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Sebastin M, Odgis J, Suckiel S, Bonini K, Di Biase M, Brown K, Marathe P, Kelly N, Ramos M, Rodriguez J, Aguiniga KL, Lopez J, Maria E, Rodriguez M, Yelton N, Cunningham-Rundles C, Gallagher K, McDonald T, McGoldrick P, Robinson M, Rubinstein A, Shulman L, Wolf S, Yozawitz E, Zinberg R, Abul-Husn N, Bauman L, Diaz G, Ferket B, Greally J, Jobanputra V, Gelb B, Horowitz C, Kenny E, Wasserstein M. eP236: TeleKidSeq: Incorporating telehealth into clinical care of children from diverse backgrounds undergoing clinical genome sequencing. Genet Med 2022. [DOI: 10.1016/j.gim.2022.01.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Belbin GM, Odgis J, Sorokin EP, Yee MC, Kohli S, Glicksberg BS, Gignoux CR, Wojcik GL, Van Vleck T, Jeff JM, Linderman M, Schurmann C, Ruderfer D, Cai X, Merkelson A, Justice AE, Young KL, Graff M, North KE, Peters U, James R, Hindorff L, Kornreich R, Edelmann L, Gottesman O, Stahl EE, Cho JH, Loos RJ, Bottinger EP, Nadkarni GN, Abul-Husn NS, Kenny EE. Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system. eLife 2017; 6:25060. [PMID: 28895531 PMCID: PMC5595434 DOI: 10.7554/elife.25060] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 08/09/2017] [Indexed: 11/16/2022] Open
Abstract
Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic BioMe biobank in New York City. By linking to medical records, we discover a locus associated with both elevated genetic relatedness and extreme short stature. We link the gene, COL27A1, with a little-known genetic disease, previously thought to be rare and recessive. We demonstrate that disease manifests in both heterozygotes and homozygotes, indicating a common collagen disorder impacting up to 2% of individuals of Puerto Rican ancestry, leading to a better understanding of the continuum of complex and Mendelian disease. Diseases often run in families. These disease are frequently linked to changes in DNA that are passed down through generations. Close family members may share these disease-causing mutations; so may distant relatives who inherited the same mutation from a common ancestor long ago. Geneticists use a method called linkage mapping to trace a disease found in multiple members of a family over generations to genetic changes in a shared ancestor. This allows scientists to pinpoint the exact place in the genome the disease-causing mutation occurred. Using computer algorithms, scientists can apply the same technique to identify mutations that distant relatives inherited from a common ancestor. Belbin et al. used this computational technique to identify a mutation that may cause unusually short stature or bone and joint problems in up to 2% of people of Puerto Rican descent. In the experiments, the genomes of about 32,000 New Yorkers who have volunteered to participate in the BioMe Biobank and their health records were used to search for genetic changes linked to extremely short stature. The search revealed that people who inherited two copies of this mutation from their parents were likely to be extremely short or to have bone and joint problems. People who inherited one copy had an increased likelihood of joint or bone problems. This mutation affects a gene responsible for making a form of protein called collagen that is important for bone growth. The analysis suggests the mutation first arose in a Native American ancestor living in Puerto Rico around the time that European colonization began. The mutation had previously been linked to a disorder called Steel syndrome that was thought to be rare. Belbin et al. showed this condition is actually fairly common in people whose ancestors recently came from Puerto Rico, but may often go undiagnosed by their physicians. The experiments emphasize the importance of including diverse populations in genetic studies, as studies of people of predominantly European descent would likely have missed the link between this disease and mutation.
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Affiliation(s)
- Gillian Morven Belbin
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Jacqueline Odgis
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Elena P Sorokin
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Sumita Kohli
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Benjamin S Glicksberg
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States.,Harris Center for Precision Wellness, Icahn School of Medicine at Mt Sinai, New York, United States
| | - Christopher R Gignoux
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Janina M Jeff
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Michael Linderman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Douglas Ruderfer
- Broad Institute, Cambridge, United States.,Division of Psychiatric Genomics, Icahn School of Medicine at Mt Sinai, New York, United States.,Center for Statistical Genetics, Icahn School of Medicine at Mt Sinai, New York, United States
| | - Xiaoqiang Cai
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Amanda Merkelson
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Misa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Epidemiology, University of Washington School of Public Health, Seattle, United States
| | - Regina James
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, United States
| | - Lucia Hindorff
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Ruth Kornreich
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Lisa Edelmann
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Eli Ea Stahl
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States.,Harris Center for Precision Wellness, Icahn School of Medicine at Mt Sinai, New York, United States.,Broad Institute, Cambridge, United States
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ruth Jf Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Noura S Abul-Husn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Eimear E Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States.,Center for Statistical Genetics, Icahn School of Medicine at Mt Sinai, New York, United States
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Weitzel KW, Alexander M, Bernhardt BA, Calman N, Carey DJ, Cavallari LH, Field JR, Hauser D, Junkins HA, Levin PA, Levy K, Madden EB, Manolio TA, Odgis J, Orlando LA, Pyeritz R, Wu RR, Shuldiner AR, Bottinger EP, Denny JC, Dexter PR, Flockhart DA, Horowitz CR, Johnson JA, Kimmel SE, Levy MA, Pollin TI, Ginsburg GS. The IGNITE network: a model for genomic medicine implementation and research. BMC Med Genomics 2016; 9:1. [PMID: 26729011 PMCID: PMC4700677 DOI: 10.1186/s12920-015-0162-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/17/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Patients, clinicians, researchers and payers are seeking to understand the value of using genomic information (as reflected by genotyping, sequencing, family history or other data) to inform clinical decision-making. However, challenges exist to widespread clinical implementation of genomic medicine, a prerequisite for developing evidence of its real-world utility. METHODS To address these challenges, the National Institutes of Health-funded IGNITE (Implementing GeNomics In pracTicE; www.ignite-genomics.org ) Network, comprised of six projects and a coordinating center, was established in 2013 to support the development, investigation and dissemination of genomic medicine practice models that seamlessly integrate genomic data into the electronic health record and that deploy tools for point of care decision making. IGNITE site projects are aligned in their purpose of testing these models, but individual projects vary in scope and design, including exploring genetic markers for disease risk prediction and prevention, developing tools for using family history data, incorporating pharmacogenomic data into clinical care, refining disease diagnosis using sequence-based mutation discovery, and creating novel educational approaches. RESULTS This paper describes the IGNITE Network and member projects, including network structure, collaborative initiatives, clinical decision support strategies, methods for return of genomic test results, and educational initiatives for patients and providers. Clinical and outcomes data from individual sites and network-wide projects are anticipated to begin being published over the next few years. CONCLUSIONS The IGNITE Network is an innovative series of projects and pilot demonstrations aiming to enhance translation of validated actionable genomic information into clinical settings and develop and use measures of outcome in response to genome-based clinical interventions using a pragmatic framework to provide early data and proofs of concept on the utility of these interventions. Through these efforts and collaboration with other stakeholders, IGNITE is poised to have a significant impact on the acceleration of genomic information into medical practice.
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Affiliation(s)
- Kristin Wiisanen Weitzel
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida (UF) College of Pharmacy, Gainesville, FL, USA.
| | - Madeline Alexander
- Center for Therapeutic Effectiveness Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Neil Calman
- Institute for Family Health, New York, NY, USA.
| | - David J Carey
- Weis Center for Research, Geisinger Health System, Danville, PA, USA.
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida (UF) College of Pharmacy, Gainesville, FL, USA.
| | - Julie R Field
- Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, TN, USA.
| | | | - Heather A Junkins
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Phillip A Levin
- Bay West Endocrinology Associates and MODEL Clinical Research, Baltimore, MD, USA.
| | - Kenneth Levy
- Department of Medicine, Indiana University School of Medicine, Indiana, IN, USA.
| | - Ebony B Madden
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Jacqueline Odgis
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lori A Orlando
- Division of General Internal Medicine, Department of Medicine, Duke University Medical Center, Durham, NC, USA.
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, 101 Science Dr, Rm 2111, CIEMAS Bldg, Durham, NC, 27708, USA.
| | - Reed Pyeritz
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - R Ryanne Wu
- Division of General Internal Medicine, Department of Medicine, Duke University Medical Center, Durham, NC, USA.
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, 101 Science Dr, Rm 2111, CIEMAS Bldg, Durham, NC, 27708, USA.
| | - Alan R Shuldiner
- University of Maryland School of Medicine, Baltimore, MD, USA.
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Joshua C Denny
- Departments of Biomedical Informatics and Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of General Internal Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Paul R Dexter
- Department of Medicine, Indiana University School of Medicine, Indiana, IN, USA.
| | - David A Flockhart
- Department of Medicine, Indiana University School of Medicine, Indiana, IN, USA.
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida (UF) College of Pharmacy, Gainesville, FL, USA.
| | - Stephen E Kimmel
- Center for Therapeutic Effectiveness Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Clinical Epidemiology and Biostatistics, Center for Therapeutic Effectiveness Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mia A Levy
- Departments of Biomedical Informatics and Medicine, Division of Hematology and Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Toni I Pollin
- University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics and Precision Medicine, Duke University Medical Center, 101 Science Dr, Rm 2111, CIEMAS Bldg, Durham, NC, 27708, USA.
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