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Syed FJ, Bekbolsynov D, Stepkowski S, Kaur D, Green RC. Maximizing matching, equity and survival in kidney transplantation using molecular HLA immunogenicity quantitation. Comput Biol Med 2024; 174:108452. [PMID: 38640635 DOI: 10.1016/j.compbiomed.2024.108452] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/11/2024] [Accepted: 04/07/2024] [Indexed: 04/21/2024]
Abstract
HLA matching improves long-term outcomes of kidney transplantation, yet implementation challenges persist, particularly within the African American (Black) patient demographic due to donor scarcity. Consequently, kidney survival rates among Black patients significantly lag behind those of other racial groups. A refined matching scheme holds promise for improving kidney survival, with prioritized matching for Black patients potentially bolstering rates of HLA-matched transplants. To facilitate quantity, quality and equity in kidney transplants, we propose two matching algorithms based on quantification of HLA immunogenicity using the hydrophobic mismatch score (HMS) for prospective transplants. We mined the national transplant patient database (SRTR) for a diverse group of donors and recipients with known racial backgrounds. Additionally, we use novel methods to infer survival assessment in the simulated transplants generated by our matching algorithms, in the absence of actual target outcomes, utilizing modified unsupervised clustering techniques. Our allocation algorithms demonstrated the ability to match 87.7% of Black and 86.1% of White recipients under the HLA immunogenicity threshold of 10. Notably, at the lowest HMS threshold of 0, 4.4% of Black and 12.1% of White recipients were matched, a marked increase from the 1.8% and 6.6% matched under the prevailing allocation scheme. Furthermore, our allocation algorithms yielded similar or improved survival rates, as illustrated by Kaplan-Meier (KM) curves, and enhanced survival prediction accuracy, evidenced by C-indices and Integrated Brier Scores.
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Affiliation(s)
- Fayeq Jeelani Syed
- Electrical Engineering and Computer Science Department, University of Toledo, 2801 W Bancroft St., Toledo, 43606, OH, USA
| | - Dulat Bekbolsynov
- Department of Medical Microbiology and Immunology, University of Toledo Medical Center, 3000 Arlington Ave., Toledo, 43614, OH, USA
| | - Stanislaw Stepkowski
- Department of Medical Microbiology and Immunology, University of Toledo Medical Center, 3000 Arlington Ave., Toledo, 43614, OH, USA
| | - Devinder Kaur
- Electrical Engineering and Computer Science Department, University of Toledo, 2801 W Bancroft St., Toledo, 43606, OH, USA
| | - Robert C Green
- Department of Computer Science, Bowling Green State University, 1001 E Wooster St., Bowling Green, 43403, OH, USA.
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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 B, 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] [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
| | - Beth 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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3
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Minten T, Gold NB, Bick S, Adelson S, Gehlenborg N, Amendola LM, Boemer F, Coffey AJ, Encina N, Russell BE, Servais L, Sund KL, Tsipouras P, Bick D, Taft RJ, Green RC. Determining the characteristics of genetic disorders that predict inclusion in newborn genomic sequencing programs. medRxiv 2024:2024.03.24.24304797. [PMID: 38585998 PMCID: PMC10996735 DOI: 10.1101/2024.03.24.24304797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Over 30 international research studies and commercial laboratories are exploring the use of genomic sequencing to screen apparently healthy newborns for genetic disorders. These programs have individualized processes for determining which genes and genetic disorders are queried and reported in newborns. We compared lists of genes from 26 research and commercial newborn screening programs and found substantial heterogeneity among the genes included. A total of 1,750 genes were included in at least one newborn genome sequencing program, but only 74 genes were included on >80% of gene lists, 16 of which are not associated with conditions on the Recommended Uniform Screening Panel. We used a linear regression model to explore factors related to the inclusion of individual genes across programs, finding that a high evidence base as well as treatment efficacy were two of the most important factors for inclusion. We applied a machine learning model to predict how suitable a gene is for newborn sequencing. As knowledge about and treatments for genetic disorders expand, this model provides a dynamic tool to reassess genes for newborn screening implementation. This study highlights the complex landscape of gene list curation among genomic newborn screening programs and proposes an empirical path forward for determining the genes and disorders of highest priority for newborn screening programs.
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Massmann A, Christensen KD, Van Heukelom J, Schultz A, Shaukat MHS, Hajek C, Weaver M, Green RC, Wu AC, Hickingbotham MR, Zoltick ES, Stys A, Stys TP. Clinical impact of preemptive pharmacogenomic testing on antiplatelet therapy in a real-world setting. Eur J Hum Genet 2024:10.1038/s41431-024-01567-1. [PMID: 38424298 DOI: 10.1038/s41431-024-01567-1] [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: 10/12/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
CYP2C19 genotyping to guide antiplatelet therapy after patients develop acute coronary syndromes (ACS) or require percutaneous coronary interventions (PCIs) reduces the likelihood of major adverse cardiovascular events (MACE). Evidence about the impact of preemptive testing, where genotyping occurs while patients are healthy, is lacking. In patients initiating antiplatelet therapy for ACS or PCI, we compared medical records data from 67 patients who received CYP2C19 genotyping preemptively (results >7 days before need), against medical records data from 67 propensity score-matched patients who received early genotyping (results within 7 days of need). We also examined data from 140 patients who received late genotyping (results >7 days after need). We compared the impact of genotyping approaches on medication selections, specialty visits, MACE and bleeding events over 1 year. Patients with CYP2C19 loss-of-function alleles were less likely to be initiated on clopidogrel if they received preemptive rather than early or late genotyping (18.2%, 66.7%, and 73.2% respectively, p = 0.001). No differences were observed by genotyping approach in the number of specialty visits or likelihood of MACE or bleeding events (all p > 0.21). Preemptive genotyping had a strong impact on initial antiplatelet selection and a comparable impact on patient outcomes and healthcare utilization, compared to genotyping ordered after a need for antiplatelet therapy had been identified.
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Affiliation(s)
- Amanda Massmann
- Sanford Imagenetics, Sioux Falls, SD, 57105, USA.
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, 57069, USA.
| | - Kurt D Christensen
- Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, 02215, USA
- Department of Population Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - Joel Van Heukelom
- Sanford Imagenetics, Sioux Falls, SD, 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, 57069, USA
| | - April Schultz
- Sanford Imagenetics, Sioux Falls, SD, 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, 57069, USA
| | - Muhammad Hamza Saad Shaukat
- Minneapolis Heart Institute/Abbott Northwestern Hospital Institute, Minneapolis, MN, 55407, USA
- Sanford Cardiovascular Institute, Sioux Falls, SD, 57105, USA
| | - Catherine Hajek
- Sanford Imagenetics, Sioux Falls, SD, 57105, USA
- Helix OpCo, LLC, San Mateo, CA, 94401, USA
| | - Max Weaver
- Sanford Imagenetics, Sioux Falls, SD, 57105, USA
| | - Robert C Green
- Broad Institute of Harvard and MIT, Cambridge, MA, 02141, USA
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Ariadne Labs, Boston, MA, 02215, USA
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, 02215, USA
- Department of Population Medicine, Harvard Medical School, Boston, MA, 02215, USA
| | - Madison R Hickingbotham
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, 02215, USA
| | - Emilie S Zoltick
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, 02215, USA
| | - Adam Stys
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, 57069, USA
- Sanford Cardiovascular Institute, Sioux Falls, SD, 57105, USA
| | - Tomasz P Stys
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD, 57069, USA
- Sanford Cardiovascular Institute, Sioux Falls, SD, 57105, USA
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5
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Gold NB, Nadel A, Green RC. Ready or not, genomic screening of fetuses is already here. Genet Med 2024; 26:101008. [PMID: 37860970 PMCID: PMC10842943 DOI: 10.1016/j.gim.2023.101008] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023] Open
Affiliation(s)
- Nina B Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, MA; Harvard Medical School, Boston, MA.
| | - Allan Nadel
- Harvard Medical School, Boston, MA; Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Ariadne Labs, Boston, MA; Department of Medicine, Harvard Medical School, Boston, MA; Broad Institute, Boston, MA
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6
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Veitch DP, Weiner MW, Miller M, Aisen PS, Ashford MA, Beckett LA, Green RC, Harvey D, Jack CR, Jagust W, Landau SM, Morris JC, Nho KT, Nosheny R, Okonkwo O, Perrin RJ, Petersen RC, Rivera Mindt M, Saykin A, Shaw LM, Toga AW, Tosun D. The Alzheimer's Disease Neuroimaging Initiative in the era of Alzheimer's disease treatment: A review of ADNI studies from 2021 to 2022. Alzheimers Dement 2024; 20:652-694. [PMID: 37698424 PMCID: PMC10841343 DOI: 10.1002/alz.13449] [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: 04/24/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 09/13/2023]
Abstract
The Alzheimer's Disease Neuroimaging Initiative (ADNI) aims to improve Alzheimer's disease (AD) clinical trials. Since 2006, ADNI has shared clinical, neuroimaging, and cognitive data, and biofluid samples. We used conventional search methods to identify 1459 publications from 2021 to 2022 using ADNI data/samples and reviewed 291 impactful studies. This review details how ADNI studies improved disease progression understanding and clinical trial efficiency. Advances in subject selection, detection of treatment effects, harmonization, and modeling improved clinical trials and plasma biomarkers like phosphorylated tau showed promise for clinical use. Biomarkers of amyloid beta, tau, neurodegeneration, inflammation, and others were prognostic with individualized prediction algorithms available online. Studies supported the amyloid cascade, emphasized the importance of neuroinflammation, and detailed widespread heterogeneity in disease, linked to genetic and vascular risk, co-pathologies, sex, and resilience. Biological subtypes were consistently observed. Generalizability of ADNI results is limited by lack of cohort diversity, an issue ADNI-4 aims to address by enrolling a diverse cohort.
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Affiliation(s)
- Dallas P. Veitch
- Department of Veterans Affairs Medical CenterNorthern California Institute for Research and Education (NCIRE)San FranciscoCaliforniaUSA
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
| | - Michael W. Weiner
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of Psychiatry and Behavioral SciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Melanie Miller
- Department of Veterans Affairs Medical CenterNorthern California Institute for Research and Education (NCIRE)San FranciscoCaliforniaUSA
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
| | - Paul S. Aisen
- Alzheimer's Therapeutic Research InstituteUniversity of Southern CaliforniaSan DiegoCaliforniaUSA
| | - Miriam A. Ashford
- Department of Veterans Affairs Medical CenterNorthern California Institute for Research and Education (NCIRE)San FranciscoCaliforniaUSA
| | - Laurel A. Beckett
- Division of BiostatisticsDepartment of Public Health SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Robert C. Green
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalBroad Institute Ariadne Labs and Harvard Medical SchoolBostonMassachusettsUSA
| | - Danielle Harvey
- Division of BiostatisticsDepartment of Public Health SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | | | - William Jagust
- Helen Wills Neuroscience InstituteUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Susan M. Landau
- Helen Wills Neuroscience InstituteUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - John C. Morris
- Knight Alzheimer's Disease Research CenterWashington University School of MedicineSaint LouisMissouriUSA
- Department of NeurologyWashington University School of MedicineSaint LouisMissouriUSA
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMissouriUSA
| | - Kwangsik T. Nho
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer's Disease Research CenterIndiana University School of MedicineIndianapolisIndianaUSA
- Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Rachel Nosheny
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Department of Psychiatry and Behavioral SciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Ozioma Okonkwo
- Wisconsin Alzheimer's Disease Research Center and Department of MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Richard J. Perrin
- Knight Alzheimer's Disease Research CenterWashington University School of MedicineSaint LouisMissouriUSA
- Department of NeurologyWashington University School of MedicineSaint LouisMissouriUSA
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMissouriUSA
| | | | - Monica Rivera Mindt
- Department of PsychologyLatin American and Latino Studies InstituteAfrican and African American StudiesFordham UniversityNew YorkNew YorkUSA
- Department of NeurologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Andrew Saykin
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer's Disease Research CenterIndiana University School of MedicineIndianapolisIndianaUSA
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Leslie M. Shaw
- Department of Pathology and Laboratory Medicine and the PENN Alzheimer's Disease Research CenterCenter for Neurodegenerative ResearchPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Arthur W. Toga
- Laboratory of Neuro ImagingInstitute of Neuroimaging and InformaticsKeck School of Medicine of University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Duygu Tosun
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCaliforniaUSA
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Lacaze P, Marquina C, Tiller J, Brotchie A, Kang YJ, Merritt MA, Green RC, Watts GF, Nowak KJ, Manchanda R, Canfell K, James P, Winship I, McNeil JJ, Ademi Z. Combined population genomic screening for three high-risk conditions in Australia: a modelling study. EClinicalMedicine 2023; 66:102297. [PMID: 38192593 PMCID: PMC10772163 DOI: 10.1016/j.eclinm.2023.102297] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 01/10/2024] Open
Abstract
Background No previous health-economic evaluation has assessed the impact and cost-effectiveness of offering combined adult population genomic screening for mutliple high-risk conditions in a national public healthcare system. Methods This modeling study assessed the impact of offering combined genomic screening for hereditary breast and ovarian cancer, Lynch syndrome and familial hypercholesterolaemia to all young adults in Australia, compared with the current practice of clinical criteria-based testing for each condition separately. The intervention of genomic screening, assumed as an up-front single cost in the first annual model cycle, would detect pathogenic variants in seven high-risk genes. The simulated population was 18-40 year-olds (8,324,242 individuals), modelling per-sample test costs ranging AU$100-$1200 (base-case AU$200) from the year 2023 onwards with testing uptake of 50%. Interventions for identified high-risk variant carriers follow current Australian guidelines, modelling imperfect uptake and adherence. Outcome measures were morbidity and mortality due to cancer (breast, ovarian, colorectal and endometrial) and coronary heart disease (CHD) over a lifetime horizon, from healthcare-system and societal perspectives. Outcomes included quality-adjusted life years (QALYs) and incremental cost-effectiveness ratio (ICER), discounted 5% annually (with 3% discounting in scenario analysis). Findings Over the population lifetime (to age 80 years), the model estimated that genomic screening per-100,000 individuals would lead to 747 QALYs gained by preventing 63 cancers, 31 CHD cases and 97 deaths. In the total model population, this would translate to 31,094 QALYs gained by preventing 2612 cancers, 542 non-fatal CHD events and 4047 total deaths. At AU$200 per-test, genomic screening would require an investment of AU$832 million for screening of 50% of the population. Our findings suggest that this intervention would be cost-effective from a healthcare-system perspective, yielding an ICER of AU$23,926 (∼£12,050/€14,110/US$15,345) per QALY gained over the status quo. In scenario analysis with 3% discounting, an ICER of AU$4758/QALY was obtained. Sensitivity analysis for the base case indicated that combined genomic screening would be cost-effective under 70% of simulations, cost-saving under 25% and not cost-effective under 5%. Threshold analysis showed that genomic screening would be cost-effective under the AU$50,000/QALY willingness-to-pay threshold at per-test costs up to AU$325 (∼£164/€192/US$208). Interpretation Our findings suggest that offering combined genomic screening for high-risk conditions to young adults would be cost-effective in the Australian public healthcare system, at currently realistic testing costs. Other matters, including psychosocial impacts, ethical and societal issues, and implementation challenges, also need consideration. Funding Australian Government, Department of Health, Medical Research Future Fund, Genomics Health Futures Mission (APP2009024). National Heart Foundation Future Leader Fellowship (102604).
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Affiliation(s)
- Paul Lacaze
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Clara Marquina
- Health Economics and Policy Evaluation Research (HEPER) Group, Centre for Medicine Use and Safety, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
| | - Jane Tiller
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Adam Brotchie
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Yoon-Jung Kang
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW 2011, Australia
| | - Melissa A. Merritt
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW 2011, Australia
| | - Robert C. Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA, 02114, USA
| | - Gerald F. Watts
- School of Medicine, University of Western Australia, Perth, WA 6009, Australia
- Departments of Cardiology and Internal Medicine, Royal Perth Hospital, Perth, WA, 6001, Australia
| | - Kristen J. Nowak
- Public and Aboriginal Health Division, Western Australia Department of Health, East Perth, WA, 6004, Australia
- Centre for Medical Research, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Karen Canfell
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, NSW 2011, Australia
| | - Paul James
- Parkville Familial Cancer Centre, Peter McCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, VIC, 3050, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, 3050, Australia
| | - Ingrid Winship
- Department of Genomic Medicine, Royal Melbourne Hospital City Campus, Parkville, VIC, 3050, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, 3050, Australia
| | - John J. McNeil
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Zanfina Ademi
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
- Health Economics and Policy Evaluation Research (HEPER) Group, Centre for Medicine Use and Safety, Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
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8
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Vassy JL, Brunette CA, Lebo MS, MacIsaac K, Yi T, Danowski ME, Alexander NVJ, Cardellino MP, Christensen KD, Gala M, Green RC, Harris E, Jones NE, Kerman BJ, Kraft P, Kulkarni P, Lewis ACF, Lubitz SA, Natarajan P, Antwi AA. The GenoVA study: Equitable implementation of a pragmatic randomized trial of polygenic-risk scoring in primary care. Am J Hum Genet 2023; 110:1841-1852. [PMID: 37922883 PMCID: PMC10645559 DOI: 10.1016/j.ajhg.2023.10.001] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Polygenic risk scores (PRSs) hold promise for disease risk assessment and prevention. The Genomic Medicine at Veterans Affairs (GenoVA) Study is addressing three main challenges to the clinical implementation of PRSs in preventive care: defining and determining their clinical utility, implementing them in time-constrained primary care settings, and countering their potential to exacerbate healthcare disparities. The study processes used to test patients, report their PRS results to them and their primary care providers (PCPs), and promote the use of those results in clinical decision-making are modeled on common practices in primary care. The following diseases were chosen for their prevalence and familiarity to PCPs: coronary artery disease; type 2 diabetes; atrial fibrillation; and breast, colorectal, and prostate cancers. A randomized clinical trial (RCT) design and primary outcome of time-to-new-diagnosis of a target disease bring methodological rigor to the question of the clinical utility of PRS implementation. The study's pragmatic RCT design enhances its relevance to how PRS might reasonably be implemented in primary care. Steps the study has taken to promote health equity include the thoughtful handling of genetic ancestry in PRS construction and reporting and enhanced recruitment strategies to address underrepresentation in research participation. To date, enhanced recruitment efforts have been both necessary and successful: participants of underrepresented race and ethnicity groups have been less likely to enroll in the study than expected but ultimately achieved proportional representation through targeted efforts. The GenoVA Study experience to date offers insights for evaluating the clinical utility of equitable PRS implementation in adult primary care.
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Affiliation(s)
- Jason L Vassy
- VA Boston Healthcare System, Boston, MA, USA; Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA.
| | - Charles A Brunette
- VA Boston Healthcare System, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Matthew S Lebo
- Harvard Medical School, Boston, MA, USA; Laboratory for Molecular Medicine, Mass General Brigham, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Thomas Yi
- VA Boston Healthcare System, Boston, MA, USA
| | | | - Nicholas V J Alexander
- VA Boston Healthcare System, Boston, MA, USA; Bucharest University Emergency Hospital, Bucharest, Romania; Bucharest University of Economic Studies, Bucharest, Romania
| | | | - Kurt D Christensen
- Harvard Medical School, Boston, MA, USA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Manish Gala
- Harvard Medical School, Boston, MA, USA; Division of Gastroenterology and Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Ariadne Labs, Boston, MA, USA; Department of Medicine (Genetics), Mass General Brigham, Boston, MA, USA
| | | | - Natalie E Jones
- VA Boston Healthcare System, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Benjamin J Kerman
- Division of General Internal Medicine and Primary Care, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Peter Kraft
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Anna C F Lewis
- Department of Medicine (Genetics), Mass General Brigham, Boston, MA, USA; Edmond and Lily Safra Center for Ethics, Harvard University, Boston, MA, USA
| | - Steven A Lubitz
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA; Novartis Institutes for BioMedical Research, Novartis, Basel, Basel-Stadt, Switzerland
| | - Pradeep Natarajan
- Harvard Medical School, Boston, MA, USA; Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
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9
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Koyama S, Wang Y, Paruchuri K, Uddin MM, Cho SMJ, Urbut SM, Haidermota S, Hornsby WE, Green RC, Daly MJ, Neale BM, Ellinor PT, Smoller JW, Lebo MS, Karlson EW, Martin AR, Natarajan P. Decoding Genetics, Ancestry, and Geospatial Context for Precision Health. medRxiv 2023:2023.10.24.23297096. [PMID: 37961173 PMCID: PMC10635180 DOI: 10.1101/2023.10.24.23297096] [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: 11/15/2023]
Abstract
Mass General Brigham, an integrated healthcare system based in the Greater Boston area of Massachusetts, annually serves 1.5 million patients. We established the Mass General Brigham Biobank (MGBB), encompassing 142,238 participants, to unravel the intricate relationships among genomic profiles, environmental context, and disease manifestations within clinical practice. In this study, we highlight the impact of ancestral diversity in the MGBB by employing population genetics, geospatial assessment, and association analyses of rare and common genetic variants. The population structures captured by the genetics mirror the sequential immigration to the Greater Boston area throughout American history, highlighting communities tied to shared genetic and environmental factors. Our investigation underscores the potency of unbiased, large-scale analyses in a healthcare-affiliated biobank, elucidating the dynamic interplay across genetics, immigration, structural geospatial factors, and health outcomes in one of the earliest American sites of European colonization.
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Affiliation(s)
- Satoshi Koyama
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ying Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kaavya Paruchuri
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Md Mesbah Uddin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - So Mi J. Cho
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Integrative Research Center for Cerebrovascular and Cardiovascular Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sarah M. Urbut
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sara Haidermota
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Whitney E. Hornsby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert C. Green
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine (Genetics), MassGeneralBrigham, Boston, MA, USA
- Broad Institute and Ariadne Labs, Boston, MA, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland (FIMM), Finland
- University of Helsinki, Helsinki, Finland
| | - Benjamin M. Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick T. Ellinor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jordan W. Smoller
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center for Precision Psychiatry, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew S. Lebo
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Elizabeth W. Karlson
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Department of Medicine, Brigham and Women’s Hospital., Boston, MA, USA
| | - Alicia R. Martin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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10
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Gold JI, Madhavan S, Park J, Zouk H, Perez E, Strong A, Drivas TG, Karaa A, Yudkoff M, Rader D, Green RC, Gold NB. Phenotypes of undiagnosed adults with actionable OTC and GLA variants. HGG Adv 2023; 4:100226. [PMID: 37593415 PMCID: PMC10428110 DOI: 10.1016/j.xhgg.2023.100226] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/21/2023] [Indexed: 08/19/2023] Open
Abstract
Inherited metabolic disorders (IMDs) are variably expressive, complicating identification of affected individuals. A genotype-first approach can identify individuals at risk for morbidity and mortality from undiagnosed IMDs and can lead to protocols that improve clinical detection, counseling, and management. Using data from 57,340 participants in two hospital biobanks, we assessed the frequency and phenotypes of individuals with pathogenic/likely pathogenic variants (PLPVs) in two IMD genes: GLA, associated with Fabry disease, and OTC, associated with ornithine transcarbamylase deficiency. Approximately 1 in 19,100 participants harbored an undiagnosed PLPV in GLA or OTC. We identified three individuals (2 male, 1 female) with PLPVs in GLA, all of whom were undiagnosed, and three individuals (3 female) with PLPVs in OTC, two of whom were undiagnosed. All three individuals with PLPVs in GLA (100%) had symptoms suggestive of mild Fabry disease, and one individual (14.2%) had an ischemic stroke at age 33, likely indicating the presence of classic disease. No individuals with PLPVs in OTC had documented hyperammonemia despite exposure to catabolic states, but all (100%) had chronic symptoms suggestive of attenuated disease, including mood disorders and migraines. Our findings suggest that GLA and OTC variants identified via a genotype-first approach are of high penetrance and that population screening of these genes can be used to facilitate stepwise phenotyping and appropriate care.
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Affiliation(s)
- Jessica I. Gold
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
| | - Sarina Madhavan
- Harvard Medical School, Boston, MA, USA
- Harvard Business School, Cambridge, MA, USA
| | - Joseph Park
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hana Zouk
- Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Emma Perez
- Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Alanna Strong
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Theodore G. Drivas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Amel Karaa
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Marc Yudkoff
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel Rader
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Regeneron Genetics Center
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Harvard Medical School, Boston, MA, USA
- Harvard Business School, Cambridge, MA, USA
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Broad Institute, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
| | - Penn Medicine BioBank
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia; Philadelphia, PA, USA
- Harvard Medical School, Boston, MA, USA
- Harvard Business School, Cambridge, MA, USA
- Department of Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Mass General Brigham Personalized Medicine, Cambridge MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Broad Institute, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
| | - Robert C. Green
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
| | - Nina B. Gold
- Massachusetts General Hospital for Children, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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11
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Vockley J, Brunetti-Pierri N, Chung WK, Clarke AJ, Gold N, Green RC, Kagan S, Moroz T, Schaaf CP, Schulz M, De Baere E. Response to Beretich and Beretich. Genet Med 2023; 25:100903. [PMID: 37245089 DOI: 10.1016/j.gim.2023.100903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Affiliation(s)
- Jerry Vockley
- University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA.
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Wendy K Chung
- Division of Molecular Genetics, Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - Angus J Clarke
- Cancer & Genetics, School of Medicine, Cardiff University, Wales, United Kingdom
| | - Nina Gold
- Mass General Hospital for Children, Division of Medical Genetics and Metabolism and Harvard Medical School, Boston, MA
| | - Robert C Green
- MassGeneralBrigham, Ariadne Labs, Broad Institute and Harvard Medical School, Boston, MA
| | - Stephen Kagan
- Gene Therapy Platform and Cross Portfolio, Global Medical Affairs, Rare Disease, Pfizer Inc
| | - Tara Moroz
- Gene Therapy Platform and Cross Portfolio, Global Medical Affairs, Rare Disease, Pfizer Inc
| | | | - Martin Schulz
- Gene Therapy Platform and Cross Portfolio, Global Medical Affairs, Rare Disease, Pfizer Inc
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital and Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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12
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Abstract
Genome sequencing is increasingly used in research and integrated into clinical care. In the research domain, large-scale analyses, including whole genome sequencing with variant interpretation and curation, virtually guarantee identification of variants that are pathogenic or likely pathogenic and actionable. Multiple guidelines recommend that findings associated with actionable conditions be offered to research participants in order to demonstrate respect for autonomy, reciprocity, and participant interests in health and privacy. Some recommendations go further and support offering a wider range of findings, including those that are not immediately actionable. In addition, entities covered by the US Health Insurance Portability and Accountability Act (HIPAA) may be required to provide a participant's raw genomic data on request. Despite these widely endorsed guidelines and requirements, the implementation of return of genomic results and data by researchers remains uneven. This article analyzes the ethical and legal foundations for researcher duties to offer adult participants their interpreted results and raw data as the new normal in genomic research.
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Affiliation(s)
- Susan M Wolf
- Law School and Medical School, University of Minnesota, Minneapolis, Minnesota, USA;
| | - Robert C Green
- Genomes2People Research Program, Harvard Medical School, Mass General Brigham, Broad Institute, and Ariadne Labs, Boston, Massachusetts, USA;
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13
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Rajabli F, Benchek P, Tosto G, Kushch N, Sha J, Bazemore K, Zhu C, Lee WP, Haut J, Hamilton-Nelson KL, Wheeler NR, Zhao Y, Farrell JJ, Grunin MA, Leung YY, Kuksa PP, Li D, Lucio da Fonseca E, Mez JB, Palmer EL, Pillai J, Sherva RM, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Abner E, Adams PM, Aguirre A, Albert MS, Albin RL, Allen M, Alvarez L, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Ayres G, Baldwin CT, Barber RC, Barnes LL, Barral S, Beach TG, Becker JT, Beecham GW, Beekly D, Benitez BA, Bennett D, Bertelson J, Bird TD, Blacker D, Boeve BF, Bowen JD, Boxer A, Brewer J, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Chasse S, Chesselet MF, Chin NA, Chui HC, Chung J, Craft S, Crane PK, Cribbs DH, Crocco EA, Cruchaga C, Cuccaro ML, Cullum M, Darby E, Davis B, De Jager PL, DeCarli C, DeToledo J, Dick M, Dickson DW, Dombroski BA, Doody RS, Duara R, Ertekin-Taner NI, Evans DA, Faber KM, Fairchild TJ, Fallon KB, Fardo DW, Farlow MR, Fernandez-Hernandez V, Ferris S, Foroud TM, Frosch MP, Fulton-Howard B, Galasko DR, Gamboa A, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Goate AM, Grabowski TJ, Graff-Radford NR, Green RC, Growdon JH, Hakonarson H, Hall J, Hamilton RL, Harari O, Hardy J, Harrell LE, Head E, Henderson VW, Hernandez M, Hohman T, Honig LS, Huebinger RM, Huentelman MJ, Hulette CM, Hyman BT, Hynan LS, Ibanez L, Jarvik GP, Jayadev S, Jin LW, Johnson K, Johnson L, Kamboh MI, Karydas AM, Katz MJ, Kauwe JS, Kaye JA, Keene CD, Khaleeq A, Kim R, Knebl J, Kowall NW, Kramer JH, Kukull WA, LaFerla FM, Lah JJ, Larson EB, Lerner A, Leverenz JB, Levey AI, Lieberman AP, Lipton RB, Logue M, Lopez OL, Lunetta KL, Lyketsos CG, Mains D, Margaret FE, Marson DC, Martin ERR, Martiniuk F, Mash DC, Masliah E, Massman P, Masurkar A, McCormick WC, McCurry SM, McDavid AN, McDonough S, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Montine TJ, Monuki ES, Morris JC, Mukherjee S, Myers AJ, Nguyen T, O'Bryant S, Olichney JM, Ory M, Palmer R, Parisi JE, Paulson HL, Pavlik V, Paydarfar D, Perez V, Peskind E, Petersen RC, Pierce A, Polk M, Poon WW, Potter H, Qu L, Quiceno M, Quinn JF, Raj A, Raskind M, Reiman EM, Reisberg B, Reisch JS, Ringman JM, Roberson ED, Rodriguear M, Rogaeva E, Rosen HJ, Rosenberg RN, Royall DR, Sager MA, Sano M, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Slifer SH, Small S, Smith AG, Smith JP, Sonnen JA, Spina S, St George-Hyslop P, Stern RA, Stevens AB, Strittmatter SM, Sultzer D, Swerdlow RH, Tanzi RE, Tilson JL, Trojanowski JQ, Troncoso JC, Tsuang DW, Van Deerlin VM, van Eldik LJ, Vance JM, Vardarajan BN, Vassar R, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Whitehead PL, Wijsman EM, Wilhelmsen KC, Williams B, Williamson J, Wilms H, Wingo TS, Wisniewski T, Woltjer RL, Woon M, Wright CB, Wu CK, Younkin SG, Yu CE, Yu L, Zhu X, Kunkle BW, Bush WS, Wang LS, Farrer LA, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Jun GR, Reitz C, Naj AC. Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies LRRC4C, LHX5-AS1 and nominates ancestry-specific loci PTPRK , GRB14 , and KIAA0825 as novel risk loci for Alzheimer's disease: the Alzheimer's Disease Genetics Consortium. medRxiv 2023:2023.07.06.23292311. [PMID: 37461624 PMCID: PMC10350126 DOI: 10.1101/2023.07.06.23292311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Limited ancestral diversity has impaired our ability to detect risk variants more prevalent in non-European ancestry groups in genome-wide association studies (GWAS). We constructed and analyzed a multi-ancestry GWAS dataset in the Alzheimer's Disease (AD) Genetics Consortium (ADGC) to test for novel shared and ancestry-specific AD susceptibility loci and evaluate underlying genetic architecture in 37,382 non-Hispanic White (NHW), 6,728 African American, 8,899 Hispanic (HIS), and 3,232 East Asian individuals, performing within-ancestry fixed-effects meta-analysis followed by a cross-ancestry random-effects meta-analysis. We identified 13 loci with cross-ancestry associations including known loci at/near CR1 , BIN1 , TREM2 , CD2AP , PTK2B , CLU , SHARPIN , MS4A6A , PICALM , ABCA7 , APOE and two novel loci not previously reported at 11p12 ( LRRC4C ) and 12q24.13 ( LHX5-AS1 ). Reflecting the power of diverse ancestry in GWAS, we observed the SHARPIN locus using 7.1% the sample size of the original discovering single-ancestry GWAS (n=788,989). We additionally identified three GWS ancestry-specific loci at/near ( PTPRK ( P =2.4×10 -8 ) and GRB14 ( P =1.7×10 -8 ) in HIS), and KIAA0825 ( P =2.9×10 -8 in NHW). Pathway analysis implicated multiple amyloid regulation pathways (strongest with P adjusted =1.6×10 -4 ) and the classical complement pathway ( P adjusted =1.3×10 -3 ). Genes at/near our novel loci have known roles in neuronal development ( LRRC4C, LHX5-AS1 , and PTPRK ) and insulin receptor activity regulation ( GRB14 ). These findings provide compelling support for using traditionally-underrepresented populations for gene discovery, even with smaller sample sizes.
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Green RC, Shah N, Genetti CA, Yu T, Zettler B, Uveges MK, Ceyhan-Birsoy O, Lebo MS, Pereira S, Agrawal PB, Parad RB, McGuire AL, Christensen KD, Schwartz TS, Rehm HL, Holm IA, Beggs AH. Actionability of unanticipated monogenic disease risks in newborn genomic screening: Findings from the BabySeq Project. Am J Hum Genet 2023; 110:1034-1045. [PMID: 37279760 PMCID: PMC10357495 DOI: 10.1016/j.ajhg.2023.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 02/03/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
Newborn genomic sequencing (NBSeq) to screen for medically important genetic information is of considerable interest but data characterizing the actionability of such findings, and the downstream medical efforts in response to discovery of unanticipated genetic risk variants, are lacking. From a clinical trial of comprehensive exome sequencing in 127 apparently healthy infants and 32 infants in intensive care, we previously identified 17 infants (10.7%) with unanticipated monogenic disease risks (uMDRs). In this analysis, we assessed actionability for each of these uMDRs with a modified ClinGen actionability semiquantitative metric (CASQM) and created radar plots representing degrees of penetrance of the condition, severity of the condition, effectiveness of intervention, and tolerability of intervention. In addition, we followed each of these infants for 3-5 years after disclosure and tracked the medical actions prompted by these findings. All 17 uMDR findings were scored as moderately or highly actionable on the CASQM (mean 9, range: 7-11 on a 0-12 scale) and several distinctive visual patterns emerged on the radar plots. In three infants, uMDRs revealed unsuspected genetic etiologies for existing phenotypes, and in the remaining 14 infants, uMDRs provided risk stratification for future medical surveillance. In 13 infants, uMDRs prompted screening for at-risk family members, three of whom underwent cancer-risk-reducing surgeries. Although assessments of clinical utility and cost-effectiveness will require larger datasets, these findings suggest that large-scale comprehensive sequencing of newborns will reveal numerous actionable uMDRs and precipitate substantial, and in some cases lifesaving, downstream medical care in newborns and their family members.
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Affiliation(s)
- Robert C Green
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ariadne Labs, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA.
| | - Nidhi Shah
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Dartmouth Health Children's, Lebanon, NH 03756, USA
| | - Casie A Genetti
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Timothy Yu
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Bethany Zettler
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Ariadne Labs, Boston, MA 02215, USA
| | - Melissa K Uveges
- William F. Connell School of Nursing, Boston College, Chestnut Hill, MA 02467, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew S Lebo
- Department of Medicine, Mass General Brigham, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine; Houston, TX, USA
| | - Pankaj B Agrawal
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Division of Neonatology, Department of Pediatrics, University of Miami Miller School of Medicine and Holtz Children's Hospital, Jackson Health System, Miami, FL, USA
| | - Richard B Parad
- Harvard Medical School, Boston, MA 02215, USA; Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine; Houston, TX, USA
| | - Kurt D Christensen
- Harvard Medical School, Boston, MA 02215, USA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Talia S Schwartz
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alan H Beggs
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02215, USA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
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15
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Preys CL, Blout Zawatsky CL, Massmann A, Heukelom JV, Green RC, Hajek C, Hickingbotham MR, Zoltick ES, Schultz A, Christensen KD. Attitudes about pharmacogenomic testing vary by healthcare specialty. Pharmacogenomics 2023; 24:539-549. [PMID: 37458095 PMCID: PMC10621761 DOI: 10.2217/pgs-2023-0039] [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: 03/06/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Aim: To understand how attitudes toward pharmacogenomic (PGx) testing among healthcare providers varies by specialty. Methods: Providers reported comfort ordering PGx testing and its perceived utility on web-based surveys before and after genetics education. Primary quantitative analyses compared primary care providers (PCPs) to specialty providers at both timepoints. Results: PCPs were more likely than specialty care providers to rate PGx testing as useful at both timepoints. Education increased comfort ordering PGx tests, with larger improvements among PCPs than specialty providers. Over 90% of cardiology and internal medicine providers rated PGx testing as useful at pre- and post-education. Conclusion: PCPs overwhelmingly perceive PGx to be useful, and provider education is particularly effective for improving PCPs' confidence. Education for all specialties will be essential to ensure appropriate integration into routine practice.
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Affiliation(s)
- Charlene L Preys
- MGH Institute of Health Professions, Charlestown, MA 02129, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Carrie L Blout Zawatsky
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Ariadne Labs, Boston, MA 02215, USA
| | - Amanda Massmann
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermilion, SD 57069, USA
| | - Joel Van Heukelom
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermilion, SD 57069, USA
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Ariadne Labs, Boston, MA 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Catherine Hajek
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Helix OpCo, LLC, San Diego, CA 92121, USA
| | - Madison R Hickingbotham
- Precision Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Emilie S Zoltick
- Precision Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - April Schultz
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermilion, SD 57069, USA
| | - Kurt D Christensen
- Ariadne Labs, Boston, MA 02215, USA
- Precision Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Population Medicine, Harvard Medical School, Boston, MA 02115, USA
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16
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Kingsmore SF, Smith LD, Kunard CM, Bainbridge M, Batalov S, Benson W, Blincow E, Caylor S, Chambers C, Del Angel G, Dimmock DP, Ding Y, Ellsworth K, Feigenbaum A, Frise E, Green RC, Guidugli L, Hall KP, Hansen C, Hobbs CA, Kahn SD, Kiel M, Van Der Kraan L, Krilow C, Kwon YH, Madhavrao L, Le J, Lefebvre S, Mardach R, Mowrey WR, Oh D, Owen MJ, Powley G, Scharer G, Shelnutt S, Tokita M, Mehtalia SS, Oriol A, Papadopoulos S, Perry J, Rosales E, Sanford E, Schwartz S, Tran D, Reese MG, Wright M, Veeraraghavan N, Wigby K, Willis MJ, Wolen AR, Defay T. Response to Grosse et al. Am J Hum Genet 2023; 110:1017. [PMID: 37267897 PMCID: PMC10256999 DOI: 10.1016/j.ajhg.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Keck Graduate Institute, Claremont, CA 91711, USA.
| | - Laurie D Smith
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Matthew Bainbridge
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sergey Batalov
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Wendy Benson
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Eric Blincow
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Sara Caylor
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Christina Chambers
- Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Katarzyna Ellsworth
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Annette Feigenbaum
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612, USA
| | - Robert C Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA 02115, USA
| | - Lucia Guidugli
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Christian Hansen
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Mark Kiel
- Genomenon, Inc., Ann Arbor, MI 48108, USA
| | - Lucita Van Der Kraan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Yong H Kwon
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Lakshminarasimha Madhavrao
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Jennie Le
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Rebecca Mardach
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Danny Oh
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Mallory J Owen
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Gunter Scharer
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Mari Tokita
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - Albert Oriol
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | | | - James Perry
- Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Edwin Rosales
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Duke Tran
- Illumina, Inc., San Diego, CA 92122, USA
| | | | - Meredith Wright
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Narayanan Veeraraghavan
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA; Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mary J Willis
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay
- Alexion, Astra Zeneca Rare Disease, Boston, MA 02210, USA
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17
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Gold NB, Adelson SM, Shah N, Williams S, Bick SL, Zoltick ES, Gold JI, Strong A, Ganetzky R, Roberts AE, Walker M, Holtz AM, Sankaran VG, Delmonte O, Tan W, Holm IA, Thiagarajah JR, Kamihara J, Comander J, Place E, Wiggs J, Green RC. Perspectives of Rare Disease Experts on Newborn Genome Sequencing. JAMA Netw Open 2023; 6:e2312231. [PMID: 37155167 PMCID: PMC10167563 DOI: 10.1001/jamanetworkopen.2023.12231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/23/2023] [Indexed: 05/10/2023] Open
Abstract
Importance Newborn genome sequencing (NBSeq) can detect infants at risk for treatable disorders currently undetected by conventional newborn screening. Despite broad stakeholder support for NBSeq, the perspectives of rare disease experts regarding which diseases should be screened have not been ascertained. Objective To query rare disease experts about their perspectives on NBSeq and which gene-disease pairs they consider appropriate to evaluate in apparently healthy newborns. Design, Setting, and Participants This survey study, designed between November 2, 2021, and February 11, 2022, assessed experts' perspectives on 6 statements related to NBSeq. Experts were also asked to indicate whether they would recommend including each of 649 gene-disease pairs associated with potentially treatable conditions in NBSeq. The survey was administered between February 11 and September 23, 2022, to 386 experts, including all 144 directors of accredited medical and laboratory genetics training programs in the US. Exposures Expert perspectives on newborn screening using genome sequencing. Main Outcomes and Measures The proportion of experts indicating agreement or disagreement with each survey statement and those who selected inclusion of each gene-disease pair were tabulated. Exploratory analyses of responses by gender and age were conducted using t and χ2 tests. Results Of 386 experts invited, 238 (61.7%) responded (mean [SD] age, 52.6 [12.8] years [range 27-93 years]; 126 [52.9%] women and 112 [47.1%] men). Among the experts who responded, 161 (87.9%) agreed that NBSeq for monogenic treatable disorders should be made available to all newborns; 107 (58.5%) agreed that NBSeq should include genes associated with treatable disorders, even if those conditions were low penetrance; 68 (37.2%) agreed that actionable adult-onset conditions should be sequenced in newborns to facilitate cascade testing in parents, and 51 (27.9%) agreed that NBSeq should include screening for conditions with no established therapies or management guidelines. The following 25 genes were recommended by 85% or more of the experts: OTC, G6PC, SLC37A4, CYP11B1, ARSB, F8, F9, SLC2A1, CYP17A1, RB1, IDS, GUSB, DMD, GLUD1, CYP11A1, GALNS, CPS1, PLPBP, ALDH7A1, SLC26A3, SLC25A15, SMPD1, GATM, SLC7A7, and NAGS. Including these, 42 gene-disease pairs were endorsed by at least 80% of experts, and 432 genes were endorsed by at least 50% of experts. Conclusions and Relevance In this survey study, rare disease experts broadly supported NBSeq for treatable conditions and demonstrated substantial concordance regarding the inclusion of a specific subset of genes in NBSeq.
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Affiliation(s)
- Nina B. Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Sophia M. Adelson
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
| | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
- Geisel School of Medicine, Hanover, New Hampshire
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
| | - Shardae Williams
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
| | - Sarah L. Bick
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
| | - Emilie S. Zoltick
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Center for Healthcare Research in Pediatrics, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jessica I. Gold
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alanna Strong
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Rebecca Ganetzky
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Amy E. Roberts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Department of Cardiology and Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts
| | - Melissa Walker
- Division of Pediatric Neurology, Massachusetts General Hospital for Children, Boston
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Alexander M. Holtz
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
| | - Vijay G. Sankaran
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ottavia Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Weizhen Tan
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Pediatric Nephrology, Massachusetts General Hospital for Children, Boston
| | - Ingrid A. Holm
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts
- Manton Center for Orphan Diseases Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Jay R. Thiagarajah
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | - Junne Kamihara
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jason Comander
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Emily Place
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Janey Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts
| | - Robert C. Green
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Ariadne Labs, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute, Boston, Massachusetts
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18
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Massmann A, Van Heukelom J, Green RC, Hajek C, Hickingbotham MR, Larson EA, Lu CY, Wu AC, Zoltick ES, Christensen KD, Schultz A. SLCO1B1 gene-based clinical decision support reduces statin-associated muscle symptoms risk with simvastatin. Pharmacogenomics 2023; 24:399-409. [PMID: 37232094 PMCID: PMC10242433 DOI: 10.2217/pgs-2023-0056] [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: 04/03/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
Background: SLCO1B1 variants are known to be a strong predictor of statin-associated muscle symptoms (SAMS) risk with simvastatin. Methods: The authors conducted a retrospective chart review on 20,341 patients who had SLCO1B1 genotyping to quantify the uptake of clinical decision support (CDS) for genetic variants known to impact SAMS risk. Results: A total of 182 patients had 417 CDS alerts generated, and 150 of these patients (82.4%) received pharmacotherapy that did not increase risks for SAMS. Providers were more likely to cancel simvastatin orders in response to CDS alerts if genotyping had been done prior to the first simvastatin prescription than after (94.1% vs 28.5%, respectively; p < 0.001). Conclusion: CDS significantly reduces simvastatin prescribing at doses associated with SAMS.
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Affiliation(s)
- Amanda Massmann
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD 57069, USA
| | - Joel Van Heukelom
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD 57069, USA
| | - Robert C Green
- Department of Medicine, Brigham & Women's Hospital & Harvard Medical School, Boston, MA 02115, USA
- Ariadne Labs, Boston, MA 02215, USA
- Broad Institute of Harvard & MIT, Cambridge, MA 02142, USA
| | - Catherine Hajek
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Helix OpCo, LLC, San Mateo, CA 94401, USA
| | - Madison R Hickingbotham
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Eric A Larson
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD 57069, USA
| | - Christine Y Lu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Population Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Ann Chen Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Population Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Emilie S Zoltick
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Kurt D Christensen
- Broad Institute of Harvard & MIT, Cambridge, MA 02142, USA
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Population Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - April Schultz
- Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57105, USA
- Department of Internal Medicine, University of South Dakota School of Medicine, Vermillion, SD 57069, USA
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19
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Vockley J, Brunetti-Pierri N, Chung WK, Clarke AJ, Gold N, Green RC, Kagan S, Moroz T, Schaaf CP, Schulz M, De Baere E. The evolving role of medical geneticists in the era of gene therapy: An urgency to prepare. Genet Med 2023; 25:100022. [PMID: 36681872 PMCID: PMC10643995 DOI: 10.1016/j.gim.2023.100022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Affiliation(s)
- Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA.
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Naples, Italy; Department of Translational Medicine, Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Wendy K Chung
- Division of Molecular Genetics, Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - Angus J Clarke
- Cancer and Genetics, School of Medicine, Cardiff University, Wales, United Kingdom
| | - Nina Gold
- Division of Medical Genetics and Metabolism, Pediatrics, Mass General Hospital for Children, Harvard Medical School, Boston, MA
| | - Robert C Green
- Department of Medicine (Genetics), Mass General Brigham, Ariadne Labs, Broad Institute and Harvard Medical School, Boston, MA
| | - Stephen Kagan
- Genetic Medicine and Pipeline, Global Medical Affairs, Rare Disease, Pfizer Inc, New York, NY
| | - Tara Moroz
- Genetic Medicine and Pipeline, Global Medical Affairs, Rare Disease, Pfizer Inc, New York, NY
| | | | - Martin Schulz
- Genetic Medicine and Pipeline, Global Medical Affairs, Rare Disease, Pfizer Inc, New York, NY
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital and Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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20
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Affiliation(s)
- Paul Lacaze
- Public Health Genomics, Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia.
| | - Ranjit Manchanda
- Wolfson Institute of Population Health, CRUK Barts Centre, Queen Mary University of London, London, UK
- Department of Gynaecological Oncology, St Bartholomew's Hospital, London, UK
- Department of Health Services Research, Faculty of Public Health & Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Robert C Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA, USA
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21
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Pereira S, Gutierrez AM, Robinson JO, Christensen KD, Genetti CA, Blout Zawatsky CL, Hsu RL, Zettler B, Uveges MK, Parad RB, Beggs AH, Holm IA, Green RC, McGuire AL. Parents' decision-making regarding whether to receive adult-onset only genetic findings for their children: Findings from the BabySeq Project. Genet Med 2023; 25:100002. [PMID: 36549595 PMCID: PMC9992280 DOI: 10.1016/j.gim.2022.100002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/02/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Most professional guidelines recommend against genetic screening for adult-onset only (AO) conditions until adulthood, yet others argue that there may be benefit to disclosing such results. We explored parents' decision-making on this issue in the BabySeq Project, a clinical trial of newborn genomic sequencing. METHODS We conducted interviews with parents (N = 24) who were given the option to receive actionable AO results for their children. Interviews explored parents' motivations to receive and reasons to decline AO genetic disease risk information, their decision-making process, and their suggestions for supporting parents in making this decision. RESULTS Parents noted several motivations to receive and reasons to decline AO results. Most commonly, parents cited early intervention/surveillance (n = 11), implications for family health (n = 7), and the ability to prepare (n = 6) as motivations to receive these results. The most common reasons to decline were protection of the child's future autonomy (n = 4), negative effect on parenting (n = 3), and anxiety about future disease (n = 3). Parents identified a number of ways to support parents in making this decision. CONCLUSION Results show considerations to better support parental decision-making that aligns with their values when offering AO genetic information because it is more commonly integrated into pediatric clinical care.
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Affiliation(s)
- Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX.
| | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Jill Oliver Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine at Harvard Pilgrim Health Care Institute, Boston, MA; Department of Population Medicine, Harvard Medical School, Boston, MA
| | - Casie A Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
| | - Carrie L Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Medical and Population Genetics, The Broad Institute, Cambridge, MA; Brigham and Women's Hospital and the Harvard T.H. Chan School of Public Health, Ariadne Labs, Boston, MA; The MGH Institute of Health Professions, Boston, MA
| | - Rebecca L Hsu
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
| | - Bethany Zettler
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | | | - Richard B Parad
- Department of Pediatrics, Harvard Medical School, Boston, MA; Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Boston, MA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA; The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ingrid A Holm
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA; Harvard Medical School, Boston, MA; The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Brigham and Women's Hospital and the Harvard T.H. Chan School of Public Health, Ariadne Labs, Boston, MA; Harvard Medical School, Boston, MA; The Broad Institute of MIT and Harvard, Cambridge, MA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX
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22
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Yu TW, Kingsmore SF, Green RC, MacKenzie T, Wasserstein M, Caggana M, Gold NB, Kennedy A, Kishnani PS, Might M, Brooks PJ, Morris JA, Parisi MA, Urv TK. Are we prepared to deliver gene-targeted therapies for rare diseases? Am J Med Genet C Semin Med Genet 2023; 193:7-12. [PMID: 36691939 DOI: 10.1002/ajmg.c.32029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 01/25/2023]
Abstract
The cost and time needed to conduct whole-genome sequencing (WGS) have decreased significantly in the last 20 years. At the same time, the number of conditions with a known molecular basis has steadily increased, as has the number of investigational new drug applications for novel gene-based therapeutics. The prospect of precision gene-targeted therapy for all seems in reach… or is it? Here we consider practical and strategic considerations that need to be addressed to establish a foundation for the early, effective, and equitable delivery of these treatments.
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Affiliation(s)
- Timothy W Yu
- Division of Genetics and Genomics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Robert C Green
- Department of Genetics-Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tippi MacKenzie
- Department of Surgery and the Center for Maternal-Fetal Precision Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Melissa Wasserstein
- Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore, New York, New York, USA
| | - Michele Caggana
- Division of Genetics, New York State Department of Health, Albany, New York, USA
| | - Nina B Gold
- Massachusetts General Hospital Department of Pediatrics, Boston, Massachusetts, USA
| | - Annie Kennedy
- EveryLife Foundation for Rare Diseases, Washington, District of Columbia, USA
| | - Priya S Kishnani
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Matthew Might
- Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Phillip J Brooks
- Office of Rare Disease Research, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, Maryland, USA
| | - Jill A Morris
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Melissa A Parisi
- Intellectual and Developmental Disabilities Branch, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Tiina K Urv
- Office of Rare Disease Research, National Center for Advancing Translational Science, National Institutes of Health, Bethesda, Maryland, USA
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23
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Lekstrom-Himes J, Brooks PJ, Koeberl DD, Brower A, Goldenberg A, Green RC, Morris JA, Orsini JJ, Yu TW, Augustine EF. Moving away from one disease at a time: Screening, trial design, and regulatory implications of novel platform technologies. Am J Med Genet C Semin Med Genet 2023; 193:30-43. [PMID: 36738469 PMCID: PMC10038900 DOI: 10.1002/ajmg.c.32031] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/16/2022] [Accepted: 01/04/2023] [Indexed: 02/06/2023]
Abstract
Most rare diseases are caused by single-gene mutations, and as such, lend themselves to a host of new gene-targeted therapies and technologies including antisense oligonucleotides, phosphomorpholinos, small interfering RNAs, and a variety of gene delivery and gene editing systems. Early successes are encouraging, however, given the substantial number of distinct rare diseases, the ability to scale these successes will be unsustainable without new development efficiencies. Herein, we discuss the need for genomic newborn screening to match pace with the growing development of targeted therapeutics and ability to rapidly develop individualized therapies for rare variants. We offer approaches to move beyond conventional "one disease at a time" preclinical and clinical drug development and discuss planned regulatory innovations that are necessary to speed therapy delivery to individuals in need. These proposals leverage the shared properties of platform classes of therapeutics and innovative trial designs including master and platform protocols to better serve patients and accelerate drug development. Ultimately, there are risks to these novel approaches; however, we believe that close partnership and transparency between health authorities, patients, researchers, and drug developers present the path forward to overcome these challenges and deliver on the promise of gene-targeted therapies for rare diseases.
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Affiliation(s)
| | - P J Brooks
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Dwight D Koeberl
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Amy Brower
- American College of Medical Genetics and Genomics, Bethesda, Maryland, USA
| | - Aaron Goldenberg
- Department of Bioethics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robert C Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA, USA
| | - Jill A Morris
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph J Orsini
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, Harvard Medical School, Boston, Massachusetts, USA
| | - Erika F Augustine
- Department of Neurology and Neurodevelopmental Medicine, Kennedy Krieger Institute, Baltimore, Maryland, USA
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24
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Weiner MW, Veitch DP, Miller MJ, Aisen PS, Albala B, Beckett LA, Green RC, Harvey D, Jack CR, Jagust W, Landau SM, Morris JC, Nosheny R, Okonkwo OC, Perrin RJ, Petersen RC, Rivera‐Mindt M, Saykin AJ, Shaw LM, Toga AW, Tosun D, Trojanowski JQ. Increasing participant diversity in AD research: Plans for digital screening, blood testing, and a community-engaged approach in the Alzheimer's Disease Neuroimaging Initiative 4. Alzheimers Dement 2023; 19:307-317. [PMID: 36209495 PMCID: PMC10042173 DOI: 10.1002/alz.12797] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [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: 04/19/2022] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 01/18/2023]
Abstract
INTRODUCTION The Alzheimer's Disease Neuroimaging Initiative (ADNI) aims to validate biomarkers for Alzheimer's disease (AD) clinical trials. To improve generalizability, ADNI4 aims to enroll 50-60% of its new participants from underrepresented populations (URPs) using new biofluid and digital technologies. ADNI4 has received funding from the National Institute on Aging beginning September 2022. METHODS ADNI4 will recruit URPs using community-engaged approaches. An online portal will screen 20,000 participants, 4000 of whom (50-60% URPs) will be tested for plasma biomarkers and APOE. From this, 500 new participants will undergo in-clinic assessment joining 500 ADNI3 rollover participants. Remaining participants (∼3500) will undergo longitudinal plasma and digital cognitive testing. ADNI4 will add MRI sequences and new PET tracers. Project 1 will optimize biomarkers in AD clinical trials. RESULTS AND DISCUSSION ADNI4 will improve generalizability of results, use remote digital and blood screening, and continue providing longitudinal clinical, biomarker, and autopsy data to investigators.
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Affiliation(s)
- Michael W. Weiner
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of Psychiatry and Behavioral SciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Dallas P. Veitch
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Northern California Institute for Research and Education (NCIRE)Department of Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
| | - Melanie J. Miller
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Northern California Institute for Research and Education (NCIRE)Department of Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
| | - Paul S. Aisen
- Alzheimer's Therapeutic Research InstituteUniversity of Southern CaliforniaSan DiegoCaliforniaUSA
| | - Bruce Albala
- Department of NeurologyUniversity of California Irvine School of MedicineIrvineCaliforniaUSA
| | - Laurel A. Beckett
- Division of BiostatisticsDepartment of Public Health SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Robert C. Green
- Division of GeneticsDepartment of MedicineBrigham and Women's Hospital, Broad Institute Ariadne Labs and Harvard Medical SchoolBostonMassachusettsUSA
| | - Danielle Harvey
- Division of BiostatisticsDepartment of Public Health SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | | | - William Jagust
- Helen Wills Neuroscience InstituteUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Susan M. Landau
- Helen Wills Neuroscience InstituteUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - John C. Morris
- Knight Alzheimer's Disease Research CenterWashington University School of MedicineSaint LouisMissouriUSA
- Department of NeurologyWashington University School of MedicineSaint LouisMissouriUSA
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMissouriUSA
| | - Rachel Nosheny
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Department of Psychiatry and Behavioral SciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Ozioma C. Okonkwo
- Wisconsin Alzheimer's Disease Research Center and Department of MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Richard J. Perrin
- Knight Alzheimer's Disease Research CenterWashington University School of MedicineSaint LouisMissouriUSA
- Department of NeurologyWashington University School of MedicineSaint LouisMissouriUSA
- Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMissouriUSA
| | | | - Monica Rivera‐Mindt
- Department of PsychologyLatin American and Latino Studies Institute, & African and African American StudiesFordham UniversityNew YorkNew YorkUSA
- Department of NeurologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer's Disease Research CenterIndiana University School of MedicineIndianapolisINUSA
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Leslie M Shaw
- Department of Pathology and Laboratory Medicine and the PENN Alzheimer's Disease Research CenterCenter for Neurodegenerative ResearchPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Arthur W. Toga
- Laboratory of Neuro ImagingInstitute of Neuroimaging and InformaticsKeck School of Medicine of University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Duygu Tosun
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - John Q. Trojanowski
- Department of Pathology and Laboratory Medicine and the PENN Alzheimer's Disease Research CenterCenter for Neurodegenerative ResearchPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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25
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Lewis ACF, Molina SJ, Appelbaum PS, Dauda B, Fuentes A, Fullerton SM, Garrison NA, Ghosh N, Green RC, Hammonds EM, Jeff JM, Jones DS, Kenny EE, Kraft P, Mauro M, Ori APS, Panofsky A, Sohail M, Neale BM, Allen DS. An Ethical Framework for Research Using Genetic Ancestry. Perspect Biol Med 2023; 66:225-248. [PMID: 37755714 DOI: 10.1353/pbm.2023.0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
A wide range of research uses patterns of genetic variation to infer genetic similarity between individuals, typically referred to as genetic ancestry. This research includes inference of human demographic history, understanding the genetic architecture of traits, and predicting disease risk. Researchers are not just structuring an intellectual inquiry when using genetic ancestry, they are also creating analytical frameworks with broader societal ramifications. This essay presents an ethics framework in the spirit of virtue ethics for these researchers: rather than focus on rule following, the framework is designed to build researchers' capacities to react to the ethical dimensions of their work. The authors identify one overarching principle of intellectual freedom and responsibility, noting that freedom in all its guises comes with responsibility, and they identify and define four principles that collectively uphold researchers' intellectual responsibility: truthfulness, justice and fairness, anti-racism, and public beneficence. Researchers should bring their practices into alignment with these principles, and to aid this, the authors name three common ways research practices infringe these principles, suggest a step-by-step process for aligning research choices with the principles, provide rules of thumb for achieving alignment, and give a worked case. The essay concludes by identifying support needed by researchers to act in accord with the proposed framework.
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26
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Tiller JM, Bakshi A, Brotchie AR, Green RC, Winship IM, Lacaze P. Public willingness to participate in population DNA screening in Australia. J Med Genet 2022:jmg-2022-108921. [DOI: 10.1136/jmg-2022-108921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/01/2022] [Indexed: 12/02/2022]
Abstract
BackgroundPopulation-based DNA screening for medically actionable conditions has the potential to improve public health by enabling early detection, treatment and/or prevention; however, public attitudes and willingness to participate in DNA screening have not been well investigated.MethodsWe presented a scenario to members of the Australian public, randomly selected from the electoral roll via the Australian Survey of Societal Attitudes, describing an adult population DNA screening programme currently under development, to detect risk of medically actionable cancers and heart disease. We asked questions regarding willingness to participate and pay, preferred delivery methods and concerns.ResultsWe received 1060 completed questionnaires (response rate 23%, mean age 58 years). The vast majority (>92%) expressed willingness to undertake DNA screening. When asked about the optimal age of screening, most (56%) favoured early adulthood (aged 18–40 years) rather than at birth or childhood. Many respondents would prefer samples and data be kept for re-screening (36%) or research use (43%); some preferred samples to be destroyed (21%). Issues that decrease likelihood of participation included privacy (75%) and insurance (86%) implications.ConclusionOur study demonstrates public willingness to participate in population DNA screening in Australia, and identifies barriers to participation, to be addressed in the design of screening programmes. Results are informing the development of a pilot national DNA screening programme.
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27
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Blout Zawatsky CL, Leonhard JR, Bell M, Moore MM, Petry NJ, Platt DM, Green RC, Hajek C, Christensen KD. Workforce Considerations When Building a Precision Medicine Program. J Pers Med 2022; 12:jpm12111929. [PMID: 36422106 PMCID: PMC9692406 DOI: 10.3390/jpm12111929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/11/2022] [Accepted: 11/12/2022] [Indexed: 11/22/2022] Open
Abstract
This paper describes one healthcare system’s approach to strategically deploying genetic specialists and pharmacists to support the implementation of a precision medicine program. In 2013, Sanford Health initiated the development of a healthcare system-wide precision medicine program. Here, we report the necessary staffing including the genetic counselors, genetic counseling assistants, pharmacists, and geneticists. We examined the administrative and electronic medical records data to summarize genetic referrals over time as well as the uptake and results of an enterprise-wide genetic screening test. Between 2013 and 2020, the number of genetic specialists employed at Sanford Health increased by 190%, from 10.1 full-time equivalents (FTEs) to 29.3 FTEs. Over the same period, referrals from multiple provider types to genetic services increased by 423%, from 1438 referrals to 7517 referrals. Between 2018 and 2020, 11,771 patients received a genetic screening, with 4% identified with potential monogenic medically actionable predisposition (MAP) findings and 95% identified with at least one informative pharmacogenetic result. Of the MAP-positive patients, 85% had completed a session with a genetics provider. A strategic workforce staffing and deployment allowed Sanford Health to manage a new genetic screening program, which prompted a large increase in genetic referrals. This approach can be used as a template for other healthcare systems interested in the development of a precision medicine program.
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Affiliation(s)
- Carrie L. Blout Zawatsky
- Genomes2People, Department of Medicine (Genetics), Brigham and Women’s Hospital, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
- Precision Population Health, Ariadne Labs, Boston, MA 02115, USA
- The MGH Institute of Health Professions, Boston, MA 02115, USA
| | - Jennifer R. Leonhard
- Department of Genetics, Sanford Health, Bemidji, MN 56601, USA
- Correspondence: ; Tel.: +1-218-333-5068
| | - Megan Bell
- Department of Genetics, Sanford Health, Sioux Falls, SD 57117, USA
- Department of Genetic Counseling, Augustana University, Sioux Falls, SD 57117, USA
| | | | - Natasha J. Petry
- Department of Sanford Imagenetics, Sanford Health, Sioux Falls, SD 57117, USA
- Department of Pharmacy Practice, North Dakota State University, Fargo, ND 58105, USA
| | - Dylan M. Platt
- Department of Genetics, Sanford Health, Sioux Falls, SD 57117, USA
- Department of Genetic Counseling, Augustana University, Sioux Falls, SD 57117, USA
| | - Robert C. Green
- Genomes2People, Department of Medicine (Genetics), Brigham and Women’s Hospital, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
- Precision Population Health, Ariadne Labs, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Catherine Hajek
- Department of Genetics, Sanford Health, Sioux Falls, SD 57117, USA
- Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57117, USA
- Helix, San Mateo, CA 94401, USA
| | - Kurt D. Christensen
- Broad Institute, Cambridge, MA 02142, USA
- Department of Population Medicine, Harvard Medical School, Boston, MA 02215, USA
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
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28
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Christensen KD, Zhang M, Galbraith LN, Granot-Hershkovitz E, Nelson SC, Gonzalez S, Argos M, Perreira KM, Daviglus ML, Isasi CR, Cai J, Talavera GA, Blout Zawatsky CL, Green RC, Isasi R, Kaplan R, Sofer T. Awareness and Utilization of Genetic Testing among Hispanic/Latino Adults Living in the US: The Hispanic Community Health Study/Study of Latinos. Human Genetics and Genomics Advances 2022; 4:100160. [DOI: 10.1016/j.xhgg.2022.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022] Open
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29
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Leppig KA, Rahm AK, Appelbaum P, Aufox S, Bland ST, Buchanan A, Christensen KD, Chung WK, Clayton EW, Crosslin D, Denny J, DeVange S, Gordon A, Green RC, Hakonarson H, Harr MH, Henrikson N, Hoell C, Holm IA, Kullo IJ, Jarvik GP, Lammers PE, Larson EB, Lindor NM, Marasa M, Myers MF, Perez E, Peterson JF, Pratap S, Prows CA, Ralston JD, Rasouly HM, Roden DM, Sharp RR, Singh R, Shaibi G, Smith ME, Sturm A, Thiese HA, Van Driest SL, Williams J, Williams MS, Wynn J, Blout Zawatsky CL, Wiesner GL. The Reckoning: The Return of Genomic Results to 1444 Participants Across the eMERGE3 Network. Obstet Gynecol Surv 2022. [DOI: 10.1097/01.ogx.0000899476.28549.ef] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Lewis ACF, Perez EF, Prince AER, Flaxman HR, Gomez L, Brockman DG, Chandler PD, Kerman BJ, Lebo MS, Smoller JW, Weiss ST, Blout Zawatksy CL, Meigs JB, Green RC, Vassy JL, Karlson EW. Patient and provider perspectives on polygenic risk scores: implications for clinical reporting and utilization. Genome Med 2022; 14:114. [PMID: 36207733 PMCID: PMC9540716 DOI: 10.1186/s13073-022-01117-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 04/20/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polygenic risk scores (PRS), which offer information about genomic risk for common diseases, have been proposed for clinical implementation. The ways in which PRS information may influence a patient's health trajectory depend on how both the patient and their primary care provider (PCP) interpret and act on PRS information. We aimed to probe patient and PCP responses to PRS clinical reporting choices METHODS: Qualitative semi-structured interviews of both patients (N=25) and PCPs (N=21) exploring responses to mock PRS clinical reports of two different designs: binary and continuous representations of PRS. RESULTS Many patients did not understand the numbers representing risk, with high numeracy patients being the exception. However, all the patients still understood a key takeaway that they should ask their PCP about actions to lower their disease risk. PCPs described a diverse range of heuristics they would use to interpret and act on PRS information. Three separate use cases for PRS emerged: to aid in gray-area clinical decision-making, to encourage patients to do what PCPs think patients should be doing anyway (such as exercising regularly), and to identify previously unrecognized high-risk patients. PCPs indicated that receiving "below average risk" information could be both beneficial and potentially harmful, depending on the use case. For "increased risk" patients, PCPs were favorable towards integrating PRS information into their practice, though some would only act in the presence of evidence-based guidelines. PCPs describe the report as more than a way to convey information, viewing it as something to structure the whole interaction with the patient. Both patients and PCPs preferred the continuous over the binary representation of PRS (23/25 and 17/21, respectively). We offer recommendations for the developers of PRS to consider for PRS clinical report design in the light of these patient and PCP viewpoints. CONCLUSIONS PCPs saw PRS information as a natural extension of their current practice. The most pressing gap for PRS implementation is evidence for clinical utility. Careful clinical report design can help ensure that benefits are realized and harms are minimized.
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Affiliation(s)
- Anna C F Lewis
- E.J. Safra Center for Ethics, Harvard University, Cambridge, USA. .,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Emma F Perez
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Mass General Brigham Personalized Medicine, Boston, MA, USA
| | | | | | - Lizbeth Gomez
- Mass General Brigham Personalized Medicine, Boston, MA, USA
| | | | | | - Benjamin J Kerman
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew S Lebo
- Mass General Brigham Personalized Medicine, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jordan W Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Scott T Weiss
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Boston, MA, USA
| | - Carrie L Blout Zawatksy
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Population Precision Health, Ariadne Labs, Boston, MA, USA.,The MGH Institute of Health Professions, Boston, MA, USA
| | - James B Meigs
- Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Robert C Green
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Population Precision Health, Ariadne Labs, Boston, MA, USA.,Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Jason L Vassy
- Harvard Medical School, Boston, MA, USA.,Population Precision Health, Ariadne Labs, Boston, MA, USA.,Veterans Affairs Boston Healthcare System, Boston, MA, USA.,Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth W Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Mass General Brigham Personalized Medicine, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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Kingsmore SF, Smith LD, Kunard CM, Bainbridge M, Batalov S, Benson W, Blincow E, Caylor S, Chambers C, Del Angel G, Dimmock DP, Ding Y, Ellsworth K, Feigenbaum A, Frise E, Green RC, Guidugli L, Hall KP, Hansen C, Hobbs CA, Kahn SD, Kiel M, Van Der Kraan L, Krilow C, Kwon YH, Madhavrao L, Le J, Lefebvre S, Mardach R, Mowrey WR, Oh D, Owen MJ, Powley G, Scharer G, Shelnutt S, Tokita M, Mehtalia SS, Oriol A, Papadopoulos S, Perry J, Rosales E, Sanford E, Schwartz S, Tran D, Reese MG, Wright M, Veeraraghavan N, Wigby K, Willis MJ, Wolen AR, Defay. T. A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases. Am J Hum Genet 2022; 109:1605-1619. [PMID: 36007526 PMCID: PMC9502059 DOI: 10.1016/j.ajhg.2022.08.003] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 12/31/2022] Open
Abstract
Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.
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Affiliation(s)
- Stephen F. Kingsmore
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Keck Graduate Institute, Claremont, CA 91711, USA,Corresponding author
| | - Laurie D. Smith
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Matthew Bainbridge
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sergey Batalov
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Wendy Benson
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Eric Blincow
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Sara Caylor
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Christina Chambers
- Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - David P. Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Yan Ding
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Katarzyna Ellsworth
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Annette Feigenbaum
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Erwin Frise
- Fabric Genomics, Inc., Oakland, CA 94612, USA
| | - Robert C. Green
- Mass General Brigham, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, MA 02115, USA
| | - Lucia Guidugli
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Christian Hansen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Mark Kiel
- Genomenon Inc., Ann Arbor, MI 48108, USA
| | - Lucita Van Der Kraan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Yong H. Kwon
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Lakshminarasimha Madhavrao
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Jennie Le
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Rebecca Mardach
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | | | - Danny Oh
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Mallory J. Owen
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Gunter Scharer
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Mari Tokita
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - Albert Oriol
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | | | - James Perry
- Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Edwin Rosales
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Erica Sanford
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Duke Tran
- Illumina, Inc., San Diego, CA 92122, USA
| | | | - Meredith Wright
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Narayanan Veeraraghavan
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Kristen Wigby
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA,Rady Children’s Hospital, San Diego, CA 92123, USA,Department of Pediatrics, University of California San Diego, San Diego, CA 92093, USA
| | - Mary J. Willis
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Thomas Defay.
- Alexion, Astra Zeneca Rare Disease, Boston, MA 02210, USA
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Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Zeng C, Bastarache LA, Tao R, Venner E, Hebbring S, Andujar JD, Bland ST, Crosslin DR, Pratap S, Cooley A, Pacheco JA, Christensen KD, Perez E, Zawatsky CLB, Witkowski L, Zouk H, Weng C, Leppig KA, Sleiman PMA, Hakonarson H, Williams MS, Luo Y, Jarvik GP, Green RC, Chung WK, Gharavi AG, Lennon NJ, Rehm HL, Gibbs RA, Peterson JF, Roden DM, Wiesner GL, Denny JC. Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases. JAMA Oncol 2022; 8:835-844. [PMID: 35446370 PMCID: PMC9026237 DOI: 10.1001/jamaoncol.2022.0373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance Knowledge about the spectrum of diseases associated with hereditary cancer syndromes may improve disease diagnosis and management for patients and help to identify high-risk individuals. Objective To identify phenotypes associated with hereditary cancer genes through a phenome-wide association study. Design, Setting, and Participants This phenome-wide association study used health data from participants in 3 cohorts. The Electronic Medical Records and Genomics Sequencing (eMERGEseq) data set recruited predominantly healthy individuals from 10 US medical centers from July 16, 2016, through February 18, 2018, with a mean follow-up through electronic health records (EHRs) of 12.7 (7.4) years. The UK Biobank (UKB) cohort recruited participants from March 15, 2006, through August 1, 2010, with a mean (SD) follow-up of 12.4 (1.0) years. The Hereditary Cancer Registry (HCR) recruited patients undergoing clinical genetic testing at Vanderbilt University Medical Center from May 1, 2012, through December 31, 2019, with a mean (SD) follow-up through EHRs of 8.8 (6.5) years. Exposures Germline variants in 23 hereditary cancer genes. Pathogenic and likely pathogenic variants for each gene were aggregated for association analyses. Main Outcomes and Measures Phenotypes in the eMERGEseq and HCR cohorts were derived from the linked EHRs. Phenotypes in UKB were from multiple sources of health-related data. Results A total of 214 020 participants were identified, including 23 544 in eMERGEseq cohort (mean [SD] age, 47.8 [23.7] years; 12 611 women [53.6%]), 187 234 in the UKB cohort (mean [SD] age, 56.7 [8.1] years; 104 055 [55.6%] women), and 3242 in the HCR cohort (mean [SD] age, 52.5 [15.5] years; 2851 [87.9%] women). All 38 established gene-cancer associations were replicated, and 19 new associations were identified. These included the following 7 associations with neoplasms: CHEK2 with leukemia (odds ratio [OR], 3.81 [95% CI, 2.64-5.48]) and plasma cell neoplasms (OR, 3.12 [95% CI, 1.84-5.28]), ATM with gastric cancer (OR, 4.27 [95% CI, 2.35-7.44]) and pancreatic cancer (OR, 4.44 [95% CI, 2.66-7.40]), MUTYH (biallelic) with kidney cancer (OR, 32.28 [95% CI, 6.40-162.73]), MSH6 with bladder cancer (OR, 5.63 [95% CI, 2.75-11.49]), and APC with benign liver/intrahepatic bile duct tumors (OR, 52.01 [95% CI, 14.29-189.29]). The remaining 12 associations with nonneoplastic diseases included BRCA1/2 with ovarian cysts (OR, 3.15 [95% CI, 2.22-4.46] and 3.12 [95% CI, 2.36-4.12], respectively), MEN1 with acute pancreatitis (OR, 33.45 [95% CI, 9.25-121.02]), APC with gastritis and duodenitis (OR, 4.66 [95% CI, 2.61-8.33]), and PTEN with chronic gastritis (OR, 15.68 [95% CI, 6.01-40.92]). Conclusions and Relevance The findings of this genetic association study analyzing the EHRs of 3 large cohorts suggest that these new phenotypes associated with hereditary cancer genes may facilitate early detection and better management of cancers. This study highlights the potential benefits of using EHR data in genomic medicine.
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Affiliation(s)
- Chenjie Zeng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa A Bastarache
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ran Tao
- Department of Biostatistics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Scott Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Justin D Andujar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Sarah T Bland
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle
| | - Siddharth Pratap
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee
| | - Ayorinde Cooley
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, Tennessee
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts.,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts
| | - Emma Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Carrie L Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Leora Witkowski
- Centre Universitaire de Santé McGill, McGill University Health Centre, Montreal, Quebec, Canada
| | - Hana Zouk
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Kathleen A Leppig
- Genetic Services and Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Human Genetics, Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Human Genetics, Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington, Seattle.,Department of Genome Sciences, University of Washington, Seattle
| | - Robert C Green
- Brigham and Women's Hospital, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, Massachusetts
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Heidi L Rehm
- Medical & Population Genetics Program and Genomics Platform, Broad Institute of MIT and Harvard Cambridge, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee.,Divisions of Cardiovascular Medicine and Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee
| | - Georgia L Wiesner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Joshua C Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Hao L, Kraft P, Berriz GF, Hynes ED, Koch C, Korategere V Kumar P, Parpattedar SS, Steeves M, Yu W, Antwi AA, Brunette CA, Danowski M, Gala MK, Green RC, Jones NE, Lewis ACF, Lubitz SA, Natarajan P, Vassy JL, Lebo MS. Development of a clinical polygenic risk score assay and reporting workflow. Nat Med 2022; 28:1006-1013. [PMID: 35437332 PMCID: PMC9117136 DOI: 10.1038/s41591-022-01767-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/02/2022] [Indexed: 12/31/2022]
Abstract
Implementation of polygenic risk scores (PRS) may improve disease prevention and management but poses several challenges: the construction of clinically valid assays, interpretation for individual patients, and the development of clinical workflows and resources to support their use in patient care. For the ongoing Veterans Affairs Genomic Medicine at Veterans Affairs (GenoVA) Study we developed a clinical genotype array-based assay for six published PRS. We used data from 36,423 Mass General Brigham Biobank participants and adjustment for population structure to replicate known PRS-disease associations and published PRS thresholds for a disease odds ratio (OR) of 2 (ranging from 1.75 (95% CI: 1.57-1.95) for type 2 diabetes to 2.38 (95% CI: 2.07-2.73) for breast cancer). After confirming the high performance and robustness of the pipeline for use as a clinical assay for individual patients, we analyzed the first 227 prospective samples from the GenoVA Study and found that the frequency of PRS corresponding to published OR > 2 ranged from 13/227 (5.7%) for colorectal cancer to 23/150 (15.3%) for prostate cancer. In addition to the PRS laboratory report, we developed physician- and patient-oriented informational materials to support decision-making about PRS results. Our work illustrates the generalizable development of a clinical PRS assay for multiple conditions and the technical, reporting and clinical workflow challenges for implementing PRS information in the clinic.
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Affiliation(s)
- Limin Hao
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gabriel F Berriz
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Elizabeth D Hynes
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Christopher Koch
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | | | - Shruti S Parpattedar
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Marcie Steeves
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Medical Genetics, Massachusetts General Hospital, Boston, MA, USA
| | - Wanfeng Yu
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
| | - Ashley A Antwi
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
| | | | | | - Manish K Gala
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Robert C Green
- Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Precision Population Health, Ariadne Labs, Boston, MA, USA
| | - Natalie E Jones
- Veterans Affairs Boston Healthcare System, Boston, MA, USA
- Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna C F Lewis
- E J Safra Center for Ethics, Harvard University, Cambridge, MA, USA
| | - Steven A Lubitz
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
| | - Pradeep Natarajan
- Harvard Medical School, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jason L Vassy
- Veterans Affairs Boston Healthcare System, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Precision Population Health, Ariadne Labs, Boston, MA, USA.
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
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35
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Armstrong B, Christensen KD, Genetti CA, Parad RB, Robinson JO, Blout Zawatsky CL, Zettler B, Beggs AH, Holm IA, Green RC, McGuire AL, Smith HS, Pereira S. Parental Attitudes Toward Standard Newborn Screening and Newborn Genomic Sequencing: Findings From the BabySeq Study. Front Genet 2022; 13:867371. [PMID: 35571041 PMCID: PMC9091188 DOI: 10.3389/fgene.2022.867371] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/31/2022] [Indexed: 01/15/2023] Open
Abstract
Introduction: With increasing utility and decreasing cost of genomic sequencing, augmentation of standard newborn screening (NBS) programs with newborn genomic sequencing (nGS) has been proposed. Before nGS can be integrated into newborn screening, parents’ perspectives must be better understood. Objective: Using data from surveys administered to parents of healthy newborns who were enrolled in the BabySeq Project, a randomized clinical trial of nGS alongside NBS, this paper reports parents’ attitudes regarding population-based NBS and nGS assessed 3 months after results disclosure. Methods: Parental attitudes regarding whether all newborns should receive, and whether informed consent should be required for, NBS and nGS, as well as whether nGS should be mandated were assessed using 5-point scales from strongly disagree (=1) to strongly agree (=5). Parents’ interest in receiving types of results from nGS was assessed on a 5-point scale from not at all interested (=1) to very interested (=5). Survey responses were analyzed using Fisher’s exact tests, paired t-tests, and repeated measures ANOVA. Results: At 3 months post-disclosure, 248 parents of 174 healthy newborns submitted a survey. Support for every newborn receiving standard NBS (mean 4.67) was higher than that for every newborn receiving nGS (mean 3.60; p < 0.001). Support for required informed consent for NBS (mean 3.44) was lower than that for nGS (mean 4.27, p < 0.001). Parents’ attitudes toward NBS and nGS were not significantly associated with self-reported political orientation. If hypothetically receiving nGS outside of the BabySeq Project, most parents reported being very interested in receiving information on their baby’s risk of developing a disease in childhood that can be prevented, treated, or cured (86.8%) and their risk of developing a disease during adulthood that can be prevented, treated, or cured (84.6%). Discussion: Parents’ opinions are crucial to inform design and delivery of public health programs, as the success of the program hinges on parents’ trust and participation. To accommodate parents’ preferences without affecting the current high participation rates in NBS, an optional add-on consent to nGS in addition to NBS may be a feasible approach. Trial Registration ClinicalTrials.gov Identifier: NCT02422511.
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Affiliation(s)
- Brittan Armstrong
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Kurt D. Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Casie A. Genetti
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
| | - Richard B. Parad
- Harvard Medical School, Boston, MA, United States
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Jill Oliver Robinson
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Carrie L. Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Medical and Population Genetics, The Broad Institute, Cambridge, MA, United States
- Ariadne Labs, Boston, MA, United States
- The MGH Institute of Health Professions, Boston, MA, United States
| | - Bethany Zettler
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Alan H. Beggs
- Harvard Medical School, Boston, MA, United States
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, United States
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Robert C. Green
- Harvard Medical School, Boston, MA, United States
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Ariadne Labs, Boston, MA, United States
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Amy L. McGuire
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Hadley Stevens Smith
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
| | - Stacey Pereira
- Center for Medical Ethics and Heath Policy, Baylor College of Medicine, Houston, TX, United States
- *Correspondence: Stacey Pereira,
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Veitch DP, Weiner MW, Aisen PS, Beckett LA, DeCarli C, Green RC, Harvey D, Jack CR, Jagust W, Landau SM, Morris JC, Okonkwo O, Perrin RJ, Petersen RC, Rivera‐Mindt M, Saykin AJ, Shaw LM, Toga AW, Tosun D, Trojanowski JQ. Using the Alzheimer's Disease Neuroimaging Initiative to improve early detection, diagnosis, and treatment of Alzheimer's disease. Alzheimers Dement 2022; 18:824-857. [PMID: 34581485 PMCID: PMC9158456 DOI: 10.1002/alz.12422] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [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: 02/01/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The Alzheimer's Disease Neuroimaging Initiative (ADNI) has accumulated 15 years of clinical, neuroimaging, cognitive, biofluid biomarker and genetic data, and biofluid samples available to researchers, resulting in more than 3500 publications. This review covers studies from 2018 to 2020. METHODS We identified 1442 publications using ADNI data by conventional search methods and selected impactful studies for inclusion. RESULTS Disease progression studies supported pivotal roles for regional amyloid beta (Aβ) and tau deposition, and identified underlying genetic contributions to Alzheimer's disease (AD). Vascular disease, immune response, inflammation, resilience, and sex modulated disease course. Biologically coherent subgroups were identified at all clinical stages. Practical algorithms and methodological changes improved determination of Aβ status. Plasma Aβ, phosphorylated tau181, and neurofilament light were promising noninvasive biomarkers. Prognostic and diagnostic models were externally validated in ADNI but studies are limited by lack of ethnocultural cohort diversity. DISCUSSION ADNI has had a profound impact in improving clinical trials for AD.
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Affiliation(s)
- Dallas P. Veitch
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA,Department of Veterans Affairs Medical CenterNorthern California Institute for Research and Education (NCIRE)San FranciscoCaliforniaUSA
| | - Michael W. Weiner
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesSan FranciscoCaliforniaUSA,Department of RadiologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA,Department of MedicineUniversity of California, San FranciscoSan FranciscoCaliforniaUSA,Department of PsychiatryUniversity of California, San FranciscoSan FranciscoCaliforniaUSA,Department of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Paul S. Aisen
- Alzheimer's Therapeutic Research InstituteUniversity of Southern CaliforniaSan DiegoCaliforniaUSA
| | - Laurel A. Beckett
- Division of Biostatistics, Department of Public Health SciencesUniversity of California DavisDavisCaliforniaUSA
| | - Charles DeCarli
- Department of Neurology and Center for NeuroscienceUniversity of California DavisDavisCaliforniaUSA
| | - Robert C. Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Broad Institute, Ariadne Labsand Harvard Medical SchoolBostonMassachusettsUSA
| | - Danielle Harvey
- Division of Biostatistics, Department of Public Health SciencesUniversity of California DavisDavisCaliforniaUSA
| | | | - William Jagust
- Helen Wills Neuroscience InstituteUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Susan M. Landau
- Helen Wills Neuroscience InstituteUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - John C. Morris
- Knight Alzheimer's Disease Research CenterWashington University School of MedicineSaint LouisMissouriUSA
| | - Ozioma Okonkwo
- Wisconsin Alzheimer's Disease Research Center and Department of MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Richard J. Perrin
- Knight Alzheimer's Disease Research CenterWashington University School of MedicineSaint LouisMissouriUSA,Department of NeurologyWashington University School of MedicineSaint LouisMissouriUSA,Department of Pathology and ImmunologyWashington University School of MedicineSaint LouisMissouriUSA
| | | | | | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences and Indiana Alzheimer's Disease Research CenterIndiana University School of MedicineIndianapolisIndianaUSA,Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Leslie M. Shaw
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Research, School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Arthur W. Toga
- Laboratory of Neuroimaging, USC Stevens Institute of Neuroimaging and Informatics, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Duygu Tosun
- Department of RadiologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - John Q. Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Research, School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
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Bekbolsynov D, Mierzejewska B, Khuder S, Ekwenna O, Rees M, Green RC, Stepkowski SM. Improving Access to HLA-Matched Kidney Transplants for African American Patients. Front Immunol 2022; 13:832488. [PMID: 35401566 PMCID: PMC8989073 DOI: 10.3389/fimmu.2022.832488] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/02/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction Kidney transplants fail more often in Black than in non-Black (White, non-Black Hispanic, and Asian) recipients. We used the estimated physicochemical immunogenicity for polymorphic amino acids of donor/recipient HLAs to select weakly immunogenic kidney transplants for Black vs. White or non-Black patients. Methods OPTN data for 65,040 donor/recipient pairs over a 20-year period were used to calculate the individual physicochemical immunogenicity by hydrophobic, electrostatic and amino acid mismatch scores (HMS, EMS, AMS) and graft-survival outcomes for Black vs. White or vs. non-Black recipients, using Kaplan-Meier survival and Cox regression analyses. Simulations for re-matching recipients with donors were based on race-adjusted HMS thresholds with clinically achievable allocations. Results The retrospective median kidney graft survival was 12.0 years in Black vs. 18.6 years in White (6.6-year difference; p>0.001) and 18.4 years in non-Black (6.4-year difference; p>0.01) recipients. Only 0.7% of Blacks received transplants matched at HLA-A/B/DR/DQ (HMS=0) vs. 8.1% in Whites (p<0.001). Among fully matched Blacks (HMS=0), graft survival was 16.1-years and in well-matched Blacks (HMS ≤ 3.0) it was 14.0-years. Whites had 21.6-years survival at HMS ≤ 3.0 and 18.7-years at HMS ≤ 7.0 whereas non-Blacks had 22.0-year at HMS ≤ 3.0 and 18.7-year at HMS ≤ 7.0, confirming that higher HMS thresholds produced excellent survival. Simulation of ABO-compatible donor-recipient pairs using race-adjusted HMS thresholds identified weakly immunogenic matches at HMS=0 for 6.1% Blacks and 18.0% at HMS ≤ 3.0. Despite prioritizing Black patients, non-Black patients could be matched at the same level as in current allocation (47.0% vs 56.5%, at HMS ≤ 7.0). Conclusions Race-adjusted HMS (EMS, AMS)-based allocation increased the number of weakly immunogenic donors for Black patients, while still providing excellent options for non-Black recipients.
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Affiliation(s)
- Dulat Bekbolsynov
- Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH, United States
| | - Beata Mierzejewska
- Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH, United States
| | - Sadik Khuder
- Department of Medicine and Public Health, University of Toledo, Toledo, OH, United States
| | - Obinna Ekwenna
- Department of Urology, College of Medicine, University of Toledo, Toledo, OH, United States
| | - Michael Rees
- Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH, United States
- Department of Urology, College of Medicine, University of Toledo, Toledo, OH, United States
- The of Alliance for Paired Donation, Maumee, OH, United States
| | - Robert C. Green
- Department of Computer Science, Bowling Green State University, Bowling Green, OH, United States
- *Correspondence: Stanislaw M. Stepkowski, ; Robert C. Green II,
| | - Stanislaw M. Stepkowski
- Department of Medical Microbiology and Immunology, University of Toledo, Toledo, OH, United States
- *Correspondence: Stanislaw M. Stepkowski, ; Robert C. Green II,
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Sible IJ, Nation DA, Aisen P, Petersen R, Jack CR, Jagust W, Trojanowki JQ, Toga AW, Beckett L, Green RC, Saykin AJ, Morris J, Shaw LM. Visit-to-Visit Blood Pressure Variability and Longitudinal Tau Accumulation in Older Adults. Hypertension 2022; 79:629-637. [PMID: 34967222 PMCID: PMC8979412 DOI: 10.1161/hypertensionaha.121.18479] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Elevated blood pressure variability (BPV) is predictive of dementia, independent of average blood pressure levels, but neuropathological mechanisms remain unclear. We examined whether BPV in older adults is related to tau accumulation in brain regions vulnerable to Alzheimer disease and whether relationships are modified by apoϵ4 carrier status. METHODS Two hundred eighty-six Alzheimer's Disease Neuroimaging Initiative participants without history of dementia underwent 3 to 4 blood pressure measurements over 12 months and ≥1 tau positron emission tomography thereafter. BPV was calculated as variability independent of mean. Each scan determined tau burden (standardized uptake value ratio) for a temporal meta-region of interest, including burden from entorhinal cortex, amygdala, parahippocampus, fusiform, inferior temporal, and middle temporal. Bayesian linear growth modeling examined the role of BPV, apolipoprotein ϵ4 carrier status, and time on regional tau accumulation after controlling for several variables, including baseline hypertension. RESULTS Elevated BPV was related to tau accumulation at follow-up in a temporal meta-region, independent of average blood pressure levels (ß, 0.89 [95% credible interval, 0.86-0.92]) and especially in entorhinal cortex (ß, 2.57 [95% credible interval, 2.15-2.99]). Apoϵ4 carriers with elevated BPV had the fastest tau accumulation at follow-up (ß, 1.73 [95% credible interval, 0.47-3.03]). CONCLUSIONS BPV is related to tau accumulation in brain regions vulnerable to Alzheimer disease, independent of average blood pressure. APOEϵ4 modified this relationship. Bidirectionality of findings is possible. BPV may represent a marker of vascular dysfunction related to early-stage tau pathology contributing to Alzheimer disease.
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Affiliation(s)
- Isabel J. Sible
- Department of Psychology, University of Southern California, Los Angeles, CA 90007, USA
| | - Daniel A. Nation
- Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, CA 92697, USA,Department of Psychological Science, University of California Irvine, Irvine, CA 92697, USA,Corresponding Author Daniel A. Nation, Ph.D., Associate Professor, University of California Irvine, Department of Psychological Science, 4201 Social and Behavioral Sciences Gateway, Irvine, CA 92697-7085, Phone: (949) 824-9339,
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Schwartz TS, Christensen KD, Uveges MK, Waisbren SE, McGuire AL, Pereira S, Robinson JO, Beggs AH, Green RC, Bachmann GA, Rabson AB, Holm IA. Effects of participation in a U.S. trial of newborn genomic sequencing on parents at risk for depression. J Genet Couns 2022; 31:218-229. [PMID: 34309124 PMCID: PMC8789951 DOI: 10.1002/jgc4.1475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/14/2021] [Revised: 06/15/2021] [Accepted: 06/27/2021] [Indexed: 02/03/2023]
Abstract
Much emphasis has been placed on participant's psychological safety within genomic research studies; however, few studies have addressed parental psychological health effects associated with their child's participation in genomic studies, particularly when parents meet the threshold for clinical concern for depression. We aimed to determine if parents' depressive symptoms were associated with their child's participation in a randomized-controlled trial of newborn exome sequencing. Parents completed the Edinburgh Postnatal Depression Scale (EPDS) at baseline, immediately post-disclosure, and 3 months post-disclosure. Mothers and fathers scoring at or above thresholds for clinical concern on the EPDS, 12 and 10, respectively, indicating possible Major Depressive Disorder with Peripartum Onset, were contacted by study staff for mental health screening. Parental concerns identified in follow-up conversations were coded for themes. Forty-five parents had EPDS scores above the clinical threshold at baseline, which decreased by an average of 2.9 points immediately post-disclosure and another 1.1 points 3 months post-disclosure (both p ≤ .014). For 28 parents, EPDS scores were below the threshold for clinical concern at baseline, increased by an average of 4.7 points into the elevated range immediately post-disclosure, and decreased by 3.8 points at 3 months post-disclosure (both p < .001). Nine parents scored above thresholds only at 3 months post-disclosure after increasing an average of 5.7 points from immediately post-disclosure (p < .001). Of the 82 parents who scored above the threshold at any time point, 43 (52.4%) were reached and 30 (69.7%) of these 43 parents attributed their elevated scores to parenting stress, balancing work and family responsibilities, and/or child health concerns. Only three parents (7.0%) raised concerns about their participation in the trial, particularly their randomization to the control arm. Elevated scores on the EPDS were typically transient and parents attributed their symptomatology to life stressors in the postpartum period rather than participation in a trial of newborn exome sequencing.
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Affiliation(s)
- Talia S Schwartz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Melissa K Uveges
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Connell School of Nursing, Boston College, Chestnut Hill, Massachusetts, USA
| | - Susan E Waisbren
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Robert C Green
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Gloria A Bachmann
- Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Arnold B Rabson
- Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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40
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Gold NB, Harrison SM, Rowe JH, Gold J, Furutani E, Biffi A, Duncan CN, Shimamura A, Lehmann LE, Green RC. Low frequency of treatable pediatric disease alleles in gnomAD: An opportunity for future genomic screening of newborns. HGG Adv 2022; 3:100059. [PMID: 35047849 PMCID: PMC8756496 DOI: 10.1016/j.xhgg.2021.100059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/13/2021] [Accepted: 09/20/2021] [Indexed: 01/18/2023] Open
Abstract
Hematopoietic stem cell transplant (HSCT) can prevent progression of several genetic disorders. Although a subset of these disorders are identified on newborn screening panels, others are not identified until irreversible symptoms develop. Genetic testing is an efficient methodology to ascertain pre-symptomatic children, but the penetrance of risk-associated variants in the general population is not well understood. We developed a list of 127 genes associated with disorders treatable with HSCT. We identified likely pathogenic or pathogenic (LP/P) and loss-of-function (LoF) variants in these genes in the Genome Aggregation Database (gnomAD), a dataset containing exome and genome sequencing data from 141,456 healthy adults. Within gnomAD, we identified 59 individuals with a LP/P or LoF variant in 15 genes. Genes were associated with bone marrow failure syndromes, bleeding disorders, primary immunodeficiencies, osteopetrosis, metabolic disorders, and epidermolysis bullosa. In conclusion, few ostensibly healthy adults had genotypes associated with pediatric disorders treatable with HSCTs. Given that most of these disorders do not have biomarkers that could be cheaply and universally assessed on a standard newborn screen, our data suggest that genetic testing may be a complementary approach to traditional newborn screening methodology that has the potential to improve mortality and is not expected to lead to a high burden of false-positive results.
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Affiliation(s)
- Nina B. Gold
- Massachusetts General Hospital for Children, Division of Medical Genetics and Metabolism, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Jared H. Rowe
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Jessica Gold
- Department of Pediatrics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elissa Furutani
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
| | - Alessandra Biffi
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Christine N. Duncan
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Akiko Shimamura
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Leslie E. Lehmann
- Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Division of Hematology and Oncology, Boston, MA, USA
- Dana-Farber Cancer Institute Division of Pediatric Oncology, Boston, MA, USA
| | - Robert C. Green
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
- Ariadne Labs, Boston, MA, USA
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41
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Hajek C, Hutchinson AM, Galbraith LN, Green RC, Murray MF, Petry N, Preys CL, Zawatsky CLB, Zoltick ES, Christensen KD. Improved provider preparedness through an 8-part genetics and genomic education program. Genet Med 2022; 24:214-224. [PMID: 34906462 PMCID: PMC9121992 DOI: 10.1016/j.gim.2021.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 03/30/2021] [Revised: 06/25/2021] [Accepted: 08/13/2021] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Large-scale genetics education appropriate for general practice providers is a growing priority. We describe the content and impact of a mandatory system-wide program implemented at Sanford Health. METHODS The Imagenetics Initiative at Sanford Health developed a 2-year genetics education program with quarterly web-based modules that were mandatory for all physicians and advanced practice providers. Scores of 0 to 5 were calculated for each module on the basis of the number of objectives that the participants reported as fulfilled. In addition, the participants completed surveys before starting and after finishing the education program, which included a 7-item measure scored 7 to 28 on the perceived preparedness to practice genetics. RESULTS Between 2252 and 2822 Sanford Health employees completed each of the 8 quarterly education modules. The ratings were highest for the module about using genomics to improve patient management (mean score = 4.3) and lowest for the module about different types of genetic tests and specialists. The mean perceived preparedness scores increased from 15.7 at pre-education to 19.1 at post-education (P < .001). CONCLUSION Web-based genetics education was highly effective in increasing health care providers' confidence about using genetics. Both comfort with personal knowledge and confidence regarding access to the system's genomic medicine experts increased significantly. The results demonstrate how scalable approaches can improve provider preparedness.
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Affiliation(s)
- Catherine Hajek
- Sanford Health Imagenetics, Sioux Falls, SD; Sanford School of Medicine, University of South Dakota, Sioux Falls, SD.
| | | | - Lauren N Galbraith
- Department of Population Medicine, Center for Healthcare Research in Pediatrics (CHERP), Harvard Pilgrim Health Care Institute, Boston, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Medicine, Harvard Medical School, Boston, MA; Ariadne Labs, Boston, MA
| | | | - Natasha Petry
- Sanford Health Imagenetics, Fargo, ND; Department of Pharmacy Practice, School of Pharmacy, North Dakota State University, Fargo, ND
| | - Charlene L Preys
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; MGH Institute of Health Professions, Boston, MA
| | - Carrie L B Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Ariadne Labs, Boston, MA
| | - Emilie S Zoltick
- Department of Population Medicine, Center for Healthcare Research in Pediatrics (CHERP), Harvard Pilgrim Health Care Institute, Boston, MA
| | - Kurt D Christensen
- Department of Population Medicine, Center for Healthcare Research in Pediatrics (CHERP), Harvard Pilgrim Health Care Institute, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Population Medicine, Harvard Medical School, Boston, MA
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42
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Blout Zawatsky CL, Shah N, Machini K, Perez E, Christensen KD, Zouk H, Steeves M, Koch C, Uveges M, Shea J, Gold N, Krier J, Boutin N, Mahanta L, Rehm HL, Weiss ST, Karlson EW, Smoller JW, Lebo MS, Green RC. Returning actionable genomic results in a research biobank: Analytic validity, clinical implementation, and resource utilization. Am J Hum Genet 2021; 108:2224-2237. [PMID: 34752750 PMCID: PMC8715145 DOI: 10.1016/j.ajhg.2021.10.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
Over 100 million research participants around the world have had research array-based genotyping (GT) or genome sequencing (GS), but only a small fraction of these have been offered return of actionable genomic findings (gRoR). Between 2017 and 2021, we analyzed genomic results from 36,417 participants in the Mass General Brigham Biobank and offered to confirm and return pathogenic and likely pathogenic variants (PLPVs) in 59 genes. Variant verification prior to participant recontact revealed that GT falsely identified PLPVs in 44.9% of samples, and GT failed to identify 72.0% of PLPVs detected in a subset of samples that were also sequenced. GT and GS detected verified PLPVs in 1% and 2.5% of the cohort, respectively. Of 256 participants who were alerted that they carried actionable PLPVs, 37.5% actively or passively declined further disclosure. 76.3% of those carrying PLPVs were unaware that they were carrying the variant, and over half of those met published professional criteria for genetic testing but had never been tested. This gRoR protocol cost approximately $129,000 USD per year in laboratory testing and research staff support, representing $14 per participant whose DNA was analyzed or $3,224 per participant in whom a PLPV was confirmed and disclosed. These data provide logistical details around gRoR that could help other investigators planning to return genomic results.
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Affiliation(s)
- Carrie L Blout Zawatsky
- Brigham and Women's Hospital, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Ariadne Labs, Boston, MA 02215, USA; The MGH Institute of Health Professions, Boston, MA 02129, USA
| | - Nidhi Shah
- Brigham and Women's Hospital, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kalotina Machini
- Harvard Medical School, Boston, MA 02115, USA; Laboratory for Molecular Medicine, Cambridge, MA 02139, USA
| | - Emma Perez
- Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kurt D Christensen
- Harvard Medical School, Boston, MA 02115, USA; Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Hana Zouk
- Harvard Medical School, Boston, MA 02115, USA; Laboratory for Molecular Medicine, Cambridge, MA 02139, USA
| | - Marcie Steeves
- Laboratory for Molecular Medicine, Cambridge, MA 02139, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Melissa Uveges
- Connell School of Nursing, Boston College, Chestnut Hill, MA 02467, USA
| | - Janelle Shea
- Division of Medical Genetics, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nina Gold
- Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Joel Krier
- Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Natalie Boutin
- Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Lisa Mahanta
- Laboratory for Molecular Medicine, Cambridge, MA 02139, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Scott T Weiss
- Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Laboratory for Molecular Medicine, Cambridge, MA 02139, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Elizabeth W Karlson
- Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Jordan W Smoller
- Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Matthew S Lebo
- Brigham and Women's Hospital, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Laboratory for Molecular Medicine, Cambridge, MA 02139, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA
| | - Robert C Green
- Brigham and Women's Hospital, Boston, MA 02115, USA; Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Ariadne Labs, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Mass General Brigham Personalized Medicine, Cambridge, MA 02139, USA.
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Karlawish J, Harkins K, Chen CA, Cupples LA, Roberts JS, Welsh‐Bohmer KA, Green RC. How knowledge of elevated amyloid impacts neuropsychological performance in cognitively normal older adults: Findings from the REVEAL SCAN Study. Alzheimers Dement 2021. [DOI: 10.1002/alz.057834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Clara A Chen
- Boston University School of Public Health Boston MA USA
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44
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Gold NB, Green RC. Reevaluating the "right not to know" in genomics research. Genet Med 2021; 24:289-292. [PMID: 34906468 DOI: 10.1016/j.gim.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 10/19/2022] Open
Affiliation(s)
- Nina B Gold
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Ariadne Labs, Boston, MA; The Broad Institute of MIT and Harvard, Boston, MA; Department of Medicine, Harvard Medical School, Boston, MA.
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45
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Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
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Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
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Haverfield EV, Esplin ED, Aguilar SJ, Hatchell KE, Ormond KE, Hanson-Kahn A, Atwal PS, Macklin-Mantia S, Hines S, Sak CWM, Tucker S, Bleyl SB, Hulick PJ, Gordon OK, Velsher L, Gu JYJ, Weissman SM, Kruisselbrink T, Abel C, Kettles M, Slavotinek A, Mendelsohn BA, Green RC, Aradhya S, Nussbaum RL. Correction to: Physician-directed genetic screening to evaluate personal risk for medically actionable disorders: a large multi-center cohort study. BMC Med 2021; 19:288. [PMID: 34732190 PMCID: PMC8567716 DOI: 10.1186/s12916-021-02141-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | | | | | | | - Kelly E Ormond
- Stanford University School of Medicine, Stanford, CA, USA
| | | | - Paldeep S Atwal
- Mayo Clinic, Jacksonville, FL, USA.,Atwal Clinic, Palm Beach, FL, USA.,PWNHealth, New York, NY, USA
| | | | | | | | | | | | | | - Ora K Gordon
- Providence Research Network, St John Cancer Institute, Los Angeles, CA, USA.,University of California, Los Angeles, CA, USA
| | | | | | - Scott M Weissman
- Genome Medical, San Francisco, CA, USA.,Chicago Genetic Consultants, Northbrook, IL, USA
| | | | | | | | - Anne Slavotinek
- University of California San Francisco, San Francisco, CA, USA
| | | | - Robert C Green
- Brigham and Women's Hospital, Boston, MA, USA.,The Broad Institute, Boston, MA, USA.,Ariadne Labs, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA, 94103, USA.,Volunteer Faculty, University of California San Francisco, San Francisco, CA, USA
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47
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Pereira S, Smith HS, Frankel LA, Christensen KD, Islam R, Robinson JO, Genetti CA, Blout Zawatsky CL, Zettler B, Parad RB, Waisbren SE, Beggs AH, Green RC, Holm IA, McGuire AL. Psychosocial Effect of Newborn Genomic Sequencing on Families in the BabySeq Project: A Randomized Clinical Trial. JAMA Pediatr 2021; 175:1132-1141. [PMID: 34424265 PMCID: PMC8383160 DOI: 10.1001/jamapediatrics.2021.2829] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
IMPORTANCE Newborn genomic sequencing (nGS) may provide health benefits throughout the life span, but there are concerns that it could also have an unfavorable (ie, negative) psychosocial effect on families. OBJECTIVE To assess the psychosocial effect of nGS on families from the BabySeq Project, a randomized clinical trial evaluating the effect of nGS on the clinical care of newborns from well-baby nurseries and intensive care units. DESIGN, SETTING, AND PARTICIPANTS In this randomized clinical trial conducted from May 14, 2015, to May 21, 2019, at well-baby nurseries and intensive care units at 3 Boston, Massachusetts, area hospitals, 519 parents of 325 infants completed surveys at enrollment, immediately after disclosure of nGS results, and 3 and 10 months after results disclosure. Statistical analysis was performed on a per-protocol basis from January 16, 2019, to December 1, 2019. INTERVENTION Newborns were randomized to receive either standard newborn screening and a family history report (control group) or the same plus an nGS report of childhood-onset conditions and highly actionable adult-onset conditions (nGS group). MAIN OUTCOMES AND MEASURES Mean responses were compared between groups and, within the nGS group, between parents of children who received a monogenic disease risk finding and those who did not in 3 domains of psychosocial impact: parent-child relationship (Mother-to-Infant Bonding Scale), parents' relationship (Kansas Marital Satisfaction Scale), and parents' psychological distress (Edinburgh Postnatal Depression Scale anxiety subscale). RESULTS A total of 519 parents (275 women [53.0%]; mean [SD] age, 35.1 [4.5] years) were included in this study. Although mean scores differed for some outcomes at singular time points, generalized estimating equations models did not show meaningful differences in parent-child relationship (between-group difference in adjusted mean [SE] Mother-to-Infant Bonding Scale scores: postdisclosure, 0.04 [0.15]; 3 months, -0.18 [0.18]; 10 months, -0.07 [0.20]; joint P = .57) or parents' psychological distress (between-group ratio of adjusted mean [SE] Edinburgh Postnatal Depression Scale anxiety subscale scores: postdisclosure, 1.04 [0.08]; 3 months, 1.07 [0.11]; joint P = .80) response patterns between study groups over time for any measures analyzed in these 2 domains. Response patterns on one parents' relationship measure differed between groups over time (between-group difference in adjusted mean [SE] Kansas Marital Satisfaction Scale scores: postdisclosure, -0.19 [0.07]; 3 months, -0.04 [0.07]; and 10 months, -0.01 [0.08]; joint P = .02), but the effect decreased over time and no difference was observed on the conflict measure responses over time. We found no evidence of persistent negative psychosocial effect in any domain. CONCLUSIONS AND RELEVANCE In this randomized clinical trial of nGS, there was no persistent negative psychosocial effect on families among those who received nGS nor among those who received a monogenic disease risk finding for their infant. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02422511.
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Affiliation(s)
- Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Hadley Stevens Smith
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Leslie A. Frankel
- Department of Psychological, Health, and Learning Sciences, University of Houston, Houston, Texas
| | - Kurt D. Christensen
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Rubaiya Islam
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Jill Oliver Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
| | - Casie A. Genetti
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts,The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Carrie L. Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Bethany Zettler
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Richard B. Parad
- Department of Pediatric Newborn Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Susan E. Waisbren
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts,Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Alan H. Beggs
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts,The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts,Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert C. Green
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts,Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts,Precision Population Health Initiative, Ariadne Labs, Boston, Massachusetts,Harvard Medical School, Boston, Massachusetts
| | - Ingrid A. Holm
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts,The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts,Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Amy L. McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas
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48
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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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49
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Weiner MW, Aisen PS, Beckett LA, Green RC, Jagust W, Morris JC, Okonkwo O, Perrin RJ, Petersen RC, Rivera Mindt M, Saykin AJ, Shaw LM, Toga AW, Trojanowski JQ. Editorial: How Will Aducanumab Approval Impact AD Research? J Prev Alzheimers Dis 2021; 8:391-392. [PMID: 34585209 PMCID: PMC8295641 DOI: 10.14283/jpad.2021.46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- M W Weiner
- Michael W. Weiner, NCIRE, 4150 Clement St, San Francisco, CA 94121, USA. E-mail address:
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50
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Christensen KD, Schonman EF, Robinson JO, Roberts JS, Diamond PM, Lee KB, Green RC, McGuire AL. Behavioral and psychological impact of genome sequencing: a pilot randomized trial of primary care and cardiology patients. NPJ Genom Med 2021; 6:72. [PMID: 34429410 PMCID: PMC8384838 DOI: 10.1038/s41525-021-00236-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 07/30/2021] [Indexed: 12/20/2022] Open
Abstract
Many expect genome sequencing (GS) to become routine in patient care and preventive medicine, but uncertainties remain about its ability to motivate participants to improve health behaviors and the psychological impact of disclosing results. In a pilot trial with exploratory analyses, we randomized 100 apparently healthy, primary-care participants and 100 cardiology participants to receive a review of their family histories of disease, either alone or in addition to GS analyses. GS results included polygenic risk information for eight cardiometabolic conditions. Overall, no differences were observed between the percentage of participants in the GS and control arms, who reported changes to health behaviors such as diet and exercise at 6 months post disclosure (48% vs. 36%, respectively, p = 0.104). In the GS arm, however, the odds of reporting a behavior change increased by 52% per high-risk polygenic prediction (p = 0.032). Mean anxiety and depression scores for GS and control arms had confidence intervals within equivalence margins of ±1.5. Mediation analyses suggested an indirect impact of GS on health behaviors by causing positive psychological responses (p ≤ 0.001). Findings suggest that GS did not distress participants. Future research on GS in more diverse populations is needed to confirm that it does not raise risks for psychological harms and to confirm the ability of polygenic risk predictions to motivate preventive behaviors.
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Affiliation(s)
- Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA, USA. .,Department of Population Medicine, Harvard Medical School, Boston, MA, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Erica F Schonman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy at Baylor College of Medicine, Houston, TX, USA
| | - J Scott Roberts
- Department of Health Behavior and Health Education, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Pamela M Diamond
- Center for Health Promotion and Prevention Research, University of Texas Houston School of Public Health, Houston, TX, USA
| | - Kaitlyn B Lee
- Center for Medical Ethics and Health Policy at Baylor College of Medicine, Houston, TX, USA
| | - Robert C Green
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Partners Personalized Medicine, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Ariadne Labs, Boston, MA, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy at Baylor College of Medicine, Houston, TX, USA
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