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Waltz M, Foreman AKM, Canter C, Cadigan RJ, O'Daniel JM. Reflections on 'common' genetic medical history questions: Time to examine the what, why, and how. Patient Educ Couns 2024; 122:108190. [PMID: 38340501 DOI: 10.1016/j.pec.2024.108190] [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] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/18/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
OBJECTIVE A central goal of patient-centered care is to establish a therapeutic relationship. While remaining in tune with patient emotions, genetics providers must ask questions to understand medical histories that will inform the differential diagnosis, evaluation plan, and potential treatments. METHODS 195 audio-recorded conversations between providers and caregivers of pediatric patients with suspected genetic conditions were coded and analyzed. Coders identified sensitive history-taking questions asked by providers related to exposures and complications during pregnancy; ancestry and consanguinity; educational attainment of the caregiver; and family structure. RESULTS We highlight examples of providers: using stigmatizing language about conception or consanguinity; not clarifying the intent behind questions related to caregivers' educational attainment and work history; and making presumptions or assumptions about caregivers' race and ethnicity, family structure, and exposures during pregnancy. CONCLUSION Some questions and phrasing considered routine by genetics providers may interfere with patient-centered care by straining attempts to establish a therapeutic, trusting relationship. Additional research is needed to assess how question asking and phrasing impact rapport building and patient experience during genetics encounters. PRACTICE IMPLICATIONS Review of the purpose and need for medical history questions common to genetics practice could serve to improve patient-centered care.
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Affiliation(s)
- Margaret Waltz
- Department of Social Medicine, University of North Carolina, Chapel Hill, NC, USA.
| | | | - Courtney Canter
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
| | - R Jean Cadigan
- Department of Social Medicine, University of North Carolina, Chapel Hill, NC, USA
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2
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Tallent B, Padilla RJ, McKay C, Foreman AKM, Fan Z, Blatt J. Response of Central Giant Cell Granuloma of the Jaw to Imatinib. J Pediatr Hematol Oncol 2023; 45:278-280. [PMID: 36706268 DOI: 10.1097/mph.0000000000002608] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/02/2022] [Indexed: 01/28/2023]
Abstract
Central giant cell granuloma of the jaw (CGCJ) can be locally aggressive and result in facial and dental deformity. A child with CGCJ was treated surgically and with denosumab with a response but life-threatening toxicity. Imatinib, a tyrosine kinase inhibitor, was prescribed based on clinical similarities between CGCJ and cherubism, for which Imatinib has been effective. Within 2 months, a computed tomographic scan showed significant ossification, which increased over the following 8 months. This case suggests that tyrosine kinase inhibitors may be an effective option, and one with limited toxicity, for CGCJ.
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Affiliation(s)
| | - Ricardo J Padilla
- Division of Oral and Maxillofacial Pathology Laboratory, The University of North Carolina Adams School of Dentistry
| | | | | | - Zheng Fan
- Department of Neurology, The University of North Carolina School of Medicine, Charlotte, NC
| | - Julie Blatt
- Division of Pediatric Hematology Oncology
- The Lineberger Comprehensive Cancer Center
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3
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Waltz M, Yan H, Cadigan RJ, Canter C, Bain L, Bensen JT, Conway C, Haldeman-Englert C, Farnan L, M Foreman AK, Grant TL, Leach B, Lin FC, Mahla M, O'Daniel JM, O'Neill SC, Smith G, Powell BC, Berg JS, Rini CM. Question prompt lists and caregiver question asking in pediatric specialty appointments: A randomized controlled trial. Patient Educ Couns 2023; 109:107620. [PMID: 36689884 PMCID: PMC9931668 DOI: 10.1016/j.pec.2022.107620] [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] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/09/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVE Question prompt lists (QPLs) have been effective at increasing patient involvement and question asking in medical appointments, which is critical for shared decision making. We investigated whether pre-visit preparation (PVP), including a QPL, would increase question asking among caregivers of pediatric patients with undiagnosed, suspected genetic conditions. METHODS Caregivers were randomized to receive the PVP before their appointment (n = 59) or not (control, n = 53). Appointments were audio-recorded. Transcripts were analyzed to determine questions asked. RESULTS Caregivers in the PVP group asked more questions (MeanPVP = 4.36, SDPVP = 4.66 vs. Meancontrol = 2.83, SDcontrol = 3.03, p = 0.045), including QPL questions (MeanPVP = 1.05, SDPVP = 1.39 vs. Meancontrol = 0.36, SDcontrol = 0.81, p = 0.002). Caregivers whose child had insurance other than Medicaid in the PVP group asked more total and QPL questions than their counterparts in the control group (ps = 0.005 and 0.002); there was no intervention effect among caregivers of children with Medicaid or no insurance (ps = 0.775 and 0.166). CONCLUSION The PVP increased question asking but worked less effectively among traditionally underserved groups. Additional interventions, including provider-focused efforts, may be needed to promote engagement of underserved patients. PRACTICE IMPLICATIONS Patient/family-focused interventions may not be beneficial for all populations. Providers should be aware of potential implicit and explicit biases and encourage question asking to promote patient/family engagement.
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Affiliation(s)
- Margaret Waltz
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA.
| | - Haoyang Yan
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - R Jean Cadigan
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Courtney Canter
- Department of Anthropology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | | | - Jeannette T Bensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Carol Conway
- Parent/Advocate, Parent Advocates for Adult Children with Intellectual &/or Developmental Disabilities in NC, Chapel Hill, NC, USA
| | | | - Laura Farnan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Tracey L Grant
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Barbara Leach
- Parent/Advocate, Family Support Program, School of Social Work, UNC Chapel Hill, Chapel Hill, NC, USA
| | - Feng-Chang Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Madeline Mahla
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Bradford C Powell
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Christine M Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
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Waltz M, Canter C, Bensen JT, Berg JS, Foreman AKM, Grant TL, Lich KH, Navas A, O’Daniel JM, Powell BC, Rini CM, Staley BS, Cadigan RJ. The Burden of COVID-19 on Caregivers of Children with Suspected Genetic Conditions: A Therapeutic Odyssey. Phys Occup Ther Pediatr 2022; 43:257-271. [PMID: 36310386 PMCID: PMC10079636 DOI: 10.1080/01942638.2022.2138734] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
AIMS Children with disabilities and rare or undiagnosed conditions and their families have faced numerous hardships of living during the COVID-19 pandemic. For those with undiagnosed conditions, the diagnostic odyssey can be long, expensive, and marked by uncertainty. We, therefore, sought to understand whether and how COVID-19 impacted the trajectory of children's care. METHODS We conducted semi-structured qualitative interviews with 25 caregivers who, prior to the pandemic, were on a diagnostic odyssey for their children. RESULTS Most caregivers did not report any interruptions to their child's diagnostic odyssey. The greatest impact was access to therapy services, including the suspension or loss of their child's in-person therapeutic care and difficulties with virtual therapies. This therapy gap caused caregivers to fear that their children were not making progress. CONCLUSION Although much has been written about the challenges of diagnostic odysseys for children and their families, this study illustrates the importance of expanding the focus of these studies to include therapeutic odysseys. Because therapeutic odysseys continue regardless of whether diagnoses are made, future research should investigate how to support caregivers through children's therapies within and outside of the COVID-19 context.
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Affiliation(s)
- Margaret Waltz
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Courtney Canter
- Department of Anthropology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jeannette T. Bensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | | | - Tracey L. Grant
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Kristen Hassmiller Lich
- Department of Health Policy and Management, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Angelo Navas
- Department of Pediatrics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Julianne M. O’Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C. Powell
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Christine M. Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Brooke S. Staley
- Department of Epidemiology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - R. Jean Cadigan
- Department of Social Medicine, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
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Hunter JE, Jenkins CL, Bulkley JE, Gilmore MJ, Lee K, Pak CM, Wallace KE, Buchanan AH, Foreman AKM, Freed AS, Goehringer S, Manickam K, Meeks NJL, Ramos EM, Shah N, Steiner RD, Subramanian SL, Trotter T, Webber EM, Williams MS, Goddard KAB, Powell BC. ClinGen's Pediatric Actionability Working Group: Clinical actionability of secondary findings from genome-scale sequencing in children and adolescents. Genet Med 2022; 24:1328-1335. [PMID: 35341655 PMCID: PMC9156571 DOI: 10.1016/j.gim.2022.02.019] [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: 12/07/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE Synthesis and curation of evidence regarding the clinical actionability of secondary findings (SFs) from genome-scale sequencing are needed to support decision-making on reporting of these findings. To assess actionability of SFs in children and adolescents, the Clinical Genome Resource established the Pediatric Actionability Working Group (AWG). METHODS The Pediatric AWG modified the framework of the existing Adult AWG, which included production of summary reports of actionability for genes and associated conditions and consensus actionability scores for specific outcome-intervention pairs. Modification of the adult framework for the pediatric setting included accounting for special considerations for reporting presymptomatic or predictive genetic findings in the pediatric context, such as maintaining future autonomy by not disclosing conditions not actionable until adulthood. The Pediatric AWG then applied this new framework to genes and associated conditions with putative actionability. RESULTS As of September 2021, the Pediatric AWG applied the new framework to 70 actionability topics representing 143 genes. Reports and scores are publicly available at www.clinicalgenome.org. CONCLUSION The Pediatric AWG continues to curate gene-condition topics and build an evidence-based resource, supporting clinical communities and decision-makers with policy development on the return of SFs in pediatric populations.
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Affiliation(s)
- Jessica Ezzell Hunter
- Genomics, Ethics, and Translational Research Program, RTI International, ResearchTriangle Park, NC.
| | - Charisma L Jenkins
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Joanna E Bulkley
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Marian J Gilmore
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Kristy Lee
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christine M Pak
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Kathleen E Wallace
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Amanda S Freed
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA
| | | | - Kandamurugu Manickam
- Division of Genetic and Genomic Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH; The Ohio State University College of Medicine, Columbus, OH
| | - Naomi J L Meeks
- Section of Genetics and Metabolism, Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Erin M Ramos
- Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Neethu Shah
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Robert D Steiner
- School of Medicine and Public Health, University of Wisconsin, Madison, WI
| | | | | | | | | | - Katrina A B Goddard
- Department of Translational and Applied Genomics (TAG), Kaiser Permanente Center for Health Research, Portland, OR
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Rini C, Roche MI, Lin FC, Foreman AKM, Khan CM, Griesemer I, Waltz M, Lee K, O'Daniel JM, Evans JP, Berg JS, Henderson GE. Burden or benefit? Effects of providing education about and the option to request additional genomic findings from diagnostic exome sequencing: A randomized controlled trial. Patient Educ Couns 2021; 104:2989-2998. [PMID: 33966955 PMCID: PMC8553797 DOI: 10.1016/j.pec.2021.04.026] [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] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/31/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
OBJECTIVE Many people prefer to learn secondary or "additional" findings from genomic sequencing, including findings with limited medical actionability. Research has investigated preferences for and effects of learning such findings, but not psychosocial and behavioral effects of receiving education about them and the option to request them, which could be burdensome or beneficial (e.g., causing choice overload or satisfying strong preferences, respectively). METHODS 335 adults with suspected genetic disorders who had diagnostic exome sequencing in a research study and were randomized to receive either diagnostic findings only (DF; n = 171) or diagnostic findings plus education about additional genomic findings and the option to request them (DF + EAF; n = 164). Assessments occurred after enrollment (Time 1), after return of diagnostic results and-for DF + EAF-the education under investigation (Time 2), and three and six months later (Times 3, 4). RESULTS Time 2 test-related distress, test-related uncertainty, and generalized anxiety were lower in the DF + EAF group (ps = 0.025-0.043). There were no other differences. CONCLUSIONS Findings show limited benefits and no harms of providing education about and the option to learn additional findings with limited medical actionability. PRACTICE IMPLICATIONS Findings can inform recommendations for returning additional findings from genomic sequencing (e.g., to research participants or after commercial testing).
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Affiliation(s)
- Christine Rini
- Department of Medical Social Sciences, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611, USA.
| | - Myra I Roche
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Feng-Chang Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Cynthia M Khan
- U.S. Government Accountability Office, 441G Street NW, Washington, DC 20548, USA
| | - Ida Griesemer
- Department of Health Behavior, University of North Carolina, 135 Dauer Dr., Chapel Hill, NC 27599, USA
| | - Margaret Waltz
- Department of Social Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James P Evans
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Gail E Henderson
- Department of Social Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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Staley BS, Milko LV, Waltz M, Griesemer I, Mollison L, Grant TL, Farnan L, Roche M, Navas A, Lightfoot A, Foreman AKM, O'Daniel JM, O'Neill SC, Lin FC, Roman TS, Brandt A, Powell BC, Rini C, Berg JS, Bensen JT. Evaluating the clinical utility of early exome sequencing in diverse pediatric outpatient populations in the North Carolina Clinical Genomic Evaluation of Next-generation Exome Sequencing (NCGENES) 2 study: a randomized controlled trial. Trials 2021; 22:395. [PMID: 34127041 PMCID: PMC8201439 DOI: 10.1186/s13063-021-05341-2] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/26/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Exome sequencing (ES) has probable utility for shortening the diagnostic odyssey of children with suspected genetic disorders. This report describes the design and methods of a study evaluating the potential of ES as a routine clinical tool for pediatric patients who have suspected genetic conditions and who are in the early stages of the diagnostic odyssey. METHODS The North Carolina Clinical Genomic Evaluation by Next-generation Exome Sequencing (NCGENES) 2 study is an interdisciplinary, multi-site Phase III randomized controlled trial of two interventions: educational pre-visit preparation (PVP) and offer of first-line ES. In this full-factorial design, parent-child dyads are randomly assigned to one of four study arms (PVP + usual care, ES + usual care, PVP + ES + usual care, or usual care alone) in equal proportions. Participants are recruited from Pediatric Genetics or Neurology outpatient clinics in three North Carolina healthcare facilities. Eligible pediatric participants are < 16 years old and have a first visit to a participating clinic, a suspected genetic condition, and an eligible parent/guardian to attend the clinic visit and complete study measures. The study oversamples participants from underserved and under-represented populations. Participants assigned to the PVP arms receive an educational booklet and question prompt list before clinical interactions. Randomization to offer of first-line ES is revealed after a child's clinic visit. Parents complete measures at baseline, pre-clinic, post-clinic, and two follow-up timepoints. Study clinicians provide phenotypic data and complete measures after the clinic visit and after returning results. Reportable study-related research ES results are confirmed in a CLIA-certified clinical laboratory. Results are disclosed to the parent by the clinical team. A community consultation team contributed to the development of study materials and study implementation methods and remains engaged in the project. DISCUSSION NCGENES 2 will contribute valuable knowledge concerning technical, clinical, psychosocial, and health economic issues associated with using early diagnostic ES to shorten the diagnostic odyssey of pediatric patients with likely genetic conditions. Results will inform efforts to engage diverse populations in genomic medicine research and generate evidence that can inform policy, practice, and future research related to the utility of first-line diagnostic ES in health care. TRIAL REGISTRATION ClinicalTrials.gov NCT03548779 . Registered on June 07, 2018.
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Affiliation(s)
- Brooke S Staley
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box #7295, Chapel Hill, NC, 27599-7295, USA.
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Margaret Waltz
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ida Griesemer
- Department of Heath Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lonna Mollison
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tracey L Grant
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Laura Farnan
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Myra Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Angelo Navas
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra Lightfoot
- Department of Heath Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Center for Health Promotion and Disease Prevention, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Suzanne C O'Neill
- Department of Oncology, Georgetown University, Washington, DC, 20007, USA
| | - Feng-Chang Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christine Rini
- Department of Medical Social Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Campus Box #7295, Chapel Hill, NC, 27599-7295, USA
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8
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DeCristo DM, Milko LV, O'Daniel JM, Foreman AKM, Mollison LF, Powell BC, Powell CM, Berg JS. Actionability of commercial laboratory sequencing panels for newborn screening and the importance of transparency for parental decision-making. Genome Med 2021; 13:50. [PMID: 33781310 PMCID: PMC8008582 DOI: 10.1186/s13073-021-00867-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 08/18/2020] [Accepted: 03/12/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Newborn screening aims to identify individual patients who could benefit from early management, treatment, and/or surveillance practices. As sequencing technologies have progressed and we move into the era of precision medicine, genomic sequencing has been introduced to this area with the hopes of detecting variants related to a vastly expanded number of conditions. Though implementation of genomic sequencing for newborn screening in public health and clinical settings is limited, commercial laboratories have begun to offer genomic screening panels for neonates. METHODS We examined genes listed on four commercial laboratory genomic screening panels for neonates and assessed their clinical actionability using an established age-based semi-quantitative metric to categorize them. We identified genes that were included on multiple panels or distinct between panels. RESULTS Three hundred and nine genes appeared on one or more commercial panels: 74 (23.9%) genes were included in all four commercial panels, 45 (14.6%) were on only three panels, 76 (24.6%) were on only two panels, and 114 (36.9%) genes were listed on only one of the four panels. Eighty-two genes (26.5%) listed on one or more panels were assessed by our method to be inappropriate for newborn screening and to require additional parental decision-making. Conversely, 249 genes that we previously identified as being highly actionable were not listed on any of the four commercial laboratory genomic screening panels. CONCLUSIONS Commercial neonatal genomic screening panels have heterogeneous content and may contain some conditions with lower actionability than would be expected for public health newborn screening; conversely, some conditions with higher actionability may be omitted from these panels. The lack of transparency about how conditions are selected suggests a need for greater detail about panel content in order for parents to make informed decisions. The nuanced activity of gene list selection for genomic screening should be iteratively refined with evidence-based approaches to provide maximal benefit and minimal harm to newborns.
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Affiliation(s)
- Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Lonna F Mollison
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
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9
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Biesecker BB, Lillie SE, Amendola LM, Donohue KE, East KM, Foreman AKM, Gilmore MJ, Greve V, Liangolou B, O'Daniel JM, Odgis JA, Rego S, Rolf B, Scollon S, Suckiel SA, Zepp J, Joseph G. A review and definition of 'usual care' in genetic counseling trials to standardize use in research. J Genet Couns 2021; 30:42-50. [PMID: 33278053 PMCID: PMC7882019 DOI: 10.1002/jgc4.1363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/30/2020] [Revised: 09/30/2020] [Accepted: 10/21/2020] [Indexed: 01/16/2023]
Abstract
The descriptor 'usual care' refers to standard or routine care. Yet, no formal definition exists. The need to define what constitutes usual care arises in clinical research. Often one arm in a trial represents usual care in comparison with a novel intervention. Accordingly, usual care in genetic counseling research appears predominantly in randomized controlled trials. Recent standards for reporting genetic counseling research call for standardization, but do not address usual care. We (1) inventoried all seven studies in the Clinical Sequencing Evidence-Generating Consortium (CSER) about how genetic counseling was conceptualized, conducted, and whether a usual care arm was involved; (2) conducted a review of published randomized control trials in genetic counseling, comparing how researchers describe usual care groups; and (3) reviewed existing professionally endorsed definitions and practice descriptions of genetic counseling. We found wide variation in the content and delivery of usual care. Descriptions frequently detailed the content of usual care, most often noting assessment of genetic risk factors, collecting family histories, and offering testing. A minority included addressing psychological concerns or the risks versus benefits of testing. Descriptions of how care was delivered were vague except for mode and type of clinician, which varied. This significant variation, beyond differences expected among subspecialties, reduces the validity and generalizability of genetic counseling research. Ideally, research reflects clinical practice so that evidence generated can be used to improve clinical outcomes. To address this objective, we propose a definition of usual care in genetic counseling research that merges common elements from the National Society of Genetic Counselors' practice definition, the Reciprocal Engagement Model, and the Accreditation Council for Genetic Counselors' practice-based competencies. Promoting consistent execution of usual care in the design of genetic counseling trials can lead to more consistency in representing clinical care and facilitate the generation of evidence to improve it.
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Affiliation(s)
- Barbara B Biesecker
- Genomics, Bioinformatics and Translation, RTI International, Washington, DC, USA
| | - Sarah E Lillie
- Center for Communication Science, RTI International, Research Triangle Park, NC, USA
| | - Laura M Amendola
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Katherine E Donohue
- Institute for Genomic Health, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kelly M East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Marian J Gilmore
- Department of Translational and Applied Genomics, Kaiser Permanente - Center for Health Research, Portland, OR, USA
| | - Veronica Greve
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Jacqueline A Odgis
- Institute for Genomic Health, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shannon Rego
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Bradley Rolf
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sabrina A Suckiel
- Institute for Genomic Health, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jamilyn Zepp
- Department of Translational and Applied Genomics, Kaiser Permanente - Center for Health Research, Portland, OR, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California, San Francisco, CA, USA
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10
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Waltz M, Prince AER, O’Daniel JM, Foreman AKM, Powell BC, Berg JS. Referencing BRCA in hereditary cancer risk discussions: In search of an anchor in a sea of uncertainty. J Genet Couns 2020; 29:949-959. [PMID: 31967382 PMCID: PMC7374021 DOI: 10.1002/jgc4.1219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 01/14/2023]
Abstract
As panel testing and exome sequencing are increasingly incorporated into clinical care, clinicians must grapple with how to communicate the risks and treatment decisions surrounding breast cancer genes beyond BRCA1 and BRCA2. In this paper, we examine clinicians' practice of employing BRCA1 and BRCA2 to help contextualize less certain genetic information regarding cancer risk and the possible implications of this practice for patients within the context of an exome sequencing study, NCGENES. We audio-recorded return of results appointments for 14 women who participated in NCGENES, previously had breast cancer, and were suspected of having a hereditary cancer predisposition. These patients were also interviewed four weeks later regarding their understanding of their results. We found that BRCA1 and BRCA2 were held as the gold standard, where clinicians compared what is known about BRCA to the limited understanding of other breast cancer-related genes. BRCA1 and BRCA2 were used as anchors to shape patients' understandings of genetic knowledge, risk, and management, illustrating how the information clinicians provide to patients may work as an external anchor. Yet, presenting BRCA1 and BRCA2 as a means of scientific reassurance can run the risk of patients conflating knowledge about certainty of risk with degree of risk after receiving a result for a moderate penetrance gene. This can be further complicated by misperceptions of the precision of cancer predictability attributed to these or other described 'cancer genes' in public media.
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Affiliation(s)
- Margaret Waltz
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Julianne M. O’Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ann Katherine M. Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bradford C. Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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11
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Amendola LM, Muenzen K, Biesecker LG, Bowling KM, Cooper GM, Dorschner MO, Driscoll C, Foreman AKM, Golden-Grant K, Greally JM, Hindorff L, Kanavy D, Jobanputra V, Johnston JJ, Kenny EE, McNulty S, Murali P, Ou J, Powell BC, Rehm HL, Rolf B, Roman TS, Van Ziffle J, Guha S, Abhyankar A, Crosslin D, Venner E, Yuan B, Zouk H, Jarvik GP, Jarvik GP. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies. Am J Hum Genet 2020; 107:932-941. [PMID: 33108757 DOI: 10.1016/j.ajhg.2020.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 08/03/2020] [Accepted: 09/29/2020] [Indexed: 12/31/2022] Open
Abstract
Harmonization of variant pathogenicity classification across laboratories is important for advancing clinical genomics. The two CLIA-accredited Electronic Medical Record and Genomics Network sequencing centers and the six CLIA-accredited laboratories and one research laboratory performing genome or exome sequencing in the Clinical Sequencing Evidence-Generating Research Consortium collaborated to explore current sources of discordance in classification. Eight laboratories each submitted 20 classified variants in the ACMG secondary finding v.2.0 genes. After removing duplicates, each of the 158 variants was annotated and independently classified by two additional laboratories using the ACMG-AMP guidelines. Overall concordance across three laboratories was assessed and discordant variants were reviewed via teleconference and email. The submitted variant set included 28 P/LP variants, 96 VUS, and 34 LB/B variants, mostly in cancer (40%) and cardiac (27%) risk genes. Eighty-six (54%) variants reached complete five-category (i.e., P, LP, VUS, LB, B) concordance, and 17 (11%) had a discordance that could affect clinical recommendations (P/LP versus VUS/LB/B). 21% and 63% of variants submitted as P and LP, respectively, were discordant with VUS. Of the 54 originally discordant variants that underwent further review, 32 reached agreement, for a post-review concordance rate of 84% (118/140 variants). This project provides an updated estimate of variant concordance, identifies considerations for LP classified variants, and highlights ongoing sources of discordance. Continued and increased sharing of variant classifications and evidence across laboratories, and the ongoing work of ClinGen to provide general as well as gene- and disease-specific guidance, will lead to continued increases in concordance.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, Seattle, WA 98195, USA
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12
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Roman TS, Crowley SB, Roche MI, Foreman AKM, O'Daniel JM, Seifert BA, Lee K, Brandt A, Gustafson C, DeCristo DM, Strande NT, Ramkissoon L, Milko LV, Owen P, Roy S, Xiong M, Paquin RS, Butterfield RM, Lewis MA, Souris KJ, Bailey DB, Rini C, Booker JK, Powell BC, Weck KE, Powell CM, Berg JS. Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project. Am J Hum Genet 2020; 107:596-611. [PMID: 32853555 PMCID: PMC7536575 DOI: 10.1016/j.ajhg.2020.08.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Newborn screening (NBS) was established as a public health program in the 1960s and is crucial for facilitating detection of certain medical conditions in which early intervention can prevent serious, life-threatening health problems. Genomic sequencing can potentially expand the screening for rare hereditary disorders, but many questions surround its possible use for this purpose. We examined the use of exome sequencing (ES) for NBS in the North Carolina Newborn Exome Sequencing for Universal Screening (NC NEXUS) project, comparing the yield from ES used in a screening versus a diagnostic context. We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (∼18%) children with hearing loss. We discovered actionable findings in four participants that would not have been detected by standard NBS. A subset of parents was eligible to receive additional information for their child about childhood-onset conditions with low or no clinical actionability, clinically actionable adult-onset conditions, and carrier status for autosomal-recessive conditions. We found pathogenic variants associated with hereditary breast and/or ovarian cancer in two children, a likely pathogenic variant in the gene associated with Lowe syndrome in one child, and an average of 1.8 reportable variants per child for carrier results. These results highlight the benefits and limitations of using genomic sequencing for NBS and the challenges of using such technology in future precision medicine approaches.
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Affiliation(s)
- Tamara S Roman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie B Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myra I Roche
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bryce A Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alicia Brandt
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Chelsea Gustafson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniela M DeCristo
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natasha T Strande
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura V Milko
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Phillips Owen
- Renaissance Computing Institute, Chapel Hill, NC 27517, USA
| | - Sayanty Roy
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mai Xiong
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan S Paquin
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Rita M Butterfield
- Department of Family Medicine and Community Health, Duke University School of Medicine, Durham, NC 27705, USA
| | - Megan A Lewis
- Center for Communication Science, RTI International, Research Triangle Park, NC 27709, USA
| | - Katherine J Souris
- Department of Health Behavior, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Donald B Bailey
- Genomics, Bioinformatics and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Christine Rini
- Feinberg School of Medicine, Department of Medical Social Sciences, and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Jessica K Booker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Karen E Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cynthia M Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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13
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Vora NL, Gilmore K, Brandt A, Gustafson C, Strande N, Ramkissoon L, Hardisty E, Foreman AKM, Wilhelmsen K, Owen P, Weck KE, Berg JS, Powell CM, Powell BC. Correction: An approach to integrating exome sequencing for fetal structural anomalies into clinical practice. Genet Med 2020; 22:1426. [PMID: 32555414 DOI: 10.1038/s41436-020-0870-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Gustafson
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natasha Strande
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lori Ramkissoon
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Phillips Owen
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen E Weck
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cynthia M Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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14
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Vora NL, Gilmore K, Brandt A, Gustafson C, Strande N, Ramkissoon L, Hardisty E, Foreman AKM, Wilhelmsen K, Owen P, Weck KE, Berg JS, Powell CM, Powell BC. An approach to integrating exome sequencing for fetal structural anomalies into clinical practice. Genet Med 2020; 22:954-961. [PMID: 31974414 PMCID: PMC7205580 DOI: 10.1038/s41436-020-0750-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 10/01/2019] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
PURPOSE We investigated the diagnostic and clinical performance of trio exome sequencing (ES) in parent-fetus trios where the fetus had sonographic abnormalities but normal karyotype, microarray and, in some cases, normal gene-specific sequencing. METHODS ES was performed from DNA of 102 anomalous fetuses and from peripheral blood from their parents. Parents provided consent for the return of diagnostic results in the fetus, medically actionable findings in the parents, and identification as carrier couple for significant autosomal recessive conditions. RESULTS In 21/102 (20.6%) fetuses, ES provided a positive-definitive or positive-probable diagnosis. In 10/102 (9.8%), ES provided an inconclusive-possible result. At least 2/102 (2.0%) had a repeat pregnancy during the study period and used the information from the study for prenatal diagnosis in the next pregnancy. Six of 204 (2.9%) parents received medically actionable results that affected their own health and 3/102 (2.9%) of couples received results that they were carriers for the same autosomal recessive condition. CONCLUSION ES has diagnostic utility in a select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy, variant interpretation, and various types of diagnostic results affecting both fetal and parental health must be addressed by highly tailored pre- and post-test genetic counseling.
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Affiliation(s)
- Neeta L Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chelsea Gustafson
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natasha Strande
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lori Ramkissoon
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Phillips Owen
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Karen E Weck
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cynthia M Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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15
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Masood MM, Mieczkowski P, Malc EP, Foreman AKM, Evans JP, Clark JM, Rose AS. Congenital Midline Cervical Cleft: First Report and Genetic Analysis of Two Related Patients. Ann Otol Rhinol Laryngol 2020; 129:653-656. [PMID: 32028786 DOI: 10.1177/0003489420906180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/15/2022]
Abstract
OBJECTIVES Congenital midline cervical cleft (CMCC) is a rare congenital anterior neck anatomical anomaly. We present the case of two related patients (grandchild and maternal grandmother) who were both born with a congenital midline cervical cleft along with genetic analysis. METHODS Clinical examination of both patients and surgical excision of the grandchild was performed. Genetic analysis with exome sequencing (ES) was conducted for both patients. RESULTS Genetic analysis with exome sequencing (ES) revealed apparently novel single nucleotide variants in 66 genes present in both proband and grandmother. Five of these variants are predicted to cause frameshifting in the coding region of the respective genes and truncated proteins (OVGP1, TYW1B, ZAN, SSPO, FOLR3). Two of these genes (TYW1B and SSPO) have homozygous indel mutations in both patients. CONCLUSIONS To our knowledge, this is the first case of two related patients with a congenital midline cervical cleft. The results of our genetic analysis reveal potential relevance to CMCC development.
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Affiliation(s)
- Maheer M Masood
- Department of Otolaryngology-Head and Neck Surgery, University of Kansas Medical Center, Kansas City, KS, USA
| | - Piotr Mieczkowski
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ewa P Malc
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - James P Evans
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - J Madison Clark
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Austin S Rose
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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16
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Rini C, Henderson GE, Evans JP, Berg JS, Foreman AKM, Griesemer I, Waltz M, O’Daniel JM, Roche MI. Correction: Genomic knowledge in the context of diagnostic exome sequencing: changes over time, persistent subgroup differences, and associations with psychological sequencing outcomes. Genet Med 2019; 21:2846. [DOI: 10.1038/s41436-019-0622-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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17
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Rini C, Henderson GE, Evans JP, Berg JS, Foreman AKM, Griesemer I, Waltz M, O'Daniel JM, Roche MI. Genomic knowledge in the context of diagnostic exome sequencing: changes over time, persistent subgroup differences, and associations with psychological sequencing outcomes. Genet Med 2019; 22:60-68. [PMID: 31312045 PMCID: PMC6946868 DOI: 10.1038/s41436-019-0600-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/19/2019] [Indexed: 01/26/2023] Open
Abstract
Purpose People undergoing diagnostic genome-scale sequencing are expected to have better psychological outcomes when they can incorporate and act on accurate, relevant knowledge that supports informed decision making. Methods This longitudinal study used data from the NCGENES study of diagnostic exome sequencing to evaluate associations between factual genomic knowledge (measured with the University of North Carolina Genomic Knowledge Scale at three assessments from baseline to after return of results) and sequencing outcomes that reflected participants’ perceived understanding of the study and sequencing, regret for joining the study, and responses to learning sequencing results. It also investigated differences in genomic knowledge associated with subgroups differing in race/ethnicity, income, education, health literacy, English proficiency, and prior genetic testing. Results Multivariate models revealed higher genomic knowledge at baseline for non-Hispanic Whites and those with higher income, education, and health literacy (ps<.001). These subgroup differences persisted across study assessments despite a general increase in knowledge among all groups. Greater baseline genomic knowledge was associated with lower test-related distress (p=.047) and greater perceived understanding of diagnostic genomic sequencing (ps .04 to <.001). Conclusion Findings extend understanding of the role of genomic knowledge in psychological outcomes of diagnostic exome sequencing, providing guidance for additional research and interventions.
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Affiliation(s)
- Christine Rini
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, USA.
| | - Gail E Henderson
- Center for Genomics and Society, University of North Carolina, Chapel Hill, NC, USA.,Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - James P Evans
- Center for Genomics and Society, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Center for Genomics and Society, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ann Katherine M Foreman
- Center for Genomics and Society, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ida Griesemer
- Department of Health Behavior, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margaret Waltz
- Center for Genomics and Society, University of North Carolina, Chapel Hill, NC, USA.,Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julianne M O'Daniel
- Center for Genomics and Society, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Myra I Roche
- Center for Genomics and Society, University of North Carolina, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pediatrics, University of North Carolina, Chapel Hill, NC, USA
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18
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Milko LV, O’Daniel JM, DeCristo DM, Crowley SB, Foreman AKM, Wallace KE, Mollison LF, Strande NT, Girnary ZS, Boshe LJ, Aylsworth AS, Gucsavas-Calikoglu M, Frazier DM, Vora NL, Roche MI, Powell BC, Powell CM, Berg JS. An Age-Based Framework for Evaluating Genome-Scale Sequencing Results in Newborn Screening. J Pediatr 2019; 209:68-76. [PMID: 30851990 PMCID: PMC6535354 DOI: 10.1016/j.jpeds.2018.12.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/24/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To assess the performance of a standardized, age-based metric for scoring clinical actionability to evaluate conditions for inclusion in newborn screening and compare it with the results from other contemporary methods. STUDY DESIGN The North Carolina Newborn Exome Sequencing for Universal Screening study developed an age-based, semiquantitative metric to assess the clinical actionability of gene-disease pairs and classify them with respect to age of onset or timing of interventions. This categorization was compared with the gold standard Recommended Uniform Screening Panel and other methods to evaluate gene-disease pairs for newborn genomic sequencing. RESULTS We assessed 822 gene-disease pairs, enriched for pediatric onset of disease and suspected actionability. Of these, 466 were classified as having childhood onset and high actionability, analogous to conditions selected for the Recommended Uniform Screening Panel core panel. Another 245 were classified as having childhood onset and low to no actionability, 25 were classified as having adult onset and high actionability, 19 were classified as having adult onset and low to no actionability, and 67 were excluded due to controversial evidence and/or prenatal onset. CONCLUSIONS This study describes a novel method to facilitate decisions about the potential use of genomic sequencing for newborn screening. These categories may assist parents and physicians in making informed decisions about the disclosure of results from voluntary genomic sequencing in children.
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Affiliation(s)
| | | | | | | | | | | | | | - Natasha T. Strande
- Department of Genetics, UNC Chapel Hill,Department of Pathology and Laboratory Medicine, UNC Chapel Hill
| | - Zahra S. Girnary
- Department of Genetics, UNC Chapel Hill,current affiliation: Mission Fullerton Genetics Center, Asheville, NC
| | - Lacey J. Boshe
- Department of Genetics, UNC Chapel Hill,current affiliation: School of Medicine, UNC Chapel Hill
| | - Arthur S. Aylsworth
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | | | - Dianne M. Frazier
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, UNC Chapel Hill
| | - Myra I. Roche
- Department of Genetics, UNC Chapel Hill,Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
| | | | - Cynthia M. Powell
- Department of Pediatrics, Division of Genetics and Metabolism, UNC Chapel Hill
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19
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Haverbusch VCE, Heise EM, Foreman AKM, Callanan NP. An examination of the factors contributing to the expansion of subspecialty genetic counseling. J Genet Couns 2019; 28:616-625. [PMID: 30706979 DOI: 10.1002/jgc4.1077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 11/17/2017] [Revised: 11/18/2018] [Accepted: 12/01/2018] [Indexed: 11/08/2022]
Abstract
In recent years, genetic counselors have moved into increasingly varied areas of patient care. Yet limited information is known about how these genetic counselors transitioned from more general clinical practice to subspecialized practice. This study was designed to answer three research questions: (1) What common factors establish a need for a genetic counselor in a subspecialty setting? (2) How do genetic counselors in subspecialties establish their positions? (3) Once established, how do the positions of these genetic counselors evolve as the subspecialty expands? Phone interviews with subspecialized genetic counselors led to the development of an online survey distributed through the National Society of Genetic Counselors ListServ. Sixty-eight of the 144 initial participants met eligibility criteria for participation as subspecialty genetic counselors in a clinical role. Physician interest in hiring a genetic counselor, clinical need, genetic counselor interest in subspecialty area, and available genetic testing were commonly reported as contributing factors to position creation. Most subspecialty genetic counseling positions were created as new positions, rather than evolved from a previous position. Over time, subspecialty positions drew more departmental funding and included increased clinical coordination or administrative responsibilities. The results of this study can encourage genetic counselors to collaborate with their medical institutions to utilize their skill-set in diverse areas of patient care.
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Affiliation(s)
| | | | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, North Carolina
| | - Nancy P Callanan
- MS Genetic Counseling Program, University of North Carolina at Greensboro, Greensboro, North Carolina
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20
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Vora NL, Powell B, Brandt A, Strande N, Hardisty E, Gilmore K, Foreman AKM, Wilhelmsen K, Bizon C, Reilly J, Owen P, Powell CM, Skinner D, Rini C, Lyerly AD, Boggess KA, Weck K, Berg JS, Evans JP. Prenatal exome sequencing in anomalous fetuses: new opportunities and challenges. Genet Med 2017; 19:1207-1216. [PMID: 28518170 PMCID: PMC5675748 DOI: 10.1038/gim.2017.33] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/04/2017] [Indexed: 12/13/2022] Open
Abstract
PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions. We assessed the perceptions and understanding of exome sequencing using mixed methods in 15 mother-father dyads.ResultsIn seven (47%) of 15 fetuses, exome sequencing provided a diagnosis or possible diagnosis with identification of variants in the following genes: COL1A1, MUSK, KCTD1, RTTN, TMEM67, PIEZO1 and DYNC2H1. One additional case revealed a de novo nonsense mutation in a novel candidate gene (MAP4K4). The perceived likelihood that exome sequencing would explain the results (5.2 on a 10-point scale) was higher than the approximately 30% diagnostic yield discussed in pretest counseling.ConclusionExome sequencing had diagnostic utility in a highly select population of fetuses where a genetic diagnosis was highly suspected. Challenges related to genetics literacy and variant interpretation must be addressed by highly tailored pre- and posttest genetic counseling.
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Affiliation(s)
- Neeta L. Vora
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Bradford Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alicia Brandt
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Natasha Strande
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emily Hardisty
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly Gilmore
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ann Katherine M. Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- North Carolina Translational and Clinical Sciences (NC TraCS) Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kirk Wilhelmsen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Chris Bizon
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jason Reilly
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Phil Owen
- Departments of Genetics and Neurology, Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Cynthia M. Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Debra Skinner
- FPG Child Development Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Christine Rini
- Department of Health Behavior, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anne D. Lyerly
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kim A. Boggess
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Karen Weck
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jonathan S. Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - James P. Evans
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Social Medicine and Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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21
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Rini C, Khan CM, Moore E, Roche MI, Evans JP, Berg JS, Powell BC, Corbie-Smith G, Foreman AKM, Griesemer I, Lee K, O'Daniel JM, Henderson GE. The who, what, and why of research participants' intentions to request a broad range of secondary findings in a diagnostic genomic sequencing study. Genet Med 2017; 20:760-769. [PMID: 29261173 PMCID: PMC5920790 DOI: 10.1038/gim.2017.176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 05/29/2017] [Accepted: 07/20/2017] [Indexed: 12/21/2022] Open
Abstract
PURPOSE In a diagnostic exome sequencing study (the North Carolina Clinical Genomic Evaluation by Next-Generation Exome Sequencing project, NCGENES), we investigated adult patients' intentions to request six categories of secondary findings (SFs) with low or no medical actionability and correlates of their intentions. METHODS At enrollment, eligible participants (n = 152) completed measures assessing their sociodemographic, clinical, and literacy-related characteristics. Prior to and during an in-person diagnostic result disclosure visit, they received education about categories of SFs they could request. Immediately after receiving education at the visit, participants completed measures of intention to learn SFs, interest in each category, and anticipated regret for learning and not learning each category. RESULTS Seventy-eight percent of participants intended to learn at least some SFs. Logistic regressions examined their intention to learn any or all of these findings (versus none) and interest in each of the six individual categories (yes/no). Results revealed little association between intentions and sociodemographic, clinical, or literacy-related factors. Across outcomes, participants who anticipated regret for learning SFs reported weaker intention to learn them (odds ratios (ORs) from 0.47 to 0.71), and participants who anticipated regret for not learning these findings reported stronger intention to learn them (OR 1.61-2.22). CONCLUSION Intentions to request SFs with low or no medical actionability may be strongly influenced by participants' desire to avoid regret.
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Affiliation(s)
- Christine Rini
- John Theuer Cancer Center, Hackensack University Medical Center, Hackensack, New Jersey, USA.
| | | | - Elizabeth Moore
- Blue Cross and Blue Shield of North Carolina, Durham, North Carolina, USA
| | - Myra I Roche
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James P Evans
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bradford C Powell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Giselle Corbie-Smith
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Center for Health Equity Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ann Katherine M Foreman
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ida Griesemer
- Department of Health Behavior, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julianne M O'Daniel
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gail E Henderson
- Center for Genomics and Society, University of North Carolina, Chapel Hill, North Carolina, USA.,Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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22
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Berg JS, Foreman AKM, O'Daniel JM, Booker JK, Boshe L, Carey T, Crooks KR, Jensen BC, Juengst ET, Lee K, Nelson DK, Powell BC, Powell CM, Roche MI, Skrzynia C, Strande NT, Weck KE, Wilhelmsen KC, Evans JP. A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing. Genet Med 2015; 18:467-75. [PMID: 26270767 PMCID: PMC4752935 DOI: 10.1038/gim.2015.104] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [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: 05/18/2015] [Accepted: 06/11/2015] [Indexed: 01/01/2023] Open
Abstract
PURPOSE As genome-scale sequencing is increasingly applied in clinical scenarios, a wide variety of genomic findings will be discovered as secondary or incidental findings, and there is debate about how they should be handled. The clinical actionability of such findings varies, necessitating standardized frameworks for a priori decision making about their analysis. METHODS We established a semiquantitative metric to assess five elements of actionability: severity and likelihood of the disease outcome, efficacy and burden of intervention, and knowledge base, with a total score from 0 to 15. RESULTS The semiquantitative metric was applied to a list of putative actionable conditions, the list of genes recommended by the American College of Medical Genetics and Genomics (ACMG) for return when deleterious variants are discovered as secondary/incidental findings, and a random sample of 1,000 genes. Scores from the list of putative actionable conditions (median = 12) and the ACMG list (median = 11) were both statistically different than the randomly selected genes (median = 7) (P < 0.0001, two-tailed Mann-Whitney test). CONCLUSION Gene-disease pairs having a score of 11 or higher represent the top quintile of actionability. The semiquantitative metric effectively assesses clinical actionability, promotes transparency, and may facilitate assessments of clinical actionability by various groups and in diverse contexts.Genet Med 18 5, 467-475.
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Affiliation(s)
- Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julianne M O'Daniel
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jessica K Booker
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lacey Boshe
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy Carey
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristy R Crooks
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brian C Jensen
- Division of Cardiology, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eric T Juengst
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Center for Bioethics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kristy Lee
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel K Nelson
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cynthia M Powell
- Division of Genetics and Metabolism, Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Myra I Roche
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Division of Genetics and Metabolism, Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cecile Skrzynia
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Natasha T Strande
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Karen E Weck
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kirk C Wilhelmsen
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James P Evans
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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23
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Couser NL, Masood MM, Strande NT, Foreman AKM, Crooks K, Weck KE, Lu M, Wilhelmsen KC, Roche M, Evans JP, Berg JS, Powell CM. The phenotype of multiple congenital anomalies-hypotonia-seizures syndrome 1: report and review. Am J Med Genet A 2015; 167A:2176-81. [PMID: 25920937 DOI: 10.1002/ajmg.a.37129] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 04/02/2015] [Accepted: 04/09/2015] [Indexed: 01/21/2023]
Abstract
The Multiple Congenital Anomalies-Hypotonia-Seizures Syndrome 1 (MCAHS1) has been described in two families to date. We describe a 2-year-old Mexican American boy with the syndrome and additional manifestations not yet reported as part of the phenotype. The patient presented with severe hypotonia, microphallus and left cryptorchidism, and was later diagnosed with epilepsy and severe cortical visual impairment. He also had supernumerary nipples, pectus excavatum, a short upturned nose, fleshy ear lobes, and a right auricular pit. Massively parallel exome sequencing and analysis revealed two novel compound heterozygous missense (Trp136Gly and Ser859Thr) variants in the PIGN gene. This report extends and further defines the phenotype of this syndrome.
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Affiliation(s)
- Natario L Couser
- Department of Ophthalmology, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Maheer M Masood
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Natasha T Strande
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Ann Katherine M Foreman
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kristy Crooks
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Karen E Weck
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Mei Lu
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kirk C Wilhelmsen
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Myra Roche
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - James P Evans
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Cynthia M Powell
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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24
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Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, Jarvik ER, Itsara A, Turner EH, Herman DS, Schleit J, Burt A, Jamal SM, Abrudan JL, Johnson AD, Conlin LK, Dulik MC, Santani A, Metterville DR, Kelly M, Foreman AKM, Lee K, Taylor KD, Guo X, Crooks K, Kiedrowski LA, Raffel LJ, Gordon O, Machini K, Desnick RJ, Biesecker LG, Lubitz SA, Mulchandani S, Cooper GM, Joffe S, Richards CS, Yang Y, Rotter JI, Rich SS, O'Donnell CJ, Berg JS, Spinner NB, Evans JP, Fullerton SM, Leppig KA, Bennett RL, Bird T, Sybert VP, Grady WM, Tabor HK, Kim JH, Bamshad MJ, Wilfond B, Motulsky AG, Scott CR, Pritchard CC, Walsh TD, Burke W, Raskind WH, Byers P, Hisama FM, Rehm H, Nickerson DA, Jarvik GP. Actionable exomic incidental findings in 6503 participants: challenges of variant classification. Genome Res 2015; 25:305-15. [PMID: 25637381 PMCID: PMC4352885 DOI: 10.1101/gr.183483.114] [Citation(s) in RCA: 259] [Impact Index Per Article: 28.8] [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] [Indexed: 02/02/2023]
Abstract
Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.
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Affiliation(s)
- Laura M Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Michael O Dorschner
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peggy D Robertson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Joseph S Salama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Ragan Hart
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Mitzi L Murray
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Mari J Tokita
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Carlos J Gallego
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Daniel Seung Kim
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - James T Bennett
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - David R Crosslin
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jane Ranchalis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Kelly L Jones
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Elisabeth A Rosenthal
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Ella R Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Andy Itsara
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Emily H Turner
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Daniel S Herman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Amber Burt
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Seema M Jamal
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Jenica L Abrudan
- Department of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Andrew D Johnson
- The Framingham Heart Study, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts 01702, USA
| | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Matthew C Dulik
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Avni Santani
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | - Melissa Kelly
- Partners Healthcare Personalized Medicine, Partners Healthcare, Boston, Massachusetts 02115, USA
| | - Ann Katherine M Foreman
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kristy Lee
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kent D Taylor
- Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Xiuqing Guo
- Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Kristy Crooks
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Lesli A Kiedrowski
- Department of Cancer Genetics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Leslie J Raffel
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Ora Gordon
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Kalotina Machini
- Laboratory of Molecular Medicine, Partners Healthcare, Boston, Massachusetts 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robert J Desnick
- Department of Genetic and Genomic Medicine, Division of Medical Genetics, Mount Sinai Hospital, New York, New York 10029, USA
| | - Leslie G Biesecker
- Genetic Diseases Research Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Steven A Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Surabhi Mulchandani
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Greg M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Steven Joffe
- Department of Medical Ethics and Health Policy, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Yaoping Yang
- Department of Pediatrics, Division of Infectious Disease, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Jerome I Rotter
- Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Christopher J O'Donnell
- The Framingham Heart Study, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts 01702, USA; Division of Cardiology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nancy B Spinner
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - James P Evans
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA
| | - Kathleen A Leppig
- Genetic Services, Group Health Cooperative, Seattle, Washington 98112, USA
| | - Robin L Bennett
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Thomas Bird
- Department of Neurology, University of Washington, Seattle, Washington 98195, USA; Veterans Affairs Puget Sound Health Care System Geriatric Research, Education, and Clinical Center, Seattle, Washington 98108, USA
| | - Virginia P Sybert
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Dermatology, Group Health Cooperative, Seattle, Washington 98112, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington 98195, USA
| | - Holly K Tabor
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA; Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, Seattle, Washington 98105, USA
| | - Jerry H Kim
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, Seattle, Washington 98105, USA; Department of Pediatrics, Division of Bioethics, University of Washington, Seattle, Washington 98195, USA
| | - Arno G Motulsky
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - C Ronald Scott
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Tom D Walsh
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Wylie Burke
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA
| | - Wendy H Raskind
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peter Byers
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Fuki M Hisama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Heidi Rehm
- Laboratory of Molecular Medicine, Partners Healthcare, Boston, Massachusetts 02115, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Debbie A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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Foreman AKM, Lee K, Evans JP. The NCGENES project: exploring the new world of genome sequencing. N C Med J 2013; 74:500-504. [PMID: 24316776] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Massively parallel sequencing (MPS) is now a clinical reality, promising improved diagnosis, targeted therapies, and population-based screening. To realize the potential of genomics, we must learn how to apply this technology optimally. The NCGENES project is designed to address several challenges that must be overcome in order to integrate MPS into clinical care.
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Affiliation(s)
- Ann Katherine M Foreman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, CB 7264, Chapel Hill, NC 27599, USA.
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