sousa SB, Lessel D, Arts HH, Kuijpers TW. Mutations in EXTL3 Cause Neuro-immuno-skeletal Dysplasia Syndrome. Am J Hum Genet 2017; 100:281-296. [PMID: 28132690 DOI: 10.1016/j.ajhg.2017.01.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/03/2017] [Indexed: 12/16/2022] Open
Abstract
EXTL3 regulates the biosynthesis of heparan sulfate (HS), important for both skeletal development and hematopoiesis, through the formation of HS proteoglycans (HSPGs). By whole-exome sequencing, we identified homozygous missense mutations c.1382C>T, c.1537C>T, c.1970A>G, and c.2008T>G in EXTL3 in nine affected individuals from five unrelated families. Notably, we found the identical homozygous missense mutation c.1382C>T (p.Pro461Leu) in four affected individuals from two unrelated families. Affected individuals presented with variable skeletal abnormalities and neurodevelopmental defects. Severe combined immunodeficiency (SCID) with a complete absence of T cells was observed in three families. EXTL3 was most abundant in hematopoietic stem cells and early progenitor T cells, which is in line with a SCID phenotype at the level of early T cell development in the thymus. To provide further support for the hypothesis that mutations in EXTL3 cause a neuro-immuno-skeletal dysplasia syndrome, and to gain insight into the pathogenesis of the disorder, we analyzed the localization of EXTL3 in fibroblasts derived from affected individuals and determined glycosaminoglycan concentrations in these cells as well as in urine and blood. We observed abnormal glycosaminoglycan concentrations and increased concentrations of the non-sulfated chondroitin disaccharide D0a0 and the disaccharide D0a4 in serum and urine of all analyzed affected individuals. In summary, we show that biallelic mutations in EXTL3 disturb glycosaminoglycan synthesis and thus lead to a recognizable syndrome characterized by variable expression of skeletal, neurological, and immunological abnormalities.
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Affiliation(s)
- Machteld M Oud
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands.
| | - Paul Tuijnenburg
- Department of Experimental Immunology, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands; Department of Pediatric Hematology, Immunology, and Infectious disease, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Naomi van Vlies
- Laboratory Genetic Metabolic Diseases, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Zemin Ren
- Department of Pathology, Academic Medical Center, University of Amsterdam, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Machiel H Jansen
- Department of Experimental Immunology, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands; Department of Pediatric Hematology, Immunology, and Infectious disease, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Chiara Bacchelli
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Marielle Alders
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Génome Québec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Rosalind Davies
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Lucie Dupuis
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Catherine M Cale
- Department of Immunology, Great Ormond Street Hospital, WC1N 3JH London, UK
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Steven T Pals
- Department of Pathology, Academic Medical Center, University of Amsterdam, PO Box 22660, 1100 DD Amsterdam, the Netherlands
| | - Louise Ocaka
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Chela James
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Ingo Müller
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Kai Lehmberg
- Division of Pediatric Stem Cell Transplantation and Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tim Strom
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 München, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
| | - Hywel J Williams
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Phil Beales
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Patricia Dias
- Serviςo de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, 1640-035 Lisboa, Portugal
| | - Han G Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Jan-Maarten Cobben
- Department of Pediatrics, Academic Medical Center University Hospital, PO Box 22660, 1100 DD Amsterdam, the Netherlands; Department of Clinical Genetics, St. George's University Hospital, SW19 0ER London, UK
| | - Christine Hall
- Emerita, Department of Radiology, Great Ormond Street Hospital, WC1N 3JH London, UK
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8 L1, Canada
| | - Polona Le Quesne Stabej
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Roberto Mendoza-Londono
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada
| | - E Graham Davies
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK; Department of Immunology, Great Ormond Street Hospital, WC1N 3JH London, UK
| | - Sérgio B de Sousa
- COSgene, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK; Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, 3000-602 Coimbra, Portugal; Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Heleen H Arts
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, PO Box 9101, 6500 HB Nijmegen, the Netherlands; Department of Pathology and Molecular Medicine, McMaster University Medical Centre, Hamilton, ON L8S 4J9, Canada
| | - Taco W Kuijpers
- Department of Experimental Immunology, Academic Medical Centre, PO Box 22660, 1100 DD Amsterdam, the Netherlands.
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79
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Glueck M, Gvozdik A, Chevalier F, Khan A, Brudno M, Wigdor D. PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2017; 23:191-200. [PMID: 27514055 DOI: 10.1109/tvcg.2016.2598469] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cross-sectional phenotype studies are used by genetics researchers to better understand how phenotypes vary across patients with genetic diseases, both within and between cohorts. Analyses within cohorts identify patterns between phenotypes and patients (e.g., co-occurrence) and isolate special cases (e.g., potential outliers). Comparing the variation of phenotypes between two cohorts can help distinguish how different factors affect disease manifestation (e.g., causal genes, age of onset, etc.). PhenoStacks is a novel visual analytics tool that supports the exploration of phenotype variation within and between cross-sectional patient cohorts. By leveraging the semantic hierarchy of the Human Phenotype Ontology, phenotypes are presented in context, can be grouped and clustered, and are summarized via overviews to support the exploration of phenotype distributions. The design of PhenoStacks was motivated by formative interviews with genetics researchers: we distil high-level tasks, present an algorithm for simplifying ontology topologies for visualization, and report the results of a deployment evaluation with four expert genetics researchers. The results suggest that PhenoStacks can help identify phenotype patterns, investigate data quality issues, and inform data collection design.
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80
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Taruscio D, Floridia G, Salvatore M, Groft SC, Gahl WA. Undiagnosed Diseases: Italy-US Collaboration and International Efforts to Tackle Rare and Common Diseases Lacking a Diagnosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1031:25-38. [PMID: 29214564 DOI: 10.1007/978-3-319-67144-4_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rare diseases (RD), according to European Union criteria, affect 5 per 10,000 persons, or 30 million people, in the EU; in the USA, RD are defined as conditions that affect fewer than 200,000 individuals in the population (320 million). Most known rare disorders are severe and chronic, with many being degenerative and life threatening. There are roughly 5000-8000 rare diseases (European Commission, DG Health and Food Safety, Public Health, Rare Diseases, Policy.http://ec.europa.eu/health/rare_diseases/policy/index_en.htm. Accessed 19 December 2016; NORD-The National Organization for Rare Diseases: https://rarediseases.org/). Patient populations for individual RD are small and scattered; international collaborations are crucial to pool resources fragmented across individual countries for better diagnosis and treatment. Undiagnosed RD (URD) are conditions that elude diagnosis; some patients wait years for a definitive diagnosis. URD may include groups of unnamed disorders with common characteristics, phenotypically well described diseases, diseases with an unknown molecular basis, or those due to unknown, non-genetic factors.The US NIH Undiagnosed Diseases Program arose in 2008 to provide a diagnosis for individuals who had long sought one without success; in 2013 a nationwide Undiagnosed Diseases Network was established in the United States. In 2015, the Undiagnosed Disease Network International (UDNI) was established and includes US, Australia, Canada, Japan, Italy and other European countries. Other national initiatives have also been undertaken and are in progress all over the world.
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Affiliation(s)
- Domenica Taruscio
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy.
| | - Giovanna Floridia
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy.,Bioethics Unit, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Marco Salvatore
- Centro Nazionale Malattie Rare, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italy
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- Undiagnosed Diseases Program, Common Fund, National Institutes of Health, Rockville, MD, USA.,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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81
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Improved Diagnosis and Care for Rare Diseases through Implementation of Precision Public Health Framework. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1031:55-94. [PMID: 29214566 DOI: 10.1007/978-3-319-67144-4_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Public health relies on technologies to produce and analyse data, as well as effectively develop and implement policies and practices. An example is the public health practice of epidemiology, which relies on computational technology to monitor the health status of populations, identify disadvantaged or at risk population groups and thereby inform health policy and priority setting. Critical to achieving health improvements for the underserved population of people living with rare diseases is early diagnosis and best care. In the rare diseases field, the vast majority of diseases are caused by destructive but previously difficult to identify protein-coding gene mutations. The reduction in cost of genetic testing and advances in the clinical use of genome sequencing, data science and imaging are converging to provide more precise understandings of the 'person-time-place' triad. That is: who is affected (people); when the disease is occurring (time); and where the disease is occurring (place). Consequently we are witnessing a paradigm shift in public health policy and practice towards 'precision public health'.Patient and stakeholder engagement has informed the need for a national public health policy framework for rare diseases. The engagement approach in different countries has produced highly comparable outcomes and objectives. Knowledge and experience sharing across the international rare diseases networks and partnerships has informed the development of the Western Australian Rare Diseases Strategic Framework 2015-2018 (RD Framework) and Australian government health briefings on the need for a National plan.The RD Framework is guiding the translation of genomic and other technologies into the Western Australian health system, leading to greater precision in diagnostic pathways and care, and is an example of how a precision public health framework can improve health outcomes for the rare diseases population.Five vignettes are used to illustrate how policy decisions provide the scaffolding for translation of new genomics knowledge, and catalyze transformative change in delivery of clinical services. The vignettes presented here are from an Australian perspective and are not intended to be comprehensive, but rather to provide insights into how a new and emerging 'precision public health' paradigm can improve the experiences of patients living with rare diseases, their caregivers and families.The conclusion is that genomic public health is informed by the individual and family needs, and the population health imperatives of an early and accurate diagnosis; which is the portal to best practice care. Knowledge sharing is critical for public health policy development and improving the lives of people living with rare diseases.
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Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJS, DeMare LE, Devereau AD, de Vries BBA, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MWM, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JOB, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN. The Human Phenotype Ontology in 2017. Nucleic Acids Res 2016; 45:D865-D876. [PMID: 27899602 PMCID: PMC5210535 DOI: 10.1093/nar/gkw1039] [Citation(s) in RCA: 501] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
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Affiliation(s)
- Sebastian Köhler
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Nicole A Vasilevsky
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Mark Engelstad
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erin Foster
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julie McMurry
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ségolène Aymé
- Institut du Cerveau et de la Moelle épinière-ICM, CNRS UMR 7225-Inserm U 1127-UPMC-P6 UMR S 1127, Hôpital Pitié-Salpêtrière, 47, bd de l'Hôpital, 75013 Paris, France
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital Department of Health, Government of Western Australia, Perth, WA 6008, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6008, Australia
| | - Susan M Bello
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Cornelius F Boerkoel
- Imagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.,NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Valentina Cipriani
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | | | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia
| | - Laura E DeMare
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Andrew D Devereau
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Daniel Greene
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Courtney Hum
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada
| | - Johanna A Jähn
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Roger James
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Roland Krause
- LuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Gholson J Lyon
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA
| | - Soichi Ogishima
- Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Tohoku Medical Megabank Organization Bldg 7F room #741,736, Seiryo 2-1, Aoba-ku, Sendai Miyagi 980-8573 Japan
| | - Annie Olry
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Willem H Ouwehand
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.,UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ana Rath
- Orphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France
| | - Franz Schaefer
- Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany
| | - Richard H Scott
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Segal
- SimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA
| | | | - Richard Sever
- Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA
| | - Cynthia L Smith
- The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Catherine Turner
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK
| | - Marijcke W M Veltman
- NIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Tom Vulliamy
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Julie von Ziegenweidt
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK
| | - Andreas Zankl
- Discipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.,Academic Department of Medical Genetics, Sydney Childrens Hospitals Network (Westmead), Australia
| | - Stephan Züchner
- JD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Tomasz Zemojtel
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Julius O B Jacobsen
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Tudor Groza
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.,St Vincent's Clinical School, Faculty of Medicine, UNSW Australia
| | - Damian Smedley
- Genomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa Haendel
- Library and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA .,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
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83
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Brown SA. Patient Similarity: Emerging Concepts in Systems and Precision Medicine. Front Physiol 2016; 7:561. [PMID: 27932992 PMCID: PMC5121278 DOI: 10.3389/fphys.2016.00561] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sherry-Ann Brown
- Department of Cardiovascular Diseases, Mayo Clinic Rochester, MN, USA
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84
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'IRDiRC Recognized Resources': a new mechanism to support scientists to conduct efficient, high-quality research for rare diseases. Eur J Hum Genet 2016; 25:162-165. [PMID: 27782107 PMCID: PMC5255942 DOI: 10.1038/ejhg.2016.137] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/06/2016] [Indexed: 01/25/2023] Open
Abstract
The International Rare Diseases Research Consortium (IRDiRC) has created a quality label, 'IRDiRC Recognized Resources', formerly known as 'IRDiRC Recommended'. It is a peer-reviewed quality indicator process established based on the IRDiRC Policies and Guidelines to designate resources (ie, standards, guidelines, tools, and platforms) designed to accelerate the pace of discoveries and translation into clinical applications for the rare disease (RD) research community. In its first year of implementation, 13 resources successfully applied for this designation, each focused on key areas essential to IRDiRC objectives and to the field of RD research more broadly. These included data sharing for discovery, knowledge organisation and ontologies, networking patient registries, and therapeutic development. 'IRDiRC Recognized Resources' is a mechanism aimed to provide community-approved contributions to RD research higher visibility, and encourage researchers to adopt recognised standards, guidelines, tools, and platforms that facilitate research advances guided by the principles of interoperability and sharing.
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85
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Registered access: a 'Triple-A' approach. Eur J Hum Genet 2016; 24:1676-1680. [PMID: 27677416 PMCID: PMC5117919 DOI: 10.1038/ejhg.2016.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/28/2016] [Accepted: 07/19/2016] [Indexed: 01/15/2023] Open
Abstract
We propose a standard model for a novel data access tier – registered access – to facilitate access to data that cannot be published in open access archives owing to ethical and legal risk. Based on an analysis of applicable research ethics and other legal and administrative frameworks, we discuss the general characteristics of this Registered Access Model, which would comprise a three-stage approval process: Authentication, Attestation and Authorization. We are piloting registered access with the Demonstration Projects of the Global Alliance for Genomics and Health for which it may provide a suitable mechanism for access to certain data types and to different types of data users.
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86
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Du C, Pusey BN, Adams CJ, Lau CC, Bone WP, Gahl WA, Markello TC, Adams DR. Explorations to improve the completeness of exome sequencing. BMC Med Genomics 2016; 9:56. [PMID: 27568008 PMCID: PMC5002202 DOI: 10.1186/s12920-016-0216-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 08/05/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Exome sequencing has advanced to clinical practice and proven useful for obtaining molecular diagnoses in rare diseases. In approximately 75 % of cases, however, a clinical exome study does not produce a definitive molecular diagnosis. These residual cases comprise a new diagnostic challenge for the genetics community. The Undiagnosed Diseases Program of the National Institutes of Health routinely utilizes exome sequencing for refractory clinical cases. Our preliminary data suggest that disease-causing variants may be missed by current standard-of-care clinical exome analysis. Such false negatives reflect limitations in experimental design, technical performance, and data analysis. RESULTS We present examples from our datasets to quantify the analytical performance associated with current practices, and explore strategies to improve the completeness of data analysis. In particular, we focus on patient ascertainment, exome capture, inclusion of intronic variants, and evaluation of medium-sized structural variants. CONCLUSIONS The strategies we present may recover previously-missed, disease causing variants in second-pass exome analysis. Understanding the limitations of the current clinical exome search space provides a rational basis to improve methods for disease variant detection using genome-scale sequencing techniques.
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Affiliation(s)
- Chen Du
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Barbara N Pusey
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Christopher J Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - C Christopher Lau
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William P Bone
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Thomas C Markello
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, National Institutes of Health, National Human Genome Research Institute, Bethesda, MD, USA.
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87
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Shafie AA, Chaiyakunapruk N, Supian A, Lim J, Zafra M, Hassali MAA. State of rare disease management in Southeast Asia. Orphanet J Rare Dis 2016; 11:107. [PMID: 27484654 PMCID: PMC4969672 DOI: 10.1186/s13023-016-0460-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/27/2016] [Indexed: 12/20/2022] Open
Abstract
Background Rare diseases, also referred to as orphan diseases, are characterised by their low prevalence with majority of them are chronically debilitating and life threatening. Given the low prevalence and the widely dispersed but very small patient base for each disease, there may often be a disproportion in the availability of treatments and resources to manage patients, spur research and train experts. This is especially true in Southeast Asian countries that are currently in the process of implementing or revising their universal health coverage schemes. This paper aims to examine the status of rare disease management in Southeast Asian countries. It will serve as the basis for a more active discussion on how countries in the region can address an under-recognised rare disease burden and enhance national and regional capacities. Methods The study consists of literature reviews and key stakeholders interviews in six focus countries, including the Philippines, Singapore, Malaysia, Indonesia, Vietnam, and Thailand and five countries as best practice, comprising of France, Canada, Australia, Taiwan, and South Korea. Rare disease management initiatives across each country were examined based on the World Health Organization’s framework for action in strengthening health systems. Results The results suggest rare disease management remains challenging across Southeast Asia, as many of the focus countries face fundamental issues from basic healthcare systems to funding. Nonetheless, there are substantial improvement opportunities, including leveraging best practices from around the world and organising a multi-stakeholder and regional approach and strategy. Conclusions Southeast Asian countries have made significant progress in the management of rare disease, but there remain key areas for substantial development opportunities.
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Affiliation(s)
- Asrul Akmal Shafie
- Social and Administrative Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia.
| | - Nathorn Chaiyakunapruk
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor, Malaysia.,Center of Pharmaceutical Outcomes Research, Faculty of Pharmaceutical Sciences, Naresuan University, Phitsanulok, Thailand.,School of Pharmacy, University of Wisconsin, Madison, WI, USA.,School of Population Health, University of Queensland, Brisbane, QLD, Australia
| | - Azuwana Supian
- Social and Administrative Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Jeremy Lim
- Health & Life Sciences, Asia-Pacific, Oliver Wyman, Singapore, Singapore
| | - Matt Zafra
- Health & Life Sciences, Asia-Pacific, Oliver Wyman, Singapore, Singapore
| | - Mohamed Azmi Ahmad Hassali
- Social and Administrative Pharmacy, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
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88
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Landis BJ, Ware SM. The Current Landscape of Genetic Testing in Cardiovascular Malformations: Opportunities and Challenges. Front Cardiovasc Med 2016; 3:22. [PMID: 27504451 PMCID: PMC4959014 DOI: 10.3389/fcvm.2016.00022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/30/2016] [Indexed: 12/21/2022] Open
Abstract
Human cardiovascular malformations (CVMs) frequently have a genetic contribution. Through the application of novel technologies, such as next-generation sequencing, DNA sequence variants associated with CVMs are being identified at a rapid pace. While clinicians are now able to offer testing with NGS gene panels or whole exome sequencing to any patient with a CVM, the interpretation of genetic variation remains problematic. Variable phenotypic expression, reduced penetrance, inconsistent phenotyping methods, and the lack of high-throughput functional testing of variants contribute to these challenges. This article elaborates critical issues that impact the decision to broadly implement clinical molecular genetic testing in CVMs. Major benefits of testing include establishing a genetic diagnosis, facilitating cost-effective screening of family members who may have subclinical disease, predicting recurrence risk in offsprings, enabling early diagnosis and anticipatory management of CV and non-CV disease phenotypes, predicting long-term outcomes, and facilitating the development of novel therapies aimed at disease improvement or prevention. Limitations include financial cost, psychosocial cost, and ambiguity of interpretation of results. Multiplex families and patients with syndromic features are two groups where disease causation could potentially be firmly established. However, these account for the minority of the overall CVM population, and there is increasing recognition that genotypes previously associated with syndromes also exist in patients who lack non-CV findings. In all circumstances, ongoing dialog between cardiologists and clinical geneticists will be needed to accurately interpret genetic testing and improve these patients’ health. This may be most effectively implemented by the creation and support of CV genetics services at centers committed to pursuing testing for patients.
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Affiliation(s)
- Benjamin J Landis
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Stephanie M Ware
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
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89
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Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles. Hum Mutat 2016; 36:922-7. [PMID: 26255989 DOI: 10.1002/humu.22850] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/24/2015] [Indexed: 01/28/2023]
Abstract
Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis.
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Affiliation(s)
- Orion J Buske
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chris Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Michael Brudno
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
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90
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Lelieveld SH, Veltman JA, Gilissen C. Novel bioinformatic developments for exome sequencing. Hum Genet 2016; 135:603-14. [PMID: 27075447 PMCID: PMC4883269 DOI: 10.1007/s00439-016-1658-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/15/2016] [Indexed: 01/19/2023]
Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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91
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López E, Thompson R, Gainotti S, Wang CM, Rubinstein Y, Taruscio D, Monaco L, Lochmüller H, Alonso V, Posada de la Paz M. Overview of existing initiatives to develop and improve access and data sharing in rare disease registries and biobanks worldwide. Expert Opin Orphan Drugs 2016. [DOI: 10.1080/21678707.2016.1188002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Estrella López
- Institute of Rare Diseases Research (IIER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Rachel Thompson
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Sabina Gainotti
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Yaffa Rubinstein
- Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Domenica Taruscio
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Verónica Alonso
- Institute of Rare Diseases Research (IIER), SpainRDR & CIBERER, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Manuel Posada de la Paz
- Institute of Rare Diseases Research (IIER), SpainRDR & CIBERER, Institute of Health Carlos III (ISCIII), Madrid, Spain
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92
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A Clinician's perspective on clinical exome sequencing. Hum Genet 2016; 135:643-54. [PMID: 27126233 DOI: 10.1007/s00439-016-1662-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022]
Abstract
Clinical exome sequencing has clearly improved our ability as clinicians to identify the cause of a wide variety of disorders. Prior to exome sequencing, a majority of patients with apparent syndromes never received a specific molecular genetic diagnosis despite extensive diagnostic odysseys. Even for those receiving an answer to the question of what caused their disorder, the diagnostic odyssey often spanned years to decades. Determining the particular genetic cause in an individual patient can be challenging due to inherent phenotypic and genetic heterogeneity of disease, technical limitations of testing or both. Blended phenotypes, due to multiple monogenic disorders in the same patient, are true dilemmas for traditional genetic evaluations, but are increasingly being diagnosed through clinical exome sequencing. New sequencing technologies have increased the proportion of patients receiving molecular diagnoses, while significantly shortening the time scale, providing multiple benefits for the health-care team, patient and family.
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93
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Lelieveld SH, Veltman JA, Gilissen C. Novel bioinformatic developments for exome sequencing. Hum Genet 2016. [PMID: 27075447 DOI: 10.1007/s00439‐016‐1658‐6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
With the widespread adoption of next generation sequencing technologies by the genetics community and the rapid decrease in costs per base, exome sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of exome sequencing data, many challenges still remain; especially the increasing scale at which exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for exome sequencing and the directions that this is taking us to. With these developments, exome sequencing is paving the way for the next big challenge, the application of whole genome sequencing.
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Affiliation(s)
- Stefan H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.,Department of Clinical Genetics, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboudumc, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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94
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Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features. Genet Med 2015; 18:788-95. [PMID: 26656649 PMCID: PMC4902791 DOI: 10.1038/gim.2015.161] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/30/2015] [Indexed: 01/09/2023] Open
Abstract
PURPOSE The pace of Mendelian gene discovery is slowed by the "n-of-1 problem"-the difficulty of establishing the causality of a putatively pathogenic variant in a single person or family. Identification of an unrelated person with an overlapping phenotype and suspected pathogenic variant in the same gene can overcome this barrier, but it is often impeded by lack of a convenient or widely available way to share data on candidate variants/genes among families, clinicians, and researchers. METHODS Social networking among families, clinicians, and researchers was used to identify three children with variants of unknown significance in KDM1A and similar phenotypes. RESULTS De novo variants in KDM1A underlie a new syndrome characterized by developmental delay and distinctive facial features. CONCLUSION Social networking is a potentially powerful strategy to discover genes for rare Mendelian conditions, particularly those with nonspecific phenotypic features. To facilitate the efforts of families to share phenotypic and genomic information with each other, clinicians, and researchers, we developed the Repository for Mendelian Genomics Family Portal (RMD-FP; http://uwcmg.org/#/family). Design and development of MyGene2 (http://www.mygene2.org), a Web-based tool that enables families, clinicians, and researchers to search for gene matches based on analysis of phenotype and exome data deposited into the RMD-FP, is under way.Genet Med 18 8, 788-795.
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95
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Taruscio D, Groft SC, Cederroth H, Melegh B, Lasko P, Kosaki K, Baynam G, McCray A, Gahl WA. Undiagnosed Diseases Network International (UDNI): White paper for global actions to meet patient needs. Mol Genet Metab 2015; 116:223-5. [PMID: 26596705 DOI: 10.1016/j.ymgme.2015.11.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 11/30/2022]
Abstract
In 2008, the National Institutes of Health's (NIH) Undiagnosed Disease Program (UDP) was initiated to provide diagnoses for individuals who had long sought one without success. As a result of two international conferences (Rome 2014 and Budapest 2015), the Undiagnosed Diseases Network International (UDNI) was established, modeled in part after the NIH UDP. Undiagnosed diseases are a global health issue, calling for an international scientific and healthcare effort. To meet this demand, the UDNI has built a consensus framework of principles, best practices and governance; the Board of Directors reflects its international character, as it includes experts from Australia, Canada, Hungary, Italy, Japan and the USA. The UDNI involves centers with internationally recognized expertise, and its scientific resources and know-how aim to fill the knowledge gaps that impede diagnosis. Consequently, the UDNI fosters the translation of research into medical practice. Active patient involvement is critical; the Patient Advisory Group is expected to play an increasing role in UDNI activities. All information for physicians and patients will be available at the UDNI website.
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Affiliation(s)
- Domenica Taruscio
- National Center for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, United States
| | | | - Béla Melegh
- Department of Medical Genetics, University of Pécs, Hungary
| | - Paul Lasko
- Department of Biology, McGill University, Montreal, Canada
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Gareth Baynam
- Princess Margaret and King Edward Memorial Hospitals, Perth, Australia; Office of Population Health, Public Health Division, WA Department of Health, Australia; Telethon Kids Institute, Perth, Australia; Western Australian Registry of Developmental Anomalies, Perth, Australia; School of Paediatrics and Child Health, University of Western Australia, Perth, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Alexa McCray
- Center for Biomedical Informatics, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States
| | - William A Gahl
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, United States
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96
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Human genotype–phenotype databases: aims, challenges and opportunities. Nat Rev Genet 2015; 16:702-15. [DOI: 10.1038/nrg3932] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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97
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Lawler M, Siu LL, Rehm HL, Chanock SJ, Alterovitz G, Burn J, Calvo F, Lacombe D, Teh BT, North KN, Sawyers CL. All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health. Cancer Discov 2015; 5:1133-6. [PMID: 26526696 DOI: 10.1158/2159-8290.cd-15-0821] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The recent explosion of genetic and clinical data generated from tumor genome analysis presents an unparalleled opportunity to enhance our understanding of cancer, but this opportunity is compromised by the reluctance of many in the scientific community to share datasets and the lack of interoperability between different data platforms. The Global Alliance for Genomics and Health is addressing these barriers and challenges through a cooperative framework that encourages "team science" and responsible data sharing, complemented by the development of a series of application program interfaces that link different data platforms, thus breaking down traditional silos and liberating the data to enable new discoveries and ultimately benefit patients.
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Affiliation(s)
- Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom.
| | | | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Washington, DC
| | | | - John Burn
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Fabien Calvo
- Cancer Core Europe and Institute Gustave Roussy Cancer Campus, Grand Paris, Villejuif, France
| | - Denis Lacombe
- European Organisation for the Research and Treatment of Cancer, Brussels, Belgium
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98
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Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat 2015; 36:915-21. [PMID: 26295439 PMCID: PMC4610002 DOI: 10.1002/humu.22858] [Citation(s) in RCA: 351] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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Affiliation(s)
- Anthony A. Philippakis
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cardiology, Brigham & Women's Hospital,
Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Danielle R. Azzariti
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Barcelona,
Spain
| | | | - Catherine A. Brownstein
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Han G. Brunner
- Radboud University Medical Center,Department of Human
Genetics, PO Box 9101, 6500HB Nijmegen, The Netherlands
- Maastricht University Medical Center, Department of Clinical
Genetics,PO Box 5800, 6202AZ Maastricht, The Netherlands
| | - Orion J. Buske
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Stephanie O.M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill
University, Canada
| | - Johan T. den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center,
Leiden, Nederland
| | - Helen V. Firth
- East Anglian Medical Genetics Service, Box 134, Cambridge
University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ,
UK
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Tx 77030, U.S.A
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute,
Ottawa, ON, Canada
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Joel B. Krier
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Justin Paschall
- European Molecular Biology Laboratory - European
Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD,
UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa
Cruz, CA, USA
| | - Peter N. Robinson
- Institute for Medical Genetics and Human Genetics,
Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin,
Germany
- Institute for Bioinformatics, Department of Mathematics and
Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies, 13353
Berlin, Germany
| | | | - Nara L. Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ganesh J. Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Peter E. Taschner
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | | | | | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics
and John P. Hussman Institute for Human Genomics, University of Miami Miller School of
Medicine, Miami, FL, USA
| | - Kym M. Boycott
- Department of Genetics, Children's Hospital of Eastern
Ontario, Ottawa, Ontario, Canada
| | - Heidi L. Rehm
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
- Department of Pathology, Brigham & Women's Hospital, Boston,
MA, USA
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