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Lewis ACF, Chisholm RL, Connolly JJ, Esplin ED, Glessner J, Gordon A, Green RC, Hakonarson H, Harr M, Holm IA, Jarvik GP, Karlson E, Kenny EE, Kottyan L, Lennon N, Linder JE, Luo Y, Martin LJ, Perez E, Puckelwartz MJ, Rasmussen-Torvik LJ, Sabatello M, Sharp RR, Smoller JW, Sterling R, Terek S, Wei WQ, Fullerton SM. Managing differential performance of polygenic risk scores across groups: Real-world experience of the eMERGE Network. Am J Hum Genet 2024:S0002-9297(24)00120-4. [PMID: 38688278 DOI: 10.1016/j.ajhg.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024] Open
Abstract
The differential performance of polygenic risk scores (PRSs) by group is one of the major ethical barriers to their clinical use. It is also one of the main practical challenges for any implementation effort. The social repercussions of how people are grouped in PRS research must be considered in communications with research participants, including return of results. Here, we outline the decisions faced and choices made by a large multi-site clinical implementation study returning PRSs to diverse participants in handling this issue of differential performance. Our approach to managing the complexities associated with the differential performance of PRSs serves as a case study that can help future implementers of PRSs to plot an anticipatory course in response to this issue.
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Affiliation(s)
- Anna C F Lewis
- Edmond and Lily Safra Center for Ethics, Harvard University, Cambridge, MA, USA; Department of Genetics, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Joe Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adam Gordon
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA; Department of Pharmacology, Northwestern University, Evanston, IL, USA
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA, USA
| | - Elizabeth Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Mass General Brigham Personalized Medicine, Boston, MA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine, New York City, NY, USA; Center for Clinical Translational Genomics, Icahn School of Medicine, New York City, NY, USA; Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine, New York City, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine, New York City, NY, USA
| | - Leah Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University, Evanston, IL, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Emma Perez
- Mass General Brigham Personalized Medicine, Boston, MA, USA
| | - Megan J Puckelwartz
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA; Department of Pharmacology, Northwestern University, Evanston, IL, USA
| | - Laura J Rasmussen-Torvik
- Center for Genetic Medicine, Northwestern University, Evanston, IL, USA; Department of Preventive Medicine, Northwestern University, Evanston, IL, USA
| | - Maya Sabatello
- Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Irving Medical Center, New York City, NY, USA; Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York City, NY, USA
| | | | - Jordan W Smoller
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA; Psychiatric & Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephanie M Fullerton
- Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA, USA
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2
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Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn NS, Arias J, Belbin G, Below JE, Berndt SI, Chung WK, Cimino JJ, Clayton EW, Connolly JJ, Crosslin DR, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth RR, Ge T, Glessner JT, Gordon AS, Patterson C, Hakonarson H, Harden M, Harr M, Hirschhorn JN, Hoggart C, Hsu L, Irvin MR, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos RJF, Luo Y, Malolepsza E, Manolio TA, Martin LJ, McCarthy L, McNally EM, Meigs JB, Mersha TB, Mosley JD, Musick A, Namjou B, Pai N, Pesce LL, Peters U, Peterson JF, Prows CA, Puckelwartz MJ, Rehm HL, Roden DM, Rosenthal EA, Rowley R, Sawicki KT, Schaid DJ, Smit RAJ, Smith JL, Smoller JW, Thomas M, Tiwari H, Toledo DM, Vaitinadin NS, Veenstra D, Walunas TL, Wang Z, Wei WQ, Weng C, Wiesner GL, Yin X, Kenny EE. Selection, optimization and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse US populations. Nat Med 2024; 30:480-487. [PMID: 38374346 PMCID: PMC10878968 DOI: 10.1038/s41591-024-02796-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Polygenic risk scores (PRSs) have improved in predictive performance, but several challenges remain to be addressed before PRSs can be implemented in the clinic, including reduced predictive performance of PRSs in diverse populations, and the interpretation and communication of genetic results to both providers and patients. To address these challenges, the National Human Genome Research Institute-funded Electronic Medical Records and Genomics (eMERGE) Network has developed a framework and pipeline for return of a PRS-based genome-informed risk assessment to 25,000 diverse adults and children as part of a clinical study. From an initial list of 23 conditions, ten were selected for implementation based on PRS performance, medical actionability and potential clinical utility, including cardiometabolic diseases and cancer. Standardized metrics were considered in the selection process, with additional consideration given to strength of evidence in African and Hispanic populations. We then developed a pipeline for clinical PRS implementation (score transfer to a clinical laboratory, validation and verification of score performance), and used genetic ancestry to calibrate PRS mean and variance, utilizing genetically diverse data from 13,475 participants of the All of Us Research Program cohort to train and test model parameters. Finally, we created a framework for regulatory compliance and developed a PRS clinical report for return to providers and for inclusion in an additional genome-informed risk assessment. The initial experience from eMERGE can inform the approach needed to implement PRS-based testing in diverse clinical settings.
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Affiliation(s)
| | - Leah C Kottyan
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Josh Arias
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gillian Belbin
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Sonja I Berndt
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - James J Cimino
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - David R Crosslin
- Tulane University, New Orleans, LA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - QiPing Feng
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Tian Ge
- Mass General Brigham, Boston, MA, USA
| | | | | | | | | | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Clive Hoggart
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Hsu
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | | | - Amit Khera
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nita Limdi
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Ruth J F Loos
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuan Luo
- Northwestern University, Evanston, IL, USA
| | | | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lisa J Martin
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Li McCarthy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tesfaye B Mersha
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | | | - Bahram Namjou
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | - Nihal Pai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | | | | | - Zhe Wang
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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3
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Linder JE, Tao R, Chung WK, Kiryluk K, Liu C, Weng C, Connolly JJ, Hakonarson H, Harr M, Leppig KA, Jarvik GP, Veenstra DL, Aufox S, Chisholm RL, Gordon AS, Hoell C, Rasmussen-Torvik LJ, Smith ME, Holm IA, Miller EM, Prows CA, Elskeally O, Kullo IJ, Lee C, Jose S, Manolio TA, Rowley R, Padi-Adjirackor NA, Wilmayani NK, City B, Wei WQ, Wiesner GL, Rahm AK, Williams JL, Williams MS, Peterson JF. Prospective, multi-site study of healthcare utilization after actionable monogenic findings from clinical sequencing. Am J Hum Genet 2023; 110:1950-1958. [PMID: 37883979 PMCID: PMC10645563 DOI: 10.1016/j.ajhg.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023] Open
Abstract
As large-scale genomic screening becomes increasingly prevalent, understanding the influence of actionable results on healthcare utilization is key to estimating the potential long-term clinical impact. The eMERGE network sequenced individuals for actionable genes in multiple genetic conditions and returned results to individuals, providers, and the electronic health record. Differences in recommended health services (laboratory, imaging, and procedural testing) delivered within 12 months of return were compared among individuals with pathogenic or likely pathogenic (P/LP) findings to matched individuals with negative findings before and after return of results. Of 16,218 adults, 477 unselected individuals were found to have a monogenic risk for arrhythmia (n = 95), breast cancer (n = 96), cardiomyopathy (n = 95), colorectal cancer (n = 105), or familial hypercholesterolemia (n = 86). Individuals with P/LP results more frequently received services after return (43.8%) compared to before return (25.6%) of results and compared to individuals with negative findings (24.9%; p < 0.0001). The annual cost of qualifying healthcare services increased from an average of $162 before return to $343 after return of results among the P/LP group (p < 0.0001); differences in the negative group were non-significant. The mean difference-in-differences was $149 (p < 0.0001), which describes the increased cost within the P/LP group corrected for cost changes in the negative group. When stratified by individual conditions, significant cost differences were observed for arrhythmia, breast cancer, and cardiomyopathy. In conclusion, less than half of individuals received billed health services after monogenic return, which modestly increased healthcare costs for payors in the year following return.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt University Medical Center, Nashville, TN 37203, USA.
| | - Ran Tao
- Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | | | | | - Cong Liu
- Columbia University, New York, NY 10032, USA
| | | | - John J Connolly
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kathleen A Leppig
- Genetic Services, Kaiser Permanente of Washington, Seattle, WA 98195, USA
| | - Gail P Jarvik
- University of Washington Medical Center, Departments of Medicine (Medical Genetics) and Genome Sciences, Seattle, WA 98195, USA
| | - David L Veenstra
- University of Washington, Department of Pharmacy, Seattle, WA 98195, USA
| | - Sharon Aufox
- Northwestern University, Center for Genetic Medicine, Chicago, IL 60611, USA
| | - Rex L Chisholm
- Northwestern University, Center for Genetic Medicine, Chicago, IL 60611, USA
| | - Adam S Gordon
- Northwestern University, Center for Genetic Medicine, Chicago, IL 60611, USA
| | - Christin Hoell
- Northwestern University, Center for Genetic Medicine, Chicago, IL 60611, USA
| | | | - Maureen E Smith
- Northwestern University, Center for Genetic Medicine, Chicago, IL 60611, USA
| | | | - Erin M Miller
- Division of Cardiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Cynthia A Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | | | | | - Sheethal Jose
- National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Teri A Manolio
- National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Robb Rowley
- National Human Genome Research Institute, Bethesda, MD 20892, USA
| | | | | | - Brittany City
- Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Wei-Qi Wei
- Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | | | | | - Janet L Williams
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
| | - Marc S Williams
- Department of Genomic Health, Geisinger, Danville, PA 17822, USA
| | - Josh F Peterson
- Vanderbilt University Medical Center, Nashville, TN 37203, USA
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4
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Connolly JJ, Berner ES, Smith M, Levy S, Terek S, Harr M, Karavite D, Suckiel S, Holm IA, Dufendach K, Nelson C, Khan A, Chisholm RL, Allworth A, Wei WQ, Bland HT, Clayton EW, Soper ER, Linder JE, Limdi NA, Miller A, Nigbur S, Bangash H, Hamed M, Sherafati A, Lewis ACF, Perez E, Orlando LA, Rakhra-Burris TK, Al-Dulaimi M, Cifric S, Scherr CL, Wynn J, Hakonarson H, Sabatello M. Education and electronic medical records and genomics network, challenges, and lessons learned from a large-scale clinical trial using polygenic risk scores. Genet Med 2023; 25:100906. [PMID: 37246632 PMCID: PMC10527667 DOI: 10.1016/j.gim.2023.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/30/2023] Open
Abstract
Polygenic risk scores (PRS) have potential to improve health care by identifying individuals that have elevated risk for common complex conditions. Use of PRS in clinical practice, however, requires careful assessment of the needs and capabilities of patients, providers, and health care systems. The electronic Medical Records and Genomics (eMERGE) network is conducting a collaborative study which will return PRS to 25,000 pediatric and adult participants. All participants will receive a risk report, potentially classifying them as high risk (∼2-10% per condition) for 1 or more of 10 conditions based on PRS. The study population is enriched by participants from racial and ethnic minority populations, underserved populations, and populations who experience poorer medical outcomes. All 10 eMERGE clinical sites conducted focus groups, interviews, and/or surveys to understand educational needs among key stakeholders-participants, providers, and/or study staff. Together, these studies highlighted the need for tools that address the perceived benefit/value of PRS, types of education/support needed, accessibility, and PRS-related knowledge and understanding. Based on findings from these preliminary studies, the network harmonized training initiatives and formal/informal educational resources. This paper summarizes eMERGE's collective approach to assessing educational needs and developing educational approaches for primary stakeholders. It discusses challenges encountered and solutions provided.
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Affiliation(s)
- John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA.
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - Maureen Smith
- Center for Genetic Medicine, Department of Medicine, Northwestern University, Chicago, IL
| | - Samuel Levy
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA
| | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA
| | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, PA
| | - Sabrina Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Kevin Dufendach
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Catrina Nelson
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Atlas Khan
- Division of Nephrology, Dept of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Aimee Allworth
- Department of Medical Genetics, University of Washington, Seattle, WA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Harris T Bland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Ellen Wright Clayton
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN; Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, TN; Vanderbilt University Law School, Nashville, TN
| | - Emily R Soper
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN; Department of Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Scott Nigbur
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Marwan Hamed
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alborz Sherafati
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Anna C F Lewis
- Edmond and Lily Safra Center for Ethics, Harvard, MA; Brigham and Women's Hospital, Boston, MA
| | - Emma Perez
- Mass General Brigham Personalized Medicine, Brigham and Women's Hospital, Boston, MA
| | | | | | | | - Selma Cifric
- Department of Biology, The College of Idaho, Caldwell, ID
| | - Courtney Lynam Scherr
- School of Communication | Department of Communication Studies, Northwestern University, Chicago, IL
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, PA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Maya Sabatello
- Center for Precision Medicine & Genomics, Department of Medicine, Columbia University Irving Medical Center, New York, NY; Division of Ethics, Department of Medical Humanities & Ethics, Columbia University Irving Medical Center, New York, NY.
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5
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Lennon NJ, Kottyan LC, Kachulis C, Abul-Husn N, Arias J, Belbin G, Below JE, Berndt S, Chung W, Cimino JJ, Clayton EW, Connolly JJ, Crosslin D, Dikilitas O, Velez Edwards DR, Feng Q, Fisher M, Freimuth R, Ge T, Glessner JT, Gordon A, Guiducci C, Hakonarson H, Harden M, Harr M, Hirschhorn J, Hoggart C, Hsu L, Irvin R, Jarvik GP, Karlson EW, Khan A, Khera A, Kiryluk K, Kullo I, Larkin K, Limdi N, Linder JE, Loos R, Luo Y, Malolepsza E, Manolio T, Martin LJ, McCarthy L, Meigs JB, Mersha TB, Mosley J, Namjou B, Pai N, Pesce LL, Peters U, Peterson J, Prows CA, Puckelwartz MJ, Rehm H, Roden D, Rosenthal EA, Rowley R, Sawicki KT, Schaid D, Schmidlen T, Smit R, Smith J, Smoller JW, Thomas M, Tiwari H, Toledo D, Vaitinadin NS, Veenstra D, Walunas T, Wang Z, Wei WQ, Weng C, Wiesner G, Xianyong Y, Kenny E. Selection, optimization, and validation of ten chronic disease polygenic risk scores for clinical implementation in diverse populations. medRxiv 2023:2023.05.25.23290535. [PMID: 37333246 PMCID: PMC10275001 DOI: 10.1101/2023.05.25.23290535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Polygenic risk scores (PRS) have improved in predictive performance supporting their use in clinical practice. Reduced predictive performance of PRS in diverse populations can exacerbate existing health disparities. The NHGRI-funded eMERGE Network is returning a PRS-based genome-informed risk assessment to 25,000 diverse adults and children. We assessed PRS performance, medical actionability, and potential clinical utility for 23 conditions. Standardized metrics were considered in the selection process with additional consideration given to strength of evidence in African and Hispanic populations. Ten conditions were selected with a range of high-risk thresholds: atrial fibrillation, breast cancer, chronic kidney disease, coronary heart disease, hypercholesterolemia, prostate cancer, asthma, type 1 diabetes, obesity, and type 2 diabetes. We developed a pipeline for clinical PRS implementation, used genetic ancestry to calibrate PRS mean and variance, created a framework for regulatory compliance, and developed a PRS clinical report. eMERGE's experience informs the infrastructure needed to implement PRS-based implementation in diverse clinical settings.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Li Hsu
- Fred Hutchinson Cancer Center and University of Washington
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ulrike Peters
- Fred Hutchinson Cancer Center and University of Washington
| | | | | | | | | | - Dan Roden
- Vanderbilt University Medical Center
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6
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Linder JE, Allworth A, Bland HT, Caraballo PJ, Chisholm RL, Clayton EW, Crosslin DR, Dikilitas O, DiVietro A, Esplin ED, Forman S, Freimuth RR, Gordon AS, Green R, Harden MV, Holm IA, Jarvik GP, Karlson EW, Labrecque S, Lennon NJ, Limdi NA, Mittendorf KF, Murphy SN, Orlando L, Prows CA, Rasmussen LV, Rasmussen-Torvik L, Rowley R, Sawicki KT, Schmidlen T, Terek S, Veenstra D, Velez Edwards DR, Absher D, Abul-Husn NS, Alsip J, Bangash H, Beasley M, Below JE, Berner ES, Booth J, Chung WK, Cimino JJ, Connolly J, Davis P, Devine B, Fullerton SM, Guiducci C, Habrat ML, Hain H, Hakonarson H, Harr M, Haverfield E, Hernandez V, Hoell C, Horike-Pyne M, Hripcsak G, Irvin MR, Kachulis C, Karavite D, Kenny EE, Khan A, Kiryluk K, Korf B, Kottyan L, Kullo IJ, Larkin K, Liu C, Malolepsza E, Manolio TA, May T, McNally EM, Mentch F, Miller A, Mooney SD, Murali P, Mutai B, Muthu N, Namjou B, Perez EF, Puckelwartz MJ, Rakhra-Burris T, Roden DM, Rosenthal EA, Saadatagah S, Sabatello M, Schaid DJ, Schultz B, Seabolt L, Shaibi GQ, Sharp RR, Shirts B, Smith ME, Smoller JW, Sterling R, Suckiel SA, Thayer J, Tiwari HK, Trinidad SB, Walunas T, Wei WQ, Wells QS, Weng C, Wiesner GL, Wiley K, Peterson JF. Returning integrated genomic risk and clinical recommendations: The eMERGE study. Genet Med 2023; 25:100006. [PMID: 36621880 PMCID: PMC10085845 DOI: 10.1016/j.gim.2023.100006] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk. METHODS To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report and will assess uptake of care recommendations after return of results. RESULTS GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022. CONCLUSION Return of a novel report for communicating monogenic, polygenic, and family history-based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.
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Affiliation(s)
- Jodell E Linder
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Harris T Bland
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Pedro J Caraballo
- Department of Internal Medicine and Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Rex L Chisholm
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University Medical Center, Nashville, TN
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA
| | - Ozan Dikilitas
- Mayo Clinician Investigator Training Program, Department of Internal Medicine and Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Alanna DiVietro
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Sophie Forman
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Robert R Freimuth
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, MN
| | - Adam S Gordon
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Richard Green
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | | | - Ingrid A Holm
- Division of Genetics and Genomics and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine and Department of Genome Science, University of Washington Medical Center, Seattle, WA
| | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sofia Labrecque
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | | | - Nita A Limdi
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Shawn N Murphy
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Lori Orlando
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University, Chicago, IL
| | | | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Konrad Teodor Sawicki
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Shannon Terek
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David Veenstra
- School of Pharmacy, University of Washington, Seattle, WA
| | - Digna R Velez Edwards
- Division of Quantitative Science, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | | | - Noura S Abul-Husn
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Hana Bangash
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Mark Beasley
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Jennifer E Below
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Eta S Berner
- Department of Health Services Administration, University of Alabama at Birmingham, Birmingham, AL
| | - James Booth
- Department of Emergency Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - James J Cimino
- Division of General Internal Medicine and the Informatics Institute, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Patrick Davis
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Beth Devine
- School of Pharmacy, University of Washington, Seattle, WA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | | | - Melissa L Habrat
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Christin Hoell
- Department of Obstetrics & Gynecology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Martha Horike-Pyne
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | - Dean Karavite
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Eimear E Kenny
- Institute for Genomic Health, Department of Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Atlas Khan
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Bruce Korf
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Leah Kottyan
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Katie Larkin
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cong Liu
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | | | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Thomas May
- Elson S. Floyd College of Medicine, Washington State University, Vancouver, WA
| | | | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alexandra Miller
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington Medical Center, Seattle, WA
| | - Priyanka Murali
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Brenda Mutai
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | - Naveen Muthu
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bahram Namjou
- The Center for Autoimmune Genomics and Etiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Mass General Brigham Personalized Medicine, Boston, MA
| | - Megan J Puckelwartz
- Department of Pharmacology, Feinberg School of Medicine, and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA
| | | | - Maya Sabatello
- Division of Nephrology, Department of Medicine & Division of Ethics, Department of Medical Humanities and Ethics, Columbia University Irving Medical Center, New York, NY
| | - Dan J Schaid
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN
| | - Baergen Schultz
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Lynn Seabolt
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN
| | - Gabriel Q Shaibi
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, AZ
| | - Richard R Sharp
- Biomedical Ethics Program, Department of Quantitative Health Science, Mayo Clinic, Rochester, MN
| | - Brian Shirts
- Department of Laboratory Medicine & Pathology, University of Washington Medical Center, Seattle, WA
| | - Maureen E Smith
- Department of Cardiology and Center for Genetic Medicine, Northwestern University, Chicago, IL
| | - Jordan W Smoller
- Department of Psychiatry and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Rene Sterling
- Division of Genomics and Society, National Human Genome Research Institute, Bethesda, MD
| | - Sabrina A Suckiel
- The Institute for Genomic Health, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jeritt Thayer
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hemant K Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Susan B Trinidad
- Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA
| | - Theresa Walunas
- Department of Medicine and Center for Health Information Partnerships, Northwestern University, Chicago, IL
| | - Wei-Qi Wei
- Department of Biomedical Informatics and Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Quinn S Wells
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, Columbia University, New York, NY
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN.
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7
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Varughese LA, Bhupathiraju M, Hoffecker G, Terek S, Harr M, Hakonarson H, Cambareri C, Marini J, Landgraf J, Chen J, Kanter G, Lau-Min KS, Massa RC, Damjanov N, Reddy NJ, Oyer RA, Teitelbaum UR, Tuteja S. Implementing Pharmacogenetic Testing in Gastrointestinal Cancers (IMPACT-GI): Study Protocol for a Pragmatic Implementation Trial for Establishing DPYD and UGT1A1 Screening to Guide Chemotherapy Dosing. Front Oncol 2022; 12:859846. [PMID: 35865463 PMCID: PMC9295185 DOI: 10.3389/fonc.2022.859846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Background Fluoropyrimidines (fluorouracil [5-FU], capecitabine) and irinotecan are commonly prescribed chemotherapy agents for gastrointestinal (GI) malignancies. Pharmacogenetic (PGx) testing for germline DPYD and UGT1A1 variants associated with reduced enzyme activity holds the potential to identify patients at high risk for severe chemotherapy-induced toxicity. Slow adoption of PGx testing in routine clinical care is due to implementation barriers, including long test turnaround times, lack of integration in the electronic health record (EHR), and ambiguity in test cost coverage. We sought to establish PGx testing in our health system following the Exploration, Preparation, Implementation, Sustainment (EPIS) framework as a guide. Our implementation study aims to address barriers to PGx testing. Methods The Implementing Pharmacogenetic Testing in Gastrointestinal Cancers (IMPACT-GI) study is a non-randomized, pragmatic, open-label implementation study at three sites within a major academic health system. Eligible patients with a GI malignancy indicated for treatment with 5-FU, capecitabine, or irinotecan will undergo PGx testing prior to chemotherapy initiation. Specimens will be sent to an academic clinical laboratory followed by return of results in the EHR with appropriate clinical decision support for the care team. We hypothesize that the availability of a rapid turnaround PGx test with specific dosing recommendations will increase PGx test utilization to guide pharmacotherapy decisions and improve patient safety outcomes. Primary implementation endpoints are feasibility, fidelity, and penetrance. Exploratory analyses for clinical effectiveness of genotyping will include assessing grade ≥3 treatment-related toxicity using available clinical data, patient-reported outcomes, and quality of life measures. Conclusion We describe the formative work conducted to prepare our health system for DPYD and UGT1A1 testing. Our prospective implementation study will evaluate the clinical implementation of this testing program and create the infrastructure necessary to ensure sustainability of PGx testing in our health system. The results of this study may help other institutions interested in implementing PGx testing in oncology care. Clinical Trial Registration https://clinicaltrials.gov/ct2/show/NCT04736472, identifier [NCT04736472].
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Affiliation(s)
- Lisa A. Varughese
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Madhuri Bhupathiraju
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Glenda Hoffecker
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Shannon Terek
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Margaret Harr
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Christine Cambareri
- Department of Pharmacy, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Jessica Marini
- Department of Pharmacy, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Jeffrey Landgraf
- Information Services Applications, Penn Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jinbo Chen
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Genevieve Kanter
- Division of Medical Ethics and Health Policy, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kelsey S. Lau-Min
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ryan C. Massa
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nevena Damjanov
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nandi J. Reddy
- Ann B. Barshinger Cancer Institute, Lancaster General Health, Penn Medicine, Lancaster, PA, United States
| | - Randall A. Oyer
- Ann B. Barshinger Cancer Institute, Lancaster General Health, Penn Medicine, Lancaster, PA, United States
| | - Ursina R. Teitelbaum
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sony Tuteja
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Sony Tuteja,
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8
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Wynn J, Milo Rasouly H, Vasquez-Loarte T, Saami AM, Weiss R, Ziniel SI, Appelbaum PS, Wright Clayton E, Christensen KD, Fasel D, Green RC, Hain HS, Harr M, Hoell C, Kullo IJ, Leppig KA, Myers MF, Pacyna JE, Perez EF, Prows CA, Kulchak Rahm A, Campbell-Salome G, Sharp RR, Smith ME, Wiesner GL, Williams JL, Blout Zawatsky CL, Gharavi AG, Chung WK, Holm IA. Do research participants share genomic screening results with family members? J Genet Couns 2021; 31:447-458. [PMID: 34665896 DOI: 10.1002/jgc4.1511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 01/25/2023]
Abstract
The public health impact of genomic screening can be enhanced by cascade testing. However, cascade testing depends on communication of results to family members. While the barriers and facilitators of family communication have been researched following clinical genetic testing, the factors impacting the dissemination of genomic screening results are unknown. Using the pragmatic Electronic Medical Records and Genomics Network-3 (eMERGE-3) study, we explored the reported sharing practices of participants who underwent genomic screening across the United States. Six eMERGE-3 sites returned genomic screening results for mostly dominant medically actionable disorders and surveyed adult participants regarding communication of results with first-degree relatives. Across the sites, 279 participants completed a 1-month and/or 6-month post-results survey. By 6 months, only 34% of the 156 respondents shared their results with all first-degree relatives and 4% did not share with any. Over a third (39%) first-degree relatives were not notified of the results. Half (53%) of participants who received their results from a genetics provider shared them with all first-degree relatives compared with 11% of participants who received their results from a non-genetics provider. The most frequent reasons for sharing were a feeling of obligation (72%) and that the information could help family members make medical decisions (72%). The most common reasons indicated for not sharing were that the family members were too young (38%), or they were not in contact (25%) or not close to them (25%). These data indicate that the professional returning the results may impact sharing patterns, suggesting that there is a need to continue to educate healthcare providers regarding approaches to facilitate sharing of genetic results within families. Finally, these data suggest that interventions to increase sharing may be universally effective regardless of the origin of the genetic result.
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Affiliation(s)
- Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Hila Milo Rasouly
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Tania Vasquez-Loarte
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Akilan M Saami
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Robyn Weiss
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Sonja I Ziniel
- Department of Pediatrics, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Center for Research on Ethical, Legal & Social Implications of Psychiatric, Neurologic & Behavior Genetics, Columbia University Irving Medical Center, New York, NY, USA
| | - Ellen Wright Clayton
- Center for Biomedical Ethics and Society and Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kurt D Christensen
- Department of Population Medicine, Precision Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care Institute, Boston, MA, USA.,Department of Population Medicine, Harvard Medical School, Boston, MA, USA
| | - David Fasel
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert C Green
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Heather S Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christin Hoell
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kathleen A Leppig
- Genetic Services and Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle, WA, USA
| | - Melanie F Myers
- Divisions of Human Genetics and Patient Services, Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Joel E Pacyna
- Biomedical Ethics Program, Mayo Clinic, Rochester, MN, USA
| | - Emma F Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | | | | | - Maureen E Smith
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Medicine, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Ali G Gharavi
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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9
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Khan SS, Hoell C, Castillo LM, Connolly JJ, Crosslin DR, Chung WK, Gordon AS, Harr M, Jarvik GP, Kullo I, Larson EB, Leppig KA, Manolio T, Pacheco JA, Ralston JD, Puckelwartz MJ, Smith ME, Wells Q, McNally EM, Rasmussen-Torvik LJ. Practice Patterns After Return of Rare Variants Associated With Cardiomyopathy in the Electronic Medical Records and Genomics Network. Circ Heart Fail 2021; 14:e008155. [PMID: 33951936 DOI: 10.1161/circheartfailure.120.008155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Sadiya S Khan
- Division of Cardiology, Department of Medicine (S.S.K., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Department of Preventive Medicine (S.S.K., L.J.R.-T.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Christin Hoell
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Lisa M Castillo
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, PA (J.J.C., M.H.)
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education (D.R.C.), University of Washington Medical Center, Seattle
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University School of Medicine, New York, NY (W.K.C.)
| | - Adam S Gordon
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Margaret Harr
- Center for Applied Genomics, The Children's Hospital of Philadelphia, PA (J.J.C., M.H.)
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences (G.P.J.), University of Washington Medical Center, Seattle
| | - Iftikhar Kullo
- Department of Cardiovascular Medicine and the Gonda Vascular Center, Mayo Clinic, Rochester, MN (I.K.)
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle (E.B.L., K.A.L., J.D.R.)
| | - Kathleen A Leppig
- Kaiser Permanente Washington Health Research Institute, Seattle (E.B.L., K.A.L., J.D.R.)
| | - Teri Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD (T.M.)
| | - Jennifer A Pacheco
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - James D Ralston
- Kaiser Permanente Washington Health Research Institute, Seattle (E.B.L., K.A.L., J.D.R.)
| | - Megan J Puckelwartz
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Maureen E Smith
- Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Quinn Wells
- Department of Medicine, Vanderbilt University Medical Center. Nashville, TN (Q.W.)
| | - Elizabeth M McNally
- Division of Cardiology, Department of Medicine (S.S.K., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL.,Center for Genetic Medicine (C.H., L.M.C., A.D.G., J.A.P., M.J.P., M.E.S., E.M.M.), Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine (S.S.K., L.J.R.-T.), Feinberg School of Medicine, Northwestern University, Chicago, IL
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10
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Leung ML, McAdoo S, Watson D, Stumm K, Harr M, Wang X, Chung CH, Mafra F, Nesbitt AI, Hakonarson H, Santani A. A Transparent Approach to Calculate Detection Rate and Residual Risk for Carrier Screening. J Mol Diagn 2021; 23:91-102. [PMID: 33349347 DOI: 10.1016/j.jmoldx.2020.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/05/2020] [Accepted: 10/14/2020] [Indexed: 01/25/2023] Open
Abstract
Carrier screening involves detection of carrier status for genes associated with recessive conditions. A negative carrier screening test result bears a nonzero residual risk (RR) for the individual to have an affected child. The RR depends on the prevalence of specific conditions and the detection rate (DR) of the test itself. Herein, we provide a detailed approach for calculating DR and RR. DR was calculated on the basis of the sum of disease allele frequencies (DAFs) of pathogenic variants found in published literature. As a proof of concept, DAF data for cystic fibrosis were compared with society guidelines. The DAF data calculated by this method were consistent with the published cystic fibrosis guideline. In addition, we compared DAF for four genes (ABCC8, ASPA, GAA, and MMUT) across three laboratories, and outlined the likely reasons for discrepancies between these laboratories. The utility of carrier screening is to support couples with information while making reproductive choices. Accurate development of DR and RR is therefore critical. The method described herein provides an unbiased and transparent process to collect, calculate, and report these data.
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Affiliation(s)
- Marco L Leung
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio.
| | | | - Deborah Watson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Departments of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Kallyn Stumm
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Xiang Wang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Christine H Chung
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Fernanda Mafra
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Addie I Nesbitt
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Departments of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Avni Santani
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
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11
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Hoell C, Wynn J, Rasmussen LV, Marsolo K, Aufox SA, Chung WK, Connolly JJ, Freimuth RR, Kochan D, Hakonarson H, Harr M, Holm IA, Kullo IJ, Lammers PE, Leppig KA, Leslie ND, Myers MF, Sharp RR, Smith ME, Prows CA. Participant choices for return of genomic results in the eMERGE Network. Genet Med 2020; 22:1821-1829. [PMID: 32669677 DOI: 10.1038/s41436-020-0905-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Secondary findings are typically offered in an all or none fashion when sequencing is used for clinical purposes. This study aims to describe the process of offering categorical and granular choices for results in a large research consortium. METHODS Within the third phase of the electronic MEdical Records and GEnomics (eMERGE) Network, several sites implemented studies that allowed participants to choose the type of results they wanted to receive from a multigene sequencing panel. Sites were surveyed to capture the details of the implementation protocols and results of these choices. RESULTS Across the ten eMERGE sites, 4664 participants including adolescents and adults were offered some type of choice. Categories of choices offered and methods for selecting categories varied. Most participants (94.5%) chose to learn all genetic results, while 5.5% chose subsets of results. Several sites allowed participants to change their choices at various time points, and 0.5% of participants made changes. CONCLUSION Offering choices that include learning some results is important and should be a dynamic process to allow for changes in scientific knowledge, participant age group, and individual preference.
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Affiliation(s)
- Christin Hoell
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Julia Wynn
- Columbia University Irving Medical Center, New York, NY, USA
| | - Luke V Rasmussen
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Keith Marsolo
- Department of Population Health Sciences, and Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Sharon A Aufox
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Wendy K Chung
- Columbia University Irving Medical Center, New York, NY, USA
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert R Freimuth
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - David Kochan
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Margaret Harr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Nancy D Leslie
- Division of Human Genetics, Cincinnati Children's Hospital, and University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Melanie F Myers
- Division of Human Genetics, Cincinnati Children's Hospital, and University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Richard R Sharp
- Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN, USA
| | - Maureen E Smith
- Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Cynthia A Prows
- Divisions of Human Genetics and Patient Services, Cincinnati Children's Hospital, Cincinnati, OH, USA.
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12
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Lynch JA, Sharp RR, Aufox SA, Bland ST, Blout C, Bowen DJ, Buchanan AH, Halverson C, Harr M, Hebbring SJ, Henrikson N, Hoell C, Holm IA, Jarvik G, Kullo IJ, Kochan DC, Larson EB, Lazzeri A, Leppig KA, Madden J, Marasa M, Myers MF, Peterson J, Prows CA, Kulchak Rahm A, Ralston J, Milo Rasouly H, Scrol A, Smith ME, Sturm A, Stuttgen K, Wiesner G, Williams MS, Wynn J, Williams JL. Understanding the Return of Genomic Sequencing Results Process: Content Review of Participant Summary Letters in the eMERGE Research Network. J Pers Med 2020; 10:jpm10020038. [PMID: 32413979 PMCID: PMC7354464 DOI: 10.3390/jpm10020038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/06/2020] [Accepted: 05/09/2020] [Indexed: 01/26/2023] Open
Abstract
A challenge in returning genomic test results to research participants is how best to communicate complex and clinically nuanced findings to participants in a manner that is scalable to the large numbers of participants enrolled. The purpose of this study was to examine the features of genetic results letters produced at each Electronic Medical Records and Genomics (eMERGE3) Network site to assess their readability and content. Letters were collected from each site, and a qualitative analysis of letter content and a quantitative analysis of readability statistics were performed. Because letters were produced independently at each eMERGE site, significant heterogeneity in readability and content was found. The content of letters varied widely from a baseline of notifying participants that results existed to more detailed information about positive or negative results, as well as materials for sharing with family members. Most letters were significantly above the Centers for Disease Control-suggested reading level for health communication. While continued effort should be applied to make letters easier to understand, the ongoing challenge of explaining complex genomic information, the implications of negative test results, and the uncertainty that comes with some types of test and result makes simplifying letter text challenging.
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Affiliation(s)
- John A. Lynch
- Department of Communication, University of Cincinnati, Cincinnati, OH 45220, USA
- Correspondence:
| | | | - Sharon A. Aufox
- Center for Genomic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (S.A.A.); (C.H.)
| | - Sarah T. Bland
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (S.T.B.); (J.P.)
| | - Carrie Blout
- Harvard Pilgrim Health Care Institute, Boston, MA 02115, USA;
| | - Deborah J. Bowen
- Department of Bioethics and Humanities, School of Medicine, University of Washington, Seattle, WA 98195, USA;
| | - Adam H. Buchanan
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA; (A.H.B.); (A.L.); (A.K.R.); (A.S.); (M.S.W.); (J.L.W.)
| | - Colin Halverson
- School of Medicine, Indiana University-Purdue University, Indianapolis, IN 46202, USA;
| | - Margaret Harr
- Center for Applied Genomics, Children’s Hospital of Pennsylvania, Philadelphia, PA 19104, USA;
| | | | - Nora Henrikson
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle, WA 98101, USA; (N.H.); (E.B.L.); (J.R.); (A.S.)
- Department of Health Services, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Christin Hoell
- Center for Genomic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; (S.A.A.); (C.H.)
| | - Ingrid A. Holm
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA;
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA;
| | - Gail Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA;
| | - Iftikhar J. Kullo
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55902, USA; (I.J.K.); (D.C.K.); (K.S.)
| | - David C. Kochan
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55902, USA; (I.J.K.); (D.C.K.); (K.S.)
| | - Eric B. Larson
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle, WA 98101, USA; (N.H.); (E.B.L.); (J.R.); (A.S.)
- Division of General Internal Medicine, University of Washington, Seattle, WA 98195, USA
| | - Amanda Lazzeri
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA; (A.H.B.); (A.L.); (A.K.R.); (A.S.); (M.S.W.); (J.L.W.)
| | - Kathleen A. Leppig
- Genetic Services, Kaiser Permanente of Washington, Seattle, WA 98101, USA;
- University of Washington Biomedical and Health Informatics, Seattle, WA 98195, USA
| | - Jill Madden
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA;
| | - Maddalena Marasa
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, NY 10032, USA; (M.M.); (H.M.R.)
| | - Melanie F. Myers
- College of Medicine, University of Cincinnati, Cincinnati, OH 45220, USA;
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA;
| | - Josh Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (S.T.B.); (J.P.)
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
| | - Cynthia A. Prows
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA;
| | - Alanna Kulchak Rahm
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA; (A.H.B.); (A.L.); (A.K.R.); (A.S.); (M.S.W.); (J.L.W.)
| | - James Ralston
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle, WA 98101, USA; (N.H.); (E.B.L.); (J.R.); (A.S.)
- University of Washington Biomedical and Health Informatics, Seattle, WA 98195, USA
| | - Hila Milo Rasouly
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, NY 10032, USA; (M.M.); (H.M.R.)
| | - Aaron Scrol
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle, WA 98101, USA; (N.H.); (E.B.L.); (J.R.); (A.S.)
| | - Maureen E. Smith
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Amy Sturm
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA; (A.H.B.); (A.L.); (A.K.R.); (A.S.); (M.S.W.); (J.L.W.)
| | - Kelsey Stuttgen
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN 55902, USA; (I.J.K.); (D.C.K.); (K.S.)
| | - Georgia Wiesner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA;
- Vanderbilt Clinical and Translational Hereditary Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Marc S. Williams
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA; (A.H.B.); (A.L.); (A.K.R.); (A.S.); (M.S.W.); (J.L.W.)
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10027, USA;
| | - Janet L. Williams
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA; (A.H.B.); (A.L.); (A.K.R.); (A.S.); (M.S.W.); (J.L.W.)
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Abstract
Objective: When inserting a dry needle laterally into the upper lumbar spine (L1-L3) there is an increased risk of piercing the kidney; therefore, the objective of this study was to determine a zone of safety for practitioners to needle in the upper lumbar spine.Methods: Ten cadavers were screened for inclusion. L1 spinous process was identified and confirmed with ultrasound imaging. A digital caliper was used to measure laterally at 1.5 cm, 2.0 cm, and 2.5 cm. Dry needles were inserted maximally at each point and a binary decision, yes or no, was made to determine if bony contact was made. Needle depth and abdominal width measurements were also recorded. Safety of the dry needling procedure was interpreted as such if bony contact was made by the needle. If bony contact was made, then it was assumed that the needle cannot advance further into pleura or kidney.Results: Forty-four percent of needles did not make bony contact at 2.5 cm lateral of the L1 spinous process, whereas 22% did not make bony contact at 1.5 cm and 2.0 cm. There was a weak to moderate negative correlation between abdominal width measurements and needle depth at 1.5 cm (-0.48) and 2.0 cm (-0.45), and at 2.5 cm (-0.39).Conclusion: A safety zone of needling less than 2.5 cm is likely safe, but needs to be confirmed with future study. Dry needling 2.5 cm lateral appears more risky due to the higher frequency of not contacting a bony backdrop.
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Affiliation(s)
- C J Mansfield
- School of Health and Rehabilitation Sciences, College of Medicine, The Ohio State University, Columbus, OH, USA.,OSU Sports Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - M Harr
- Neuroscience, College of Arts and Sciences, The Ohio State University, Columbus, OH, USA
| | - M Briggs
- OSU Sports Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.,Sports Medicine Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA.,Department of Orthopaedics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - J Onate
- School of Health and Rehabilitation Sciences, College of Medicine, The Ohio State University, Columbus, OH, USA.,Sports Medicine Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - L C Boucher
- School of Health and Rehabilitation Sciences, College of Medicine, The Ohio State University, Columbus, OH, USA.,Sports Medicine Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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14
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Zouk H, Venner E, Lennon NJ, Muzny DM, Abrams D, Adunyah S, Albertson-Junkans L, Ames DC, Appelbaum P, Aronson S, Aufox S, Babb LJ, Balasubramanian A, Bangash H, Basford M, Bastarache L, Baxter S, Behr M, Benoit B, Bhoj E, Bielinski SJ, Bland HT, Blout C, Borthwick K, Bottinger EP, Bowser M, Brand H, Brilliant M, Brodeur W, Caraballo P, Carrell D, Carroll A, Almoguera B, Castillo L, Castro V, Chandanavelli G, Chiang T, Chisholm RL, Christensen KD, Chung W, Chute CG, City B, Cobb BL, Connolly JJ, Crane P, Crew K, Crosslin D, De Andrade M, De la Cruz J, Denson S, Denny J, DeSmet T, Dikilitas O, Friedrich C, Fullerton SM, Funke B, Gabriel S, Gainer V, Gharavi A, Glazer AM, Glessner JT, Goehringer J, Gordon AS, Graham C, Green RC, Gundelach JH, Dayal J, Hain HS, Hakonarson H, Harden MV, Harley J, Harr M, Hartzler A, Hayes MG, Hebbring S, Henrikson N, Hershey A, Hoell C, Holm I, Howell KM, Hripcsak G, Hu J, Jarvik GP, Jayaseelan JC, Jiang Y, Joo YY, Jose S, Josyula NS, Justice AE, Kalla SE, Kalra D, Karlson E, Kelly MA, Keating BJ, Kenny EE, Key D, Kiryluk K, Kitchner T, Klanderman B, Klee E, Kochan DC, Korchina V, Kottyan L, Kovar C, Kudalkar E, Kullo IJ, Lammers P, Larson EB, Lebo MS, Leduc M, Lee MT(M, Leppig KA, Leslie ND, Li R, Liang WH, Lin CF, Linder J, Lindor NM, Lingren T, Linneman JG, Liu C, Liu W, Liu X, Lynch J, Lyon H, Macbeth A, Mahadeshwar H, Mahanta L, Malin B, Manolio T, Marasa M, Marsolo K, Dinsmore MJ, Dodge S, Hynes ED, Dunlea P, Edwards TL, Eng CM, Fasel D, Fedotov A, Feng Q, Fleharty M, Foster A, Freimuth R, McGowan ML, McNally E, Meldrim J, Mentch F, Mosley J, Mukherjee S, Mullen TE, Muniz J, Murdock DR, Murphy S, Murugan M, Myers MF, Namjou B, Ni Y, Obeng AO, Onofrio RC, Taylor CO, Person TN, Peterson JF, Petukhova L, Pisieczko CJ, Pratap S, Prows CA, Puckelwartz MJ, Rahm AK, Raj R, Ralston JD, Ramaprasan A, Ramirez A, Rasmussen L, Rasmussen-Torvik L, Rasouly HM, Raychaudhuri S, Ritchie MD, Rives C, Riza B, Roden D, Rosenthal EA, Santani A, Schaid D, Scherer S, Scott S, Scrol A, Sengupta S, Shang N, Sharma H, Sharp RR, Singh R, Sleiman PM, Slowik K, Smith JC, Smith ME, Smoller JW, Sohn S, Stanaway IB, Starren J, Stroud M, Su J, Tolwinski K, Van Driest SL, Vargas SM, Varugheese M, Veenstra D, Verbitsky M, Vicente G, Wagner M, Walker K, Walunas T, Wang L, Wang Q, Wei WQ, Weiss ST, Wiesner GL, Wells Q, Weng C, White PS, Wiley KL, Williams JL, Williams MS, Wilson MW, Witkowski L, Woods LA, Woolf B, Wu TJ, Wynn J, Yang Y, Yi V, Zhang G, Zhang L, Rehm HL, Gibbs RA. Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network. Am J Hum Genet 2019; 105:588-605. [PMID: 31447099 PMCID: PMC6731372 DOI: 10.1016/j.ajhg.2019.07.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
The advancement of precision medicine requires new methods to coordinate and deliver genetic data from heterogeneous sources to physicians and patients. The eMERGE III Network enrolled >25,000 participants from biobank and prospective cohorts of predominantly healthy individuals for clinical genetic testing to determine clinically actionable findings. The network developed protocols linking together the 11 participant collection sites and 2 clinical genetic testing laboratories. DNA capture panels targeting 109 genes were used for testing of DNA and sample collection, data generation, interpretation, reporting, delivery, and storage were each harmonized. A compliant and secure network enabled ongoing review and reconciliation of clinical interpretations, while maintaining communication and data sharing between clinicians and investigators. A total of 202 individuals had positive diagnostic findings relevant to the indication for testing and 1,294 had additional/secondary findings of medical significance deemed to be returnable, establishing data return rates for other testing endeavors. This study accomplished integration of structured genomic results into multiple electronic health record (EHR) systems, setting the stage for clinical decision support to enable genomic medicine. Further, the established processes enable different sequencing sites to harmonize technical and interpretive aspects of sequencing tests, a critical achievement toward global standardization of genomic testing. The eMERGE protocols and tools are available for widespread dissemination.
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15
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Douglas G, Cho MT, Telegrafi A, Winter S, Carmichael J, Zackai EH, Deardorff MA, Harr M, Williams L, Psychogios A, Erwin AL, Grebe T, Retterer K, Juusola J. De novo
missense variants in
MEIS2
recapitulate the microdeletion phenotype of cardiac and palate abnormalities, developmental delay, intellectual disability and dysmorphic features. Am J Med Genet A 2018; 176:1845-1851. [DOI: 10.1002/ajmg.a.40368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/14/2018] [Accepted: 05/28/2018] [Indexed: 12/23/2022]
Affiliation(s)
| | | | | | - Susan Winter
- Valley Children's Hospital Central California Madera California
| | | | - Elaine H. Zackai
- The Division of GeneticsThe Children's Hospital of Philadelphia Philadelphia Pennsylvania
- The Department of PediatricsThe Perelman School of Medicine, The University of Pennsylvania Philadelphia Pennsylvania
| | - Matthew A. Deardorff
- The Division of GeneticsThe Children's Hospital of Philadelphia Philadelphia Pennsylvania
- The Department of PediatricsThe Perelman School of Medicine, The University of Pennsylvania Philadelphia Pennsylvania
| | - Margaret Harr
- The Division of GeneticsThe Children's Hospital of Philadelphia Philadelphia Pennsylvania
| | - Linford Williams
- Children's Hospital of Pittsburgh of UPMC Pittsburgh Pennsylvania
| | - Apostolos Psychogios
- The Departments of PediatricsInternal Medicine, and Cardiology, University of Kentucky Lexington Kentucky
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16
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Williams JL, Chung WK, Fedotov A, Kiryluk K, Weng C, Connolly JJ, Harr M, Hakonarson H, Leppig KA, Larson EB, Jarvik GP, Veenstra DL, Hoell C, Smith ME, Holm IA, Peterson JF, Williams MS. Harmonizing Outcomes for Genomic Medicine: Comparison of eMERGE Outcomes to ClinGen Outcome/Intervention Pairs. Healthcare (Basel) 2018; 6:healthcare6030083. [PMID: 30011878 PMCID: PMC6164315 DOI: 10.3390/healthcare6030083] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/27/2018] [Accepted: 07/10/2018] [Indexed: 11/16/2022] Open
Abstract
Genomic medicine is moving from research to the clinic. There is a lack of evidence about the impact of genomic medicine interventions on health outcomes. This is due in part to a lack of standardized outcome measures that can be used across different programs to evaluate the impact of interventions targeted to specific genetic conditions. The eMERGE Outcomes working group (OWG) developed measures to collect information on outcomes following the return of genomic results to participants for several genetic disorders. These outcomes were compared to outcome intervention pairs for genetic disorders developed independently by the ClinGen Actionability working group (AWG). In general, there was concordance between the defined outcomes between the two groups. The ClinGen outcomes tended to be from a higher level and the AWG scored outcomes represented a subset of outcomes referenced in the accompanying AWG evidence review. eMERGE OWG outcomes were more detailed and discrete, facilitating a collection of relevant information from the health records. This paper demonstrates that common outcomes for genomic medicine interventions can be identified. Further work is needed to standardize outcomes across genomic medicine implementation projects and to make these publicly available to enhance dissemination and assist in making precision public health a reality.
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Affiliation(s)
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10025, USA.
| | - Alex Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10025, USA.
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Columbia University, New York, NY 10025, USA.
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY 10025, USA.
| | - John J Connolly
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Margaret Harr
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Hakon Hakonarson
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kathleen A Leppig
- Genetic Services, Kaiser Permanente of Washington, Seattle, WA 98101, USA.
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, USA.
| | - Gail P Jarvik
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA.
| | - David L Veenstra
- Department Pharmacy, University of Washington, Seattle, WA 98195, USA.
| | - Christin Hoell
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Maureen E Smith
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
| | - Josh F Peterson
- Departments of Biomedical Informatics and Medicine, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, PA 17822, USA.
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17
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Fossey R, Kochan D, Winkler E, Pacyna JE, Olson J, Thibodeau S, Connolly JJ, Harr M, Behr MA, Prows CA, Cobb B, Myers MF, Leslie ND, Namjou-Khales B, Milo Rasouly H, Wynn J, Fedotov A, Chung WK, Gharavi A, Williams JL, Pais L, Holm I, Aufox S, Smith ME, Scrol A, Leppig K, Jarvik GP, Wiesner GL, Li R, Stroud M, Smoller JW, Sharp RR, Kullo IJ. Ethical Considerations Related to Return of Results from Genomic Medicine Projects: The eMERGE Network (Phase III) Experience. J Pers Med 2018; 8:jpm8010002. [PMID: 29301385 PMCID: PMC5872076 DOI: 10.3390/jpm8010002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022] Open
Abstract
We examined the Institutional Review Board (IRB) process at 9 academic institutions in the electronic Medical Records and Genomics (eMERGE) Network, for proposed electronic health record-based genomic medicine studies, to identify common questions and concerns. Sequencing of 109 disease related genes and genotyping of 14 actionable variants is being performed in ~28,100 participants from the 9 sites. Pathogenic/likely pathogenic variants in actionable genes are being returned to study participants. We examined each site’s research protocols, informed-consent materials, and interactions with IRB staff. Research staff at each site completed questionnaires regarding their IRB interactions. The time to prepare protocols for IRB submission, number of revisions and time to approval ranged from 10–261 days, 0–11, and 11–90 days, respectively. IRB recommendations related to the readability of informed consent materials, specifying the full range of potential risks, providing options for receiving limited results or withdrawal, sharing of information with family members, and establishing the mechanisms to answer participant questions. IRBs reviewing studies that involve the return of results from genomic sequencing have a diverse array of concerns, and anticipating these concerns can help investigators to more effectively engage IRBs.
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Affiliation(s)
- Robyn Fossey
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA.
| | - David Kochan
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA.
| | - Erin Winkler
- Center for Individualized Medicine and Department of Medical Genomics, Mayo Clinic, Rochester, MN 55905, USA.
| | - Joel E Pacyna
- Department of Health Sciences Research, Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN 55905, USA.
| | - Janet Olson
- Department of Health Sciences Research, Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN 55905, USA.
| | - Stephen Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.
| | - John J Connolly
- The Children's Hospital of Philadelphia, Center for Applied Genomics, Philadelphia, PA 19104, USA.
| | - Margaret Harr
- The Children's Hospital of Philadelphia, Center for Applied Genomics, Philadelphia, PA 19104, USA.
| | - Meckenzie A Behr
- The Children's Hospital of Philadelphia, Center for Applied Genomics, Philadelphia, PA 19104, USA.
| | - Cynthia A Prows
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Beth Cobb
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Melanie F Myers
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Nancy D Leslie
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | | | - Hila Milo Rasouly
- Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, NY 10027, USA.
| | - Julia Wynn
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA.
| | - Alexander Fedotov
- Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA.
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA.
| | - Ali Gharavi
- Department of Medicine, Division of Nephrology, Columbia University Medical Center, New York, NY 10027, USA.
| | | | - Lynn Pais
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Ingrid Holm
- Boston Children's Hospital, Boston, MA 02115, USA.
| | - Sharon Aufox
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Maureen E Smith
- Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.
| | | | | | - Gail P Jarvik
- Division of Medical Genetics, University of Washington, Seattle, WA 98195, USA.
| | - Georgia L Wiesner
- Department of Medicine, Division of Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA.
| | - Rongling Li
- National Human Genome Research Institute, Rockville, MD 20892, USA.
| | - Mary Stroud
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA.
| | - Jordan W Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Richard R Sharp
- Department of Health Sciences Research, Biomedical Ethics Research Program, Mayo Clinic, Rochester, MN 55905, USA.
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA.
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18
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Bhoj EJ, Li D, Harr M, Edvardson S, Elpeleg O, Chisholm E, Juusola J, Douglas G, Guillen Sacoto MJ, Siquier-Pernet K, Saadi A, Bole-Feysot C, Nitschke P, Narravula A, Walke M, Horner MB, Day-Salvatore DL, Jayakar P, Vergano SAS, Tarnopolsky MA, Hegde M, Colleaux L, Crino P, Hakonarson H. Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia. Am J Hum Genet 2016; 98:782-8. [PMID: 27040691 DOI: 10.1016/j.ajhg.2016.03.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/16/2016] [Indexed: 12/15/2022] Open
Abstract
Through an international multi-center collaboration, 13 individuals from nine unrelated families and affected by likely pathogenic biallelic variants in TBC1-domain-containing kinase (TBCK) were identified through whole-exome sequencing. All affected individuals were found to share a core phenotype of intellectual disability and hypotonia, and many had seizures and showed brain atrophy and white-matter changes on neuroimaging. Minor non-specific facial dysmorphism was also noted in some individuals, including multiple older children who developed coarse features similar to those of storage disorders. TBCK has been shown to regulate the mammalian target of rapamycin (mTOR) signaling pathway, which is also stimulated by exogenous leucine supplementation. TBCK was absent in cells from affected individuals, and decreased phosphorylation of phospho-ribosomal protein S6 was also observed, a finding suggestive of downregulation of mTOR signaling. Lastly, we demonstrated that activation of the mTOR pathway in response to L-leucine supplementation was retained, suggesting a possible avenue for directed therapies for this condition.
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Affiliation(s)
- Elizabeth J Bhoj
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Margaret Harr
- Department of Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shimon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91120, Israel; Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Elizabeth Chisholm
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA 23507, USA
| | | | | | | | - Karine Siquier-Pernet
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Necker-Enfants Malades Hospital, 75015 Paris, France
| | - Abdelkrim Saadi
- Département de Neurologie, Etablissement Hospitalier Spécialisé de Benaknoun, Algers, Algeria
| | - Christine Bole-Feysot
- Genomic Platform, INSERM UMR 1163, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France
| | - Patrick Nitschke
- Plateforme de Bioinformatique, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France
| | | | - Maria Walke
- Nicklaus Children's Hospital, Miami, FL, 33155, USA
| | - Michele B Horner
- Department of Medical Genetics & Genomic Medicine, St. Peter's University Hospital, New Brunswick, NJ 08901, USA
| | - Debra-Lynn Day-Salvatore
- Department of Medical Genetics & Genomic Medicine, St. Peter's University Hospital, New Brunswick, NJ 08901, USA
| | | | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA 23507, USA
| | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada
| | - Madhuri Hegde
- Emory Genetics Laboratory, Emory University, Decatur, GA 30033, USA
| | - Laurence Colleaux
- INSERM UMR 1163, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Necker-Enfants Malades Hospital, 75015 Paris, France
| | - Peter Crino
- Department of Neurology, Temple University, Philadelphia, PA 19122, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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19
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Ganetzky R, Finn E, Bagchi A, Zollo O, Conlin L, Deardorff M, Harr M, Simpson MA, McGrath JA, Zackai E, Lemmon MA, Sondheimer N. EGFR mutations cause a lethal syndrome of epithelial dysfunction with progeroid features. Mol Genet Genomic Med 2015; 3:452-8. [PMID: 26436111 PMCID: PMC4585453 DOI: 10.1002/mgg3.156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 02/27/2015] [Revised: 04/16/2015] [Accepted: 04/21/2015] [Indexed: 12/18/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is part of a large family of receptors required for communicating extracellular signals through internal tyrosine kinases. Epidermal growth factor (EGF) signaling is required for tissue development, whereas constitutive activation of this signaling pathway is associated with oncogenic transformation. We identified homozygous c.1283G>A (p.Gly428Asp) mutations in the extracellular domain of EGFR in two siblings. The children were born prematurely, had abnormalities in skin and hair, suffered multisystem organ failure, and died in the neonatal period from intestinal perforation. EGF failed to induce mutated receptor phosphorylation in patient-derived fibroblasts and activation of downstream targets was suppressed. The heterologously expressed extracellular domain was impaired in stability and the binding of EGF. Cells from the affected patient undergo early senescence with accelerated expression of β-galactosidase and shortened telomeres at all passages when compared to controls. A comparison of homozygous inherited regions from a separate report of a patient from the same ethnic background and EGFR genotype confirms the pathogenicity of EGFR mutations in congenital disease.
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Affiliation(s)
- Rebecca Ganetzky
- Department of Pediatrics, The University of Pennsylvania Philadelphia, 19104, Pennsylvania ; Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, 19104, Pennsylvania
| | - Erin Finn
- Division of Biochemical Genetics, The Children's Hospital of Philadelphia Philadelphia, 19104, Pennsylvania
| | - Atrish Bagchi
- Department of Biochemistry and Biophysics and Graduate Group in Biochemistry and Molecular Biophysics, The University of Pennsylvania Philadelphia, 19104, Pennsylvania
| | - Ornella Zollo
- Division of Biochemical Genetics, The Children's Hospital of Philadelphia Philadelphia, 19104, Pennsylvania
| | - Laura Conlin
- Department of Pathology, The University of Pennsylvania Philadelphia, 19104, Pennsylvania
| | - Matthew Deardorff
- Department of Pediatrics, The University of Pennsylvania Philadelphia, 19104, Pennsylvania ; Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, 19104, Pennsylvania
| | - Margaret Harr
- Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, 19104, Pennsylvania
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, King's College London London, United Kingdom
| | - John A McGrath
- St. John's Institute of Dermatology, King's College London London, United Kingdom ; The Centre for Dermatology and Genetic Medicine, University of Dundee Dundee, United Kingdom
| | - Elaine Zackai
- Department of Pediatrics, The University of Pennsylvania Philadelphia, 19104, Pennsylvania ; Division of Genetics, The Children's Hospital of Philadelphia Philadelphia, 19104, Pennsylvania
| | - Mark A Lemmon
- Department of Biochemistry and Biophysics and Graduate Group in Biochemistry and Molecular Biophysics, The University of Pennsylvania Philadelphia, 19104, Pennsylvania
| | - Neal Sondheimer
- Department of Pediatrics, The University of Pennsylvania Philadelphia, 19104, Pennsylvania ; Division of Biochemical Genetics, The Children's Hospital of Philadelphia Philadelphia, 19104, Pennsylvania
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20
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Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders M, Venselaar H, Helsmoortel C, Cho M, Hoischen A, Vissers LE, Koemans T, Wissink-Lindhout W, Eichler E, Romano C, Van Esch H, Stumpel C, Vreeburg M, Smeets E, Oberndorff K, van Bon B, Shaw M, Gecz J, Haan E, Bienek M, Jensen C, Loeys B, Van Dijck A, Innes A, Racher H, Vermeer S, Di Donato N, Rump A, Tatton-Brown K, Parker M, Henderson A, Lynch S, Fryer A, Ross A, Vasudevan P, Kini U, Newbury-Ecob R, Chandler K, Male A, Dijkstra S, Schieving J, Giltay J, van Gassen K, Schuurs-Hoeijmakers J, Tan P, Pediaditakis I, Haas S, Retterer K, Reed P, Monaghan K, Haverfield E, Natowicz M, Myers A, Kruer M, Stein Q, Strauss K, Brigatti K, Keating K, Burton B, Kim K, Charrow J, Norman J, Foster-Barber A, Kline A, Kimball A, Zackai E, Harr M, Fox J, McLaughlin J, Lindstrom K, Haude K, van Roozendaal K, Brunner H, Chung W, Kooy R, Pfundt R, Kalscheuer V, Mehta S, Katsanis N, Kleefstra T, Kleefstra T. Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling. Am J Hum Genet 2015; 97:343-52. [PMID: 26235985 DOI: 10.1016/j.ajhg.2015.07.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/13/2015] [Indexed: 12/22/2022] Open
Abstract
Intellectual disability (ID) affects approximately 1%-3% of humans with a gender bias toward males. Previous studies have identified mutations in more than 100 genes on the X chromosome in males with ID, but there is less evidence for de novo mutations on the X chromosome causing ID in females. In this study we present 35 unique deleterious de novo mutations in DDX3X identified by whole exome sequencing in 38 females with ID and various other features including hypotonia, movement disorders, behavior problems, corpus callosum hypoplasia, and epilepsy. Based on our findings, mutations in DDX3X are one of the more common causes of ID, accounting for 1%-3% of unexplained ID in females. Although no de novo DDX3X mutations were identified in males, we present three families with segregating missense mutations in DDX3X, suggestive of an X-linked recessive inheritance pattern. In these families, all males with the DDX3X variant had ID, whereas carrier females were unaffected. To explore the pathogenic mechanisms accounting for the differences in disease transmission and phenotype between affected females and affected males with DDX3X missense variants, we used canonical Wnt defects in zebrafish as a surrogate measure of DDX3X function in vivo. We demonstrate a consistent loss-of-function effect of all tested de novo mutations on the Wnt pathway, and we further show a differential effect by gender. The differential activity possibly reflects a dose-dependent effect of DDX3X expression in the context of functional mosaic females versus one-copy males, which reflects the complex biological nature of DDX3X mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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21
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Wenger TL, Harr M, Ricciardi S, Bhoj E, Santani A, Adam MP, Barnett SS, Ganetzky R, McDonald-McGinn DM, Battaglia D, Bigoni S, Selicorni A, Sorge G, Monica MD, Mari F, Andreucci E, Romano S, Cocchi G, Savasta S, Malbora B, Marangi G, Garavelli L, Zollino M, Zackai EH. "CHARGE-like presentation, craniosynostosis and mild Mowat-Wilson Syndrome diagnosed by recognition of the distinctive facial gestalt in a cohort of 28 new cases" American Journal of Medical Genetics Part A. 164:2557-2566, 2014. Am J Med Genet A 2015; 167:1682-3. [PMID: 26097173 DOI: 10.1002/ajmg.a.36860] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/11/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Tara L Wenger
- Division of Craniofacial Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Margaret Harr
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stefania Ricciardi
- Istituto di Genetica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Elizabeth Bhoj
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Avni Santani
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Margaret P Adam
- Division of Genetic Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Sarah S Barnett
- Division of Genetics, University of Missouri Children's Hospital, Columbia, Missouri
| | - Rebecca Ganetzky
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Donna M McDonald-McGinn
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Domenica Battaglia
- UOC di Neuropsichiatria Infantile, Universitá Cattolica del Sacro Cuore, Rome, Italy
| | - Stefania Bigoni
- Unitá di Genetica Medica, Azienda Ospedaliero-Universitaria di Ferrara, Rome, Italy
| | - Angelo Selicorni
- Dipartimento di Pediatria, Ospedale S. Gerardo/Fondazione MBBM, Universitá di Milano-Bicocca, Monza, Italy
| | - Giovanni Sorge
- Unità Operativa Complessa di Clinica Pediatrica, Dipartimento di Scienze Mediche e Pediatriche, Azienda Ospedaliera Universitaria "Policlinico - Vittorio Emanuele", Università di Catania, Catania, Italy
| | - Matteo Della Monica
- Unità Operativa di Genetica Medica, Ospedale Gaetano Rummo, Benevento, Italy
| | - Francesca Mari
- UOC di Genetica Medica, Universitá di Siena, Siena, Italy
| | - Elena Andreucci
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Silvia Romano
- Unitá di Genetica Medica, Dipartimento di Fisiopatologia Clinica, Azienda Ospedaliero Universitaria "A. Meyer", Universitá di Firenze, Florence, Italy
| | - Guido Cocchi
- UO di neonatologia, Policlinico S. Orsola-Malpighi, Università di Bologna, Bologna, Italy
| | - Salvatore Savasta
- Dipartimento di Pediatria, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Baris Malbora
- Department of Pediatrics, Gulhane Military Medical Academy, Haydarpasa Training Hospital, Istanbul, Turkey
| | - Giuseppe Marangi
- Istituto di Genetica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Livia Garavelli
- Unitá di Genetica Clinica, Dipartimento Ostetrico-Ginecologico e Pediatrico, Istituto di Ricovero e Cura a Carattere Scientifico, Arcispedale S Maria Nuova, Reggio Emilia, Italy
| | - Marcella Zollino
- Istituto di Genetica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Elaine H Zackai
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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22
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Wenger TL, Harr M, Ricciardi S, Bhoj E, Santani A, Adam MP, Barnett SS, Ganetzky R, McDonald-McGinn DM, Battaglia D, Bigoni S, Selicorni A, Sorge G, Monica MD, Mari F, Andreucci E, Romano S, Cocchi G, Savasta S, Malbora B, Marangi G, Garavelli L, Zollino M, Zackai EH. CHARGE-like presentation, craniosynostosis and mild Mowat-Wilson Syndrome diagnosed by recognition of the distinctive facial gestalt in a cohort of 28 new cases. Am J Med Genet A 2014; 164A:2557-66. [PMID: 25123255 DOI: 10.1002/ajmg.a.36696] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 06/20/2014] [Indexed: 12/12/2022]
Abstract
Mowat-Wilson syndrome (MWS) is characterized by moderate to severe intellectual disability and distinctive facial features in association with variable structural congenital anomalies/clinical features including congenital heart disease, Hirschsprung disease, hypospadias, agenesis of the corpus callosum, short stature, epilepsy, and microcephaly. Less common clinical features include ocular anomalies, craniosynostosis, mild intellectual disability, and choanal atresia. These cases may be more difficult to diagnose. In this report, we add 28 MWS patients with molecular confirmation of ZEB2 mutation, including seven with an uncommon presenting feature. Among the "unusual" patients, two patients had clinical features of charge syndrome including choanal atresia, coloboma, cardiac defects, genitourinary anomaly (1/2), and severe intellectual disability; two patients had craniosynostosis; and three patients had mild intellectual disability. Sixteen patients have previously-unreported mutations in ZEB2. Genotype-phenotype correlations were suggested in those with mild intellectual disability (two had a novel missense mutation in ZEB2, one with novel splice site mutation). This report increases the number of reported patients with MWS with unusual features, and is the first report of MWS in children previously thought to have CHARGE syndrome. These patients highlight the importance of facial gestalt in the accurate identification of MWS when less common features are present.
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Affiliation(s)
- Tara L Wenger
- Division of Craniofacial Medicine, Seattle Children's Hospital, Seattle, WA
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