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Costanzo MC, von Grotthuss M, Massung J, Jang D, Caulkins L, Koesterer R, Gilbert C, Welch RP, Kudtarkar P, Hoang Q, Boughton AP, Singh P, Sun Y, Duby M, Moriondo A, Nguyen T, Smadbeck P, Alexander BR, Brandes M, Carmichael M, Dornbos P, Green T, Huellas-Bruskiewicz KC, Ji Y, Kluge A, McMahon AC, Mercader JM, Ruebenacker O, Sengupta S, Spalding D, Taliun D, Smith P, Thomas MK, Akolkar B, Brosnan MJ, Cherkas A, Chu AY, Fauman EB, Fox CS, Kamphaus TN, Miller MR, Nguyen L, Parsa A, Reilly DF, Ruetten H, Wholley D, Zaghloul NA, Abecasis GR, Altshuler D, Keane TM, McCarthy MI, Gaulton KJ, Florez JC, Boehnke M, Burtt NP, Flannick J. The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits. Cell Metab 2023; 35:695-710.e6. [PMID: 36963395 PMCID: PMC10231654 DOI: 10.1016/j.cmet.2023.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 10/23/2022] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results.
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Affiliation(s)
- Maria C Costanzo
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Marcin von Grotthuss
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Jeffrey Massung
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Dongkeun Jang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Lizz Caulkins
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ryan Koesterer
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Clint Gilbert
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ryan P Welch
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Parul Kudtarkar
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Quy Hoang
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Andrew P Boughton
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Preeti Singh
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Ying Sun
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Marc Duby
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Annie Moriondo
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Trang Nguyen
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Patrick Smadbeck
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Benjamin R Alexander
- Simulation and Modeling Sciences, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - MacKenzie Brandes
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Mary Carmichael
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Peter Dornbos
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Todd Green
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Kenneth C Huellas-Bruskiewicz
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Yue Ji
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Alexandria Kluge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Josep M Mercader
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Oliver Ruebenacker
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Sebanti Sengupta
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dylan Spalding
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Daniel Taliun
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Philip Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Melissa K Thomas
- Tailored Therapeutics-Diabetes, Eli Lilly and Company, Lilly Corporate Center DC 0545, Indianapolis, IN 46285, USA
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - M Julia Brosnan
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Andriy Cherkas
- Team Early Projects Type 1 Diabetes, Therapeutic Area Diabetes and Cardiovascular Medicine, Research & Development, Sanofi, Industriepark Höchst-H831, Frankfurt am Main 65926, Germany
| | - Audrey Y Chu
- Merck Research Laboratories, Boston, MA 02115, USA
| | - Eric B Fauman
- Integrative Biology, Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | | | | | - Melissa R Miller
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA 02139, USA
| | - Lynette Nguyen
- Foundation for the National Institutes of Health, North Bethesda, MD 20852, USA
| | - Afshin Parsa
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | - Hartmut Ruetten
- CardioMetabolism & Respiratory Medicine, Boehringer Ingelheim International GmbH, 55216 Ingelheim/Rhein, Germany
| | - David Wholley
- Foundation for the National Institutes of Health, North Bethesda, MD 20852, USA
| | - Norann A Zaghloul
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Gonçalo R Abecasis
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - David Altshuler
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 9DU, UK; Oxford Centre for Diabetes Endocrinology & Metabolism, University of Oxford, Oxford OX3 7BN, UK
| | - Kyle J Gaulton
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael Boehnke
- Department of Biostatistics and The Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noël P Burtt
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA.
| | - Jason Flannick
- Programs in Metabolism and Medical & Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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