1
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Hallquist MLG, Borensztein MJ, Coughlin CR, Buchanan AH, Andrew Faucett W, Peay HL, Smith ME, Tricou EP, Uhlmann WR, Wain KE, Ormond KE. Defining critical educational components of informed consent for genetic testing: views of US-based genetic counselors and medical geneticists. Eur J Hum Genet 2023; 31:1165-1174. [PMID: 37308598 PMCID: PMC10545703 DOI: 10.1038/s41431-023-01401-0] [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: 12/06/2022] [Revised: 03/22/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2023] Open
Abstract
The Clinical Genome Resource (ClinGen) Consent and Disclosure Recommendation (CADRe) framework proposes that key components of informed consent for genetic testing can be covered with a targeted discussion for many conditions rather than a time-intensive traditional genetic counseling approach. We surveyed US genetics professionals (medical geneticists and genetic counselors) on their response to scenarios that proposed core informed consent concepts for clinical genetic testing developed in a prior expert consensus process. The anonymous online survey included responses to 3 (of 6 possible) different clinical scenarios that summarized the application of the core concepts. There was a binary (yes/no) question asking respondents whether they agreed the scenarios included the minimum necessary and critical educational concepts to allow an informed decision. Respondents then provided open-ended feedback on what concepts were missing or could be removed. At least one scenario was completed by 238 respondents. For all but one scenario, over 65% of respondents agreed that the identified concepts portrayed were sufficient for an informed decision; the exome scenario had the lowest agreement (58%). Qualitative analysis of the open-ended comments showed no consistently mentioned concepts to add or remove. The level of agreement with the example scenarios suggests that the minimum critical educational components for pre-test informed consent proposed in our prior work is a reasonable starting place for targeted pre-test discussions. This may be helpful in providing consistency to the clinical practice of both genetics and non-genetics providers, meeting patients' informational needs, tailoring consent for psychosocial support, and in future guideline development.
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Affiliation(s)
| | - Maia J Borensztein
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Curtis R Coughlin
- Department of Pediatrics and Center for Bioethics and Humanities, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | | | - Holly L Peay
- RTI International, Genomics, Bioinformatics, and Translational Research Center, Raleigh, NC, USA
| | - Maureen E Smith
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Eric P Tricou
- Geisinger, Danville, PA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Wendy R Uhlmann
- Division of Genetic Medicine, Department of Internal Medicine; Department of Human Genetics; Center for Bioethics & Social Sciences in Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Kelly E Ormond
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
- Health Ethics and Policy Lab, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
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2
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Buchanan AH, Manickam K, Meyer MN, Wagner JK, Hallquist MLG, Williams JL, Rahm AK, Williams MS, Chen ZME, Shah CK, Garg TK, Lazzeri AL, Schwartz MLB, Lindbuchler DAM, Fan AL, Leeming R, Servano PO, Smith AL, Vogel VG, Abul-Husn NS, Dewey FE, Lebo MS, Mason-Suares HM, Ritchie MD, Davis FD, Carey DJ, Feinberg DT, Faucett WA, Ledbetter DH, Murray MF. Correction to: Early cancer diagnoses through BRCA1/2 screening of unselected adult biobank participants. Genet Med 2021; 23:2470. [PMID: 34646007 PMCID: PMC9119243 DOI: 10.1038/s41436-021-01304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Adam H Buchanan
- Geisinger Health System, Danville, PA, USA. .,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA.
| | - Kandamurugu Manickam
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Michelle N Meyer
- Geisinger Health System, Danville, PA, USA.,Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - Jennifer K Wagner
- Geisinger Health System, Danville, PA, USA.,Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - Miranda L G Hallquist
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Janet L Williams
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Alanna Kulchak Rahm
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Marc S Williams
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Zong-Ming E Chen
- Geisinger Health System, Danville, PA, USA.,Laboratory Medicine, Geisinger Health System, Danville, PA, USA
| | - Chaitali K Shah
- Geisinger Health System, Danville, PA, USA.,Radiology, Geisinger Health System, Danville, PA, USA
| | - Tullika K Garg
- Geisinger Health System, Danville, PA, USA.,Department of Urology, Geisinger Health System, Danville, PA, USA
| | - Amanda L Lazzeri
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Marci L B Schwartz
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - D' Andra M Lindbuchler
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Audrey L Fan
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Rosemary Leeming
- Geisinger Health System, Danville, PA, USA.,General Surgery, Geisinger Health System, Danville, PA, USA
| | - Pedro O Servano
- Geisinger Health System, Danville, PA, USA.,Family Medicine, Geisinger Health System, Danville, PA, USA
| | - Ashlee L Smith
- Geisinger Health System, Danville, PA, USA.,Women's Health, Geisinger Health System, Danville, PA, USA
| | - Victor G Vogel
- Geisinger Health System, Danville, PA, USA.,Hematology & Oncology, Geisinger Health System, Danville, PA, USA
| | | | | | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Heather M Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, MA, USA
| | - Marylyn D Ritchie
- Geisinger Health System, Danville, PA, USA.,Biomedical and Translational Informatics, Geisinger Health System, Danville, PA, USA
| | - F Daniel Davis
- Geisinger Health System, Danville, PA, USA.,Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - David J Carey
- Geisinger Health System, Danville, PA, USA.,Department of Molecular and Functional Genomics, Geisinger Health System, Danville, PA, USA
| | - David T Feinberg
- Geisinger Health System, Danville, PA, USA.,Office of the Chief Executive Officer, Geisinger Health System, Danville, PA, USA
| | - W Andrew Faucett
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - David H Ledbetter
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - Michael F Murray
- Geisinger Health System, Danville, PA, USA.,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
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3
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Hallquist MLG, Tricou EP, Ormond KE, Savatt JM, Coughlin CR, Faucett WA, Hercher L, Levy HP, O'Daniel JM, Peay HL, Stosic M, Smith M, Uhlmann WR, Wand H, Wain KE, Buchanan AH. Application of a framework to guide genetic testing communication across clinical indications. Genome Med 2021; 13:71. [PMID: 33926532 PMCID: PMC8086064 DOI: 10.1186/s13073-021-00887-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/14/2021] [Indexed: 12/20/2022] Open
Abstract
Background Genetic information is increasingly relevant across healthcare. Traditional genetic counseling (GC) may limit access to genetic information and may be more information and support than some individuals need. We report on the application and clinical implications of a framework to consistently integrate genetics expertise where it is most useful to patients. Methods The Clinical Genome Resource’s (ClinGen) Consent and Disclosure Recommendations (CADRe) workgroup designed rubrics to guide pre- and post-genetic test communication. Using a standard set of testing indications, pre- and post-test rubrics were applied to 40 genetic conditions or testing modalities with diverse features, including variability in levels of penetrance, clinical actionability, and evidence supporting a gene-disease relationship. Final communication recommendations were reached by group consensus. Results Communication recommendations were determined for 478 unique condition-indication or testing-indication pairs. For half of the conditions and indications (238/478), targeted discussions (moderate communication depth) were the recommended starting communication level for pre- and post-test conversations. Traditional GC was recommended pre-test for adult-onset neurodegenerative conditions for individuals with no personal history and post-test for most conditions when genetic testing revealed a molecular diagnosis as these situations are likely higher in complexity and uncertainty. A brief communication approach was recommended for more straightforward conditions and indications (e.g., familial hypercholesterolemia; familial variant testing). Conclusions The CADRe recommendations provide guidance for clinicians in determining the depth of pre- and post-test communication, strategically aligning the anticipated needs of patients with the starting communication approach. Shorter targeted discussions or brief communications are suggested for many tests and indications. Longer traditional GC consultations would be reserved for patients with more complex and uncertain situations where detailed information, education, and psychological support can be most beneficial. Future studies of the CADRe communication framework will be essential for determining if CADRe-informed care supports quality patient experience while improving access to genetic information across healthcare. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00887-x.
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Affiliation(s)
| | - Eric P Tricou
- Geisinger, 100 N Academy Blvd, Danville, PA, 17822, USA.,Department of Genetics and Stanford Center for Biomedical Ethics, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Stanford, CA, 94304, USA
| | - Kelly E Ormond
- Department of Genetics and Stanford Center for Biomedical Ethics, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Stanford, CA, 94304, USA
| | | | - Curtis R Coughlin
- University of Colorado Department of Pediatrics and Center for Bioethics and Humanities, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
| | | | - Laura Hercher
- Sarah Lawrence College Joan H. Marks Graduate Program in Human Genetics, 1 Mead Way, Bronxville, NY, 10708, USA
| | - Howard P Levy
- Johns Hopkins University Division of General Internal Medicine and McKusick-Nathans Institute of Genetic Medicine, 0753 Falls Rd, Suite 325, Lutherville, MD, USA
| | - Julianne M O'Daniel
- Department of Genetics Genetic Medicine Building, University of North Carolina at Chapel Hill, 120 Mason Farm Rd, CB # 7264, Chapel Hill, NC, 27514, USA
| | - Holly L Peay
- RTI International, 3040 E Cornwallis Rd, Research Triangle Park, NC, 27709, USA
| | - Melissa Stosic
- DotLab, 780 E Main St, Suite 1, Branford, CT, 06405, USA
| | - Maureen Smith
- Northwestern University Feinberg School of Medicine, 310 E. Superior St., Chicago, IL, 60611-3008, USA
| | - Wendy R Uhlmann
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan Medicine, 300 North Ingalls, NI3 A03, SPC 5419, Ann Arbor, MI, 48109-5419, USA
| | - Hannah Wand
- Department of Genetics and Stanford Center for Biomedical Ethics, Center for Academic Medicine, Stanford University School of Medicine, 453 Quarry Road, Stanford, CA, 94304, USA
| | - Karen E Wain
- Geisinger, 100 N Academy Blvd, Danville, PA, 17822, USA
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4
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Abstract
Historically, both pretest and posttest genetic counseling has been standard of care for genetic testing. This model should be adapted for primary care providers (PCPs) willing to learn critical information about the test and key concepts that patients need to make an informed testing decision. It is helpful for PCPs to discuss a few initial patients with a genetic counselor to prepare for the key concepts of pretest and posttest counseling. This article provides guidance about the recommended level of involvement of PCPs based on the test indication, test complexity, disorder management, and the potential for psychosocial sequela.
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Affiliation(s)
- W Andrew Faucett
- Office of the Chief Scientific Officer, Geisinger, MC 30-42, 100 North Academy Avenue, Danville, PA 17822, USA.
| | - Holly Peay
- Center for Newborn Screening, Ethics, and Disability Studies, RTI International, 3040 East Institute Drive, Research Triangle Park, NC 27709, USA
| | - Curtis R Coughlin
- Department of Pediatrics, Section of Genetics, University of Colorado Anschutz Medical Campus, East 17th Avenue, Aurora, CO 80045, USA
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6
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Savatt JM, Azzariti DR, Faucett WA, Harrison S, Hart J, Kattman B, Landrum MJ, Ledbetter DH, Miller VR, Palen E, Rehm HL, Rhode J, Turner S, Vidal JA, Wain KE, Riggs ER, Martin CL. ClinGen's GenomeConnect registry enables patient-centered data sharing. Hum Mutat 2019; 39:1668-1676. [PMID: 30311371 DOI: 10.1002/humu.23633] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 05/03/2018] [Revised: 07/20/2018] [Accepted: 08/23/2018] [Indexed: 01/09/2023]
Abstract
GenomeConnect, the NIH-funded Clinical Genome Resource (ClinGen) patient registry, engages patients in data sharing to support the goal of creating a genomic knowledge base to inform clinical care and research. Participant self-reported health information and genomic variants from genetic testing reports are curated and shared with public databases, such as ClinVar. There are four primary benefits of GenomeConnect: (1) sharing novel genomic data-47.9% of variants were new to ClinVar, highlighting patients as a genomic data source; (2) contributing additional phenotypic information-of the 52.1% of variants already in ClinVar, GenomeConnect provided enhanced case-level data; (3) providing a way for patients to receive variant classification updates if the reporting laboratory submits to ClinVar-97.3% of responding participants opted to receive such information and 13 updates have been identified; and (4) supporting connections with others, including other participants, clinicians, and researchers to enable the exchange of information and support-60.4% of participants have opted to partake in participant matching. Moving forward, ClinGen plans to increase patient-centric data sharing by partnering with other existing patient groups. By engaging patients, more information is contributed to the public knowledge base, benefiting both patients and the genomics community.
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Affiliation(s)
- Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts
| | - W Andrew Faucett
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Steven Harrison
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer Hart
- National Center for Biotechnology Information, Bethesda, Maryland
| | - Brandi Kattman
- National Center for Biotechnology Information, Bethesda, Maryland
| | | | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Emily Palen
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Stefanie Turner
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan
| | | | - Karen E Wain
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Erin Rooney Riggs
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania
| | - Christa Lese Martin
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, Pennsylvania.,Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
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7
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Williams MS, Buchanan AH, Davis FD, Faucett WA, Hallquist MLG, Leader JB, Martin CL, McCormick CZ, Meyer MN, Murray MF, Rahm AK, Schwartz MLB, Sturm AC, Wagner JK, Williams JL, Willard HF, Ledbetter DH. Patient-Centered Precision Health In A Learning Health Care System: Geisinger's Genomic Medicine Experience. Health Aff (Millwood) 2019; 37:757-764. [PMID: 29733722 DOI: 10.1377/hlthaff.2017.1557] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [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: 11/05/2022]
Abstract
Health care delivery is increasingly influenced by the emerging concepts of precision health and the learning health care system. Although not synonymous with precision health, genomics is a key enabler of individualized care. Delivering patient-centered, genomics-informed care based on individual-level data in the current national landscape of health care delivery is a daunting challenge. Problems to overcome include data generation, analysis, storage, and transfer; knowledge management and representation for patients and providers at the point of care; process management; and outcomes definition, collection, and analysis. Development, testing, and implementation of a genomics-informed program requires multidisciplinary collaboration and building the concepts of precision health into a multilevel implementation framework. Using the principles of a learning health care system provides a promising solution. This article describes the implementation of population-based genomic medicine in an integrated learning health care system-a working example of a precision health program.
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Affiliation(s)
- Marc S Williams
- Marc S. Williams ( ) is director of the Genomic Medicine Institute, Geisinger, in Danville, Pennsylvania
| | - Adam H Buchanan
- Adam H. Buchanan is an assistant professor at the Genomic Medicine Institute, Geisinger
| | - F Daniel Davis
- F. Daniel Davis is director of the Center for Bioethics and Healthcare Policy, Geisinger
| | - W Andrew Faucett
- W. Andrew Faucett is a professor at the Genomic Medicine Institute, Geisinger
| | - Miranda L G Hallquist
- Miranda L. G. Hallquist is a genetic counselor at the Genomic Medicine Institute, Geisinger
| | - Joseph B Leader
- Joseph B. Leader is director of the Phenomic Analytics and Clinical Data Core, Geisinger
| | - Christa L Martin
- Christa L. Martin is director of the Autism and Developmental Medicine Institute, Geisinger
| | - Cara Z McCormick
- Cara Z. McCormick is a senior assistant at the Genomic Medicine Institute, Geisinger
| | - Michelle N Meyer
- Michelle N. Meyer is associate director for research ethics at the Center for Translational Bioethics and Health Care Policy, Geisinger
| | - Michael F Murray
- Michael F. Murray was a physician in the Genomic Medicine Institute, Geisinger, at the time this work was completed. He is now at the Yale School of Medicine
| | - Alanna K Rahm
- Alanna K. Rahm is an assistant professor at the Genomic Medicine Institute, Geisinger
| | - Marci L B Schwartz
- Marci L. B. Schwartz is a genetic counselor at the Genomic Medicine Institute, Geisinger
| | - Amy C Sturm
- Amy C. Sturm is a professor at the Genomic Medicine Institute, Geisinger
| | - Jennifer K Wagner
- Jennifer K. Wagner is associate director of bioethics research, Center for Translational Bioethics and Health Care Policy, Geisinger
| | - Janet L Williams
- Janet L. Williams is director of research genetic counselors, Genomic Medicine Institute, Geisinger
| | - Huntington F Willard
- Huntington F. Willard is director of the National Precision Health Institute, Geisinger
| | - David H Ledbetter
- David H. Ledbetter is executive vice president and chief scientific officer, Geisinger
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8
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Manickam K, Buchanan AH, Schwartz MLB, Hallquist MLG, Williams JL, Rahm AK, Rocha H, Savatt JM, Evans AE, Butry LM, Lazzeri AL, Lindbuchler DM, Flansburg CN, Leeming R, Vogel VG, Lebo MS, Mason-Suares HM, Hoskinson DC, Abul-Husn NS, Dewey FE, Overton JD, Reid JG, Baras A, Willard HF, McCormick CZ, Krishnamurthy SB, Hartzel DN, Kost KA, Lavage DR, Sturm AC, Frisbie LR, Person TN, Metpally RP, Giovanni MA, Lowry LE, Leader JB, Ritchie MD, Carey DJ, Justice AE, Kirchner HL, Faucett WA, Williams MS, Ledbetter DH, Murray MF. Exome Sequencing-Based Screening for BRCA1/2 Expected Pathogenic Variants Among Adult Biobank Participants. JAMA Netw Open 2018; 1:e182140. [PMID: 30646163 PMCID: PMC6324494 DOI: 10.1001/jamanetworkopen.2018.2140] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
IMPORTANCE Detection of disease-associated variants in the BRCA1 and BRCA2 (BRCA1/2) genes allows for cancer prevention and early diagnosis in high-risk individuals. OBJECTIVES To identify pathogenic and likely pathogenic (P/LP) BRCA1/2 variants in an unselected research cohort, and to characterize the features associated with P/LP variants. DESIGN, SETTING, AND PARTICIPANTS This is a cross-sectional study of adult volunteers (n = 50 726) who underwent exome sequencing at a single health care system (Geisinger Health System, Danville, Pennsylvania) from January 1, 2014, to March 1, 2016. Participants are part of the DiscovEHR cohort and were identified through the Geisinger MyCode Community Health Initiative. They consented to a research protocol that included sequencing and return of actionable test results. Clinical data from electronic health records and clinical visits were correlated with variants. Comparisons were made between those with (cases) and those without (controls) P/LP variants in BRCA1/2. MAIN OUTCOMES Prevalence of P/LP BRCA1/2 variants in cohort, proportion of variant carriers not previously ascertained through clinical testing, and personal and family history of relevant cancers among BRCA1/2 variant carriers and noncarriers. RESULTS Of the 50 726 health system patients who underwent exome sequencing, 50 459 (99.5%) had no expected pathogenic BRCA1/2 variants and 267 (0.5%) were BRCA1/2 carriers. Of the 267 cases (148 [55.4%] were women and 119 [44.6%] were men with a mean [range] age of 58.9 [23-90] years), 183 (68.5%) received clinically confirmed results in their electronic health record. Among the 267 participants with P/LP BRCA1/2 variants, 219 (82.0%) had no prior clinical testing, 95 (35.6%) had BRCA1 variants, and 172 (64.4%) had BRCA2 variants. Syndromic cancer diagnoses were present in 11 (47.8%) of the 23 deceased BRCA1/2 carriers and in 56 (20.9%) of all 267 BRCA1/2 carriers. Among women, 31 (20.9%) of 148 variant carriers had a personal history of breast cancer, compared with 1554 (5.2%) of 29 880 noncarriers (odds ratio [OR], 5.95; 95% CI, 3.88-9.13; P < .001). Ovarian cancer history was present in 15 (10.1%) of 148 variant carriers and in 195 (0.6%) of 29 880 variant noncarriers (OR, 18.30; 95% CI, 10.48-31.4; P < .001). Among 89 BRCA1/2 carriers without prior testing but with comprehensive personal and family history data, 44 (49.4%) did not meet published guidelines for clinical testing. CONCLUSIONS AND RELEVANCE This study found that compared with previous clinical care, exome sequencing-based screening identified 5 times as many individuals with P/LP BRCA1/2 variants. These findings suggest that genomic screening may identify BRCA1/2-associated cancer risk that might otherwise remain undetected within health care systems and may provide opportunities to reduce morbidity and mortality in patients.
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Affiliation(s)
- Kandamurugu Manickam
- Molecular and Human Genetics Department, Nationwide Children’s Hospital, Columbus, Ohio
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | | | - Heather Rocha
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Alyson E. Evans
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Loren M. Butry
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | - Victor G. Vogel
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Matthew S. Lebo
- Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts
| | | | - Derick C. Hoskinson
- Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, Massachusetts
| | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York
| | | | | | | | | | - Korey A. Kost
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Amy C. Sturm
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - T. Nate Person
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | - Lacy E. Lowry
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | - Marylyn D. Ritchie
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
- Center for Translational Bioinformatics, University of Pennsylvania, Philadelphia
| | - David J. Carey
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Anne E. Justice
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | | | | | | | | | - Michael F. Murray
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
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9
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Schwartz MLB, McCormick CZ, Lazzeri AL, Lindbuchler DM, Hallquist MLG, Manickam K, Buchanan AH, Rahm AK, Giovanni MA, Frisbie L, Flansburg CN, Davis FD, Sturm AC, Nicastro C, Lebo MS, Mason-Suares H, Mahanta LM, Carey DJ, Williams JL, Williams MS, Ledbetter DH, Faucett WA, Murray MF. A Model for Genome-First Care: Returning Secondary Genomic Findings to Participants and Their Healthcare Providers in a Large Research Cohort. Am J Hum Genet 2018; 103:328-337. [PMID: 30100086 PMCID: PMC6128218 DOI: 10.1016/j.ajhg.2018.07.009] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/15/2018] [Indexed: 10/28/2022] Open
Abstract
There is growing interest in communicating clinically relevant DNA sequence findings to research participants who join projects with a primary research goal other than the clinical return of such results. Since Geisinger's MyCode Community Health Initiative (MyCode) was launched in 2007, more than 200,000 participants have been broadly consented for discovery research. In 2013 the MyCode consent was amended to include a secondary analysis of research genomic sequences that allows for delivery of clinical results. Since May 2015, pathogenic and likely pathogenic variants from a set list of genes associated with monogenic conditions have prompted "genome-first" clinical encounters. The encounters are described as genome-first because they are identified independent of any clinical parameters. This article (1) details our process for generating clinical results from research data, delivering results to participants and providers, facilitating condition-specific clinical evaluations, and promoting cascade testing of relatives, and (2) summarizes early results and participant uptake. We report on 542 participants who had results uploaded to the electronic health record as of February 1, 2018 and 291 unique clinical providers notified with one or more participant results. Of these 542 participants, 515 (95.0%) were reached to disclose their results and 27 (5.0%) were lost to follow-up. We describe an exportable model for delivery of clinical care through secondary use of research data. In addition, subject and provider participation data from the initial phase of these efforts can inform other institutions planning similar programs.
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Affiliation(s)
| | | | | | - D'Andra M Lindbuchler
- Geisinger, Danville, PA 17822, USA; Wilkes-Barre Area Career and Technical Center, Plains Township, PA 18705, USA
| | | | - Kandamurugu Manickam
- Geisinger, Danville, PA 17822, USA; Nationwide Children's Hospital, Columbus, OH 43205, USA
| | | | | | | | | | | | | | | | | | - Matthew S Lebo
- Laboratory for Molecular Medicine, Cambridge, MA 02139, USA
| | | | | | | | | | | | | | | | - Michael F Murray
- Geisinger, Danville, PA 17822, USA; Yale School of Medicine, New Haven, CT 06510, USA.
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Rocha HM, Savatt JM, Riggs ER, Wagner JK, Faucett WA, Martin CL. Incorporating Social Media into your Support Tool Box: Points to Consider from Genetics-Based Communities. J Genet Couns 2017; 27:470-480. [PMID: 29130143 DOI: 10.1007/s10897-017-0170-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023]
Abstract
Patients with newly-described or rare genetic findings are turning to social media to find and connect with others. Blogs, Facebook groups, and Twitter have all been reported as tools for patients to connect with one another. However, the preferences for social media use and privacy among patients, their families, and these communities have not been well characterized. To explore preferences about privacy and membership guidelines, an online survey was administered to two web-based patient registries, Simons Variation in Individuals Project ( www.simonsvipconnect.org ) and GenomeConnect ( www.genomeconnect.org ). Over a three-month period, invitations were sent to 2524 individuals and 103 responses (4%) were received and analyzed. Responses indicate that Facebook is the most popular resource accessed within this sample population (99%). Participants used social media to look for information about their diagnosis or test results (83%), read posts from rare disease groups or organizations (73%), participate in conversations about their diagnosis (67%), and connect with others to find support (58%). Focusing on privacy issues in social media, respondents indicate that membership and access impact the level of comfort in sharing personal or medical information. Nearly 60% of respondents felt uncomfortable sharing photos or medical information within a public Facebook group, whereas only 12% of respondents felt uncomfortable sharing in private group targeted to families alone. Using this preliminary data concerning social media use and privacy, we developed points for genetic counselors to incorporate when discussing available support resources for patients with a new, or rare, genetic diagnosis or genetic test result. Genetic counselors are trained to provide anticipatory guidance to families adapting to new genetic information, and are well-equipped to help patients consider their preferences about using social media as a source of information and support.
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Affiliation(s)
- Heather Mae Rocha
- Genomic Medicine Institute, Geisinger, 100 N Academy Ave, MC 26-20, Danville, PA, 17822, USA.
| | - Juliann M Savatt
- Genomic Medicine Institute, Geisinger, 100 N Academy Ave, MC 26-20, Danville, PA, 17822, USA.,Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Erin Rooney Riggs
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Jennifer K Wagner
- Center for Translational Bioethics & Health Care Policy, Geisinger, Danville, PA, USA
| | - W Andrew Faucett
- Genomic Medicine Institute, Geisinger, 100 N Academy Ave, MC 26-20, Danville, PA, 17822, USA
| | - Christa Lese Martin
- Genomic Medicine Institute, Geisinger, 100 N Academy Ave, MC 26-20, Danville, PA, 17822, USA.,Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
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11
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Ormond KE, Mortlock DP, Scholes DT, Bombard Y, Brody LC, Faucett WA, Garrison NA, Hercher L, Isasi R, Middleton A, Musunuru K, Shriner D, Virani A, Young CE. Human Germline Genome Editing. Am J Hum Genet 2017; 101:167-176. [PMID: 28777929 PMCID: PMC5544380 DOI: 10.1016/j.ajhg.2017.06.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [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] [Indexed: 12/24/2022] Open
Abstract
With CRISPR/Cas9 and other genome-editing technologies, successful somatic and germline genome editing are becoming feasible. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in March 2017. The workgroup included representatives from the UK Association of Genetic Nurses and Counsellors, Canadian Association of Genetic Counsellors, International Genetic Epidemiology Society, and US National Society of Genetic Counselors. These groups, as well as the American Society for Reproductive Medicine, Asia Pacific Society of Human Genetics, British Society for Genetic Medicine, Human Genetics Society of Australasia, Professional Society of Genetic Counselors in Asia, and Southern African Society for Human Genetics, endorsed the final statement. The statement includes the following positions. (1) At this time, given the nature and number of unanswered scientific, ethical, and policy questions, it is inappropriate to perform germline gene editing that culminates in human pregnancy. (2) Currently, there is no reason to prohibit in vitro germline genome editing on human embryos and gametes, with appropriate oversight and consent from donors, to facilitate research on the possible future clinical applications of gene editing. There should be no prohibition on making public funds available to support this research. (3) Future clinical application of human germline genome editing should not proceed unless, at a minimum, there is (a) a compelling medical rationale, (b) an evidence base that supports its clinical use, (c) an ethical justification, and (d) a transparent public process to solicit and incorporate stakeholder input.
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Affiliation(s)
- Kelly E Ormond
- Department of Genetics and Stanford Center for Biomedical Ethics, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Douglas P Mortlock
- Vanderbilt Genetics Institute and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Yvonne Bombard
- Li Ka Shing Knowledge Institute of St. Michael's Hospital, Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5B 1W8, Canada
| | - Lawrence C Brody
- Division of Genomics and Society, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - W Andrew Faucett
- Genomic Medicine Institute, Geisinger Health System, Danville, PA 17822, USA; National Society of Genetic Counselors
| | - Nanibaa' A Garrison
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Hospital and Research Institute, Seattle, WA 98101, USA; Division of Bioethics, Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Laura Hercher
- National Society of Genetic Counselors; Joan H. Marks Graduate Program in Human Genetics, Sarah Lawrence College, Bronxville, NY 10708, USA
| | - Rosario Isasi
- Dr. John T. Macdonald Foundation Department of Human Genetics and Institute for Bioethics and Health Policy, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Anna Middleton
- Society and Ethics Research Group, Connecting Science, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Association of Genetic Nurses and Counsellors
| | - Kiran Musunuru
- Cardiovascular Institute, Departments of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA; International Genetic Epidemiology Society
| | - Alice Virani
- Provincial Health Service Authority of British Columbia and Department of Medical Genetics, University of British Columbia, BC V6H 3N1, Canada; Canadian Association of Genetic Counsellors
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Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush J, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC. Toward clinical genomics in everyday medicine: perspectives and recommendations. Expert Rev Mol Diagn 2016; 16:521-32. [PMID: 26810587 PMCID: PMC4841021 DOI: 10.1586/14737159.2016.1146593] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Precision or personalized medicine through clinical genome and exome sequencing has been described by some as a revolution that could transform healthcare delivery, yet it is currently used in only a small fraction of patients, principally for the diagnosis of suspected Mendelian conditions and for targeting cancer treatments. Given the burden of illness in our society, it is of interest to ask how clinical genome and exome sequencing can be constructively integrated more broadly into the routine practice of medicine for the betterment of public health. In November 2014, 46 experts from academia, industry, policy and patient advocacy gathered in a conference sponsored by Illumina, Inc. to discuss this question, share viewpoints and propose recommendations. This perspective summarizes that work and identifies some of the obstacles and opportunities that must be considered in translating advances in genomics more widely into the practice of medicine.
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Affiliation(s)
- Susan K Delaney
- a Coriell Institute for Medical Research , Camden , NJ , USA
| | - Michael L Hultner
- b Lockheed Martin , Information Systems & Global Solutions , Rockville , MD , USA
| | - Howard J Jacob
- c HudsonAlpha Institute for Biotechnology , Huntsville , AL , USA
| | | | - Jeanette J McCarthy
- e Duke University , Center for Applied Genomics and Precision Medicine , Durham , NC , USA
| | | | - Kenneth B Beckman
- g University of Minnesota , Genomics Center ,, Minneapolis , MN , USA
| | - John W Belmont
- h Baylor College of Medicine , Children's Nutrition Research Center , Houston , TX , USA
| | - Cinnamon S Bloss
- i University of California, San Diego , School of Medicine , La Jolla , CA , USA
| | | | | | - Stephen A Damiani
- k Mission Massimo Foundation , Elsternwick , VIC , Australia .,l Mission Massimo Foundation Inc ., Westlake Village , CA , USA
| | | | | | - Michael J Dougherty
- o The American Society of Human Genetics , Bethesda , MD , USA.,p Department of Pediatrics , University of Colorado School of Medicine , Aurora , CO , USA
| | - Joel T Dudley
- q Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | | | - Jennifer R Friedman
- r University of California, San Diego , Departments of Neurosciences and Pediatrics and Rady Children's Hospital , San Diego , CA , USA
| | | | - Tom S Hays
- t University of Minnesota , Department of Genetics, Cell Biology and Development , Minneapolis , MN , USA
| | | | - Jeff Huber
- u Google Inc ., Mountain View , CA , USA
| | | | | | | | - Elissa Levin
- q Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | | | | | | | - David C Magnus
- y Stanford Center for Biomedical Ethics , Stanford School of Medicine , Stanford , CA , USA
| | | | | | | | - Helen Messier
- ab Healix Health, Ltd , West Vancouver , BC , Canada
| | | | | | | | | | | | | | - Michael M Su
- ai Anthem Blue Cross , Woodland Hills , CA , USA
| | | | - Steven Tucker
- ak Novena Specialist Center , Singapore , Republic of Singapore
| | | | - Robert C Green
- am Division of Genetics, Department of Medicine, Brigham and Women's Hospital , the Broad Institute, Harvard Medical School and Partners Healthcare Personalized Medicine , Boston , MA , USA
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13
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D’Angelo D, Lebon S, Chen Q, Martin-Brevet S, Snyder LG, Hippolyte L, Hanson E, Maillard AM, Faucett WA, Macé A, Pain A, Bernier R, Chawner SJRA, David A, Andrieux J, Aylward E, Baujat G, Caldeira I, Conus P, Ferrari C, Forzano F, Gérard M, Goin-Kochel RP, Grant E, Hunter JV, Isidor B, Jacquette A, Jønch AE, Keren B, Lacombe D, Le Caignec C, Martin CL, Männik K, Metspalu A, Mignot C, Mukherjee P, Owen MJ, Passeggeri M, Rooryck-Thambo C, Rosenfeld JA, Spence SJ, Steinman KJ, Tjernagel J, Van Haelst M, Shen Y, Draganski B, Sherr EH, Ledbetter DH, van den Bree MBM, Beckmann JS, Spiro JE, Reymond A, Jacquemont S, Chung WK. Defining the Effect of the 16p11.2 Duplication on Cognition, Behavior, and Medical Comorbidities. JAMA Psychiatry 2016; 73:20-30. [PMID: 26629640 PMCID: PMC5894477 DOI: 10.1001/jamapsychiatry.2015.2123] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE The 16p11.2 BP4-BP5 duplication is the copy number variant most frequently associated with autism spectrum disorder (ASD), schizophrenia, and comorbidities such as decreased body mass index (BMI). OBJECTIVES To characterize the effects of the 16p11.2 duplication on cognitive, behavioral, medical, and anthropometric traits and to understand the specificity of these effects by systematically comparing results in duplication carriers and reciprocal deletion carriers, who are also at risk for ASD. DESIGN, SETTING, AND PARTICIPANTS This international cohort study of 1006 study participants compared 270 duplication carriers with their 102 intrafamilial control individuals, 390 reciprocal deletion carriers, and 244 deletion controls from European and North American cohorts. Data were collected from August 1, 2010, to May 31, 2015 and analyzed from January 1 to August 14, 2015. Linear mixed models were used to estimate the effect of the duplication and deletion on clinical traits by comparison with noncarrier relatives. MAIN OUTCOMES AND MEASURES Findings on the Full-Scale IQ (FSIQ), Nonverbal IQ, and Verbal IQ; the presence of ASD or other DSM-IV diagnoses; BMI; head circumference; and medical data. RESULTS Among the 1006 study participants, the duplication was associated with a mean FSIQ score that was lower by 26.3 points between proband carriers and noncarrier relatives and a lower mean FSIQ score (16.2-11.4 points) in nonproband carriers. The mean overall effect of the deletion was similar (-22.1 points; P < .001). However, broad variation in FSIQ was found, with a 19.4- and 2.0-fold increase in the proportion of FSIQ scores that were very low (≤40) and higher than the mean (>100) compared with the deletion group (P < .001). Parental FSIQ predicted part of this variation (approximately 36.0% in hereditary probands). Although the frequency of ASD was similar in deletion and duplication proband carriers (16.0% and 20.0%, respectively), the FSIQ was significantly lower (by 26.3 points) in the duplication probands with ASD. There also were lower head circumference and BMI measurements among duplication carriers, which is consistent with the findings of previous studies. CONCLUSIONS AND RELEVANCE The mean effect of the duplication on cognition is similar to that of the reciprocal deletion, but the variance in the duplication is significantly higher, with severe and mild subgroups not observed with the deletion. These results suggest that additional genetic and familial factors contribute to this variability. Additional studies will be necessary to characterize the predictors of cognitive deficits.
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Affiliation(s)
- Debra D’Angelo
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | - Sébastien Lebon
- Pediatric Neurology Unit, Department of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Qixuan Chen
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, New York
| | - Sandra Martin-Brevet
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Loyse Hippolyte
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ellen Hanson
- Department of Psychiatry, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anne M. Maillard
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - W. Andrew Faucett
- Genomic Medicine Institute, Geisinger Clinic, Danville, Pennsylvania
| | - Aurélien Macé
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland7Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Aurélie Pain
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Science, University of Washington, Seattle
| | - Samuel J. R. A. Chawner
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Albert David
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France
| | - Joris Andrieux
- Institut de Génétique Médicale, Hospital Jeanne de Flandre, Centre Hospitalier Régional Universitaire (CHRU) de Lille, Lille, France
| | - Elizabeth Aylward
- Center for Integrative Brain Research, Children’s Research Institute, Seattle, Washington
| | - Genevieve Baujat
- Département de Génétique, Hôpital Necker–Enfants Malades, Assistance Publique–Hôpitaux de Paris (AP-HP), Paris, France 14INSERM U1163, Hôpital Necker–Enfants Malades, Paris, France15Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Paris
| | - Ines Caldeira
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe Conus
- Department of Psychiatry, Cery Hospital, CHU Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Carrina Ferrari
- Department of Psychiatry, Cery Hospital, CHU Vaudois and University of Lausanne, Lausanne, Switzerland
| | | | - Marion Gérard
- Departement de Génétique, AP-HP, Hôpital Robert Debré, Université Paris VII-Paris Diderot, Paris, France
| | - Robin P. Goin-Kochel
- Section of Psychology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Ellen Grant
- Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jill V. Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas
| | - Bertrand Isidor
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France
| | - Aurélia Jacquette
- Département de Génétique et de Cytogénétique, Unité fonctionnelle de Génétique Clinique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France23Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France24Groupe de Recherche Clinique, Déficie
| | - Aia E. Jønch
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Boris Keren
- Department of Genetics and Cytogenetics, Groupe Hospitalier Pitié Salpêtrière, AP-HP, Paris, France
| | - Didier Lacombe
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France26Service de Génétique Médicale, CHU de Bor
| | - Cédric Le Caignec
- Service de Génétique Médicale, Faculté de Médecine, Centre Hospitalier Universitaire (CHU) Nantes, Institut National de la Santé et de la Recherche Medicale (INSERM) Unités Mixtes de Recherche 957, Nantes, France
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - Katrin Männik
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland29Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia30Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Cyril Mignot
- Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Pratik Mukherjee
- Department of Radiology and Biomedical Imaging, University of California, San Francisco
| | - Michael J. Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Marzia Passeggeri
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Caroline Rooryck-Thambo
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France32Laboratoire Maladies Rares: Génétique et Métabolisme, Université de Bordeaux, Bordeaux, France
| | | | - Sarah J. Spence
- Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kyle J. Steinman
- Department of Neurology, Seattle Children’s Research Institute and University of Washington, Seattle
| | | | - Mieke Van Haelst
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Yiping Shen
- Genetic Diagnostic Laboratory, Department of Laboratory Medicine, Children’s Hospital, Boston, Massachusetts
| | - Bogdan Draganski
- Laboratoire de Recherche en Neuroimagerie, Department for Clinical Neurosciences, Centre Hospitalo-Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Elliott H. Sherr
- Department of Neurology, University of California, San Francisco
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - Marianne B. M. van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Jacques S. Beckmann
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland7Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sébastien Jacquemont
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland41CHU Sainte-Justine Research Center, Montreal, Canada42Department of Pediatrics, Université de Montréal, Montreal, Quebec, Canada
| | - Wendy K. Chung
- Division of Molecular Genetics, Department of Pediatrics, Columbia University, New York, New York44Department of Medicine, Columbia University, New York, New York
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Kirkpatrick BE, Riggs ER, Azzariti DR, Miller VR, Ledbetter DH, Miller DT, Rehm H, Martin CL, Faucett WA. GenomeConnect: matchmaking between patients, clinical laboratories, and researchers to improve genomic knowledge. Hum Mutat 2015; 36:974-8. [PMID: 26178529 DOI: 10.1002/humu.22838] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [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: 05/05/2015] [Accepted: 06/29/2015] [Indexed: 12/14/2022]
Abstract
As the utility of genetic and genomic testing in healthcare grows, there is need for a high-quality genomic knowledge base to improve the clinical interpretation of genomic variants. Active patient engagement can enhance communication between clinicians, patients, and researchers, contributing to knowledge building. It also encourages data sharing by patients and increases the data available for clinicians to incorporate into individualized patient care, clinical laboratories to utilize in test interpretation, and investigators to use for research. GenomeConnect is a patient portal supported by the Clinical Genome Resource (ClinGen), providing an opportunity for patients to add to the knowledge base by securely sharing their health history and genetic test results. Data can be matched with queries from clinicians, laboratory personnel, and researchers to better interpret the results of genetic testing and build a foundation to support genomic medicine. Participation is online, allowing patients to contribute regardless of location. GenomeConnect supports longitudinal, detailed clinical phenotyping and robust "matching" among research and clinical communities. Phenotype data are gathered using online health questionnaires; genotype data are obtained from genetic test reports uploaded by participants and curated by staff. GenomeConnect empowers patients to actively participate in the improvement of genomic test interpretation and clinical utility.
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Affiliation(s)
| | | | - Danielle R Azzariti
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts
| | | | | | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts.,Claritas Genomics, Cambridge, Massachusetts
| | - Heidi Rehm
- Laboratory for Molecular Medicine, Partners Personalized Medicine, Boston, Massachusetts.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
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Ormond KE, Rashkin M, Faucett WA. Standardizing Variant Interpretation in Genomic Sequencing: Implications for Genetic Counseling Practice. Curr Genet Med Rep 2015. [DOI: 10.1007/s40142-015-0073-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Moreno-De-Luca A, Evans DW, Boomer KB, Hanson E, Bernier R, Goin-Kochel RP, Myers SM, Challman TD, Moreno-De-Luca D, Slane MM, Hare AE, Chung WK, Spiro JE, Faucett WA, Martin CL, Ledbetter DH. The role of parental cognitive, behavioral, and motor profiles in clinical variability in individuals with chromosome 16p11.2 deletions. JAMA Psychiatry 2015; 72:119-26. [PMID: 25493922 DOI: 10.1001/jamapsychiatry.2014.2147] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Most disorders caused by copy number variants (CNVs) display significant clinical variability, often referred to as incomplete penetrance and variable expressivity. Genetic and environmental sources of this variability are not well understood. OBJECTIVES To investigate the contributors to phenotypic variability in probands with CNVs involving the same genomic region; to measure the effect size for de novo mutation events; and to explore the contribution of familial background to resulting cognitive, behavioral, and motor performance outcomes in probands with de novo CNVs. DESIGN, SETTING, AND PARTICIPANTS Family-based study design with a volunteer sample of 56 individuals with de novo 16p11.2 deletions and their noncarrier parents and siblings from the Simons Variation in Individuals Project. MAIN OUTCOMES AND MEASURES We used linear mixed-model analysis to measure effect size and intraclass correlation to determine the influence of family background for a de novo CNV on quantitative traits representing the following 3 neurodevelopmental domains: cognitive ability (Full-Scale IQ), social behavior (Social Responsiveness Scale), and neuromotor performance (Purdue Pegboard Test). We included an anthropometric trait, body mass index, for comparison. RESULTS A significant deleterious effect of the 16p11.2 deletion was demonstrated across all domains. Relative to the biparental mean, the effect sizes were -1.7 SD for cognitive ability, 2.2 SD for social behavior, and -1.3 SD for neuromotor performance (P < .001). Despite large deleterious effects, significant positive correlations between parents and probands were preserved for the Full-Scale IQ (0.42 [P = .03]), the verbal IQ (0.53 [P = .004]), and the Social Responsiveness Scale (0.52 [P = .009]) scores. We also observed a 1-SD increase in the body mass index of probands compared with siblings, with an intraclass correlation of 0.40 (P = .07). CONCLUSIONS AND RELEVANCE Analysis of families with de novo CNVs provides the least confounded estimate of the effect size of the 16p11.2 deletion on heritable, quantitative traits and demonstrates a 1- to 2-SD effect across all neurodevelopmental dimensions. Significant parent-proband correlations indicate that family background contributes to the phenotypic variability seen in this and perhaps other CNV disorders and may have implications for counseling families regarding their children's developmental and psychiatric prognoses. Use of biparental mean scores rather than general population mean scores may be more relevant to examine the effect of a mutation or any other cause of trait variation on a neurodevelopmental outcome and possibly on systems of diagnosis and trait ascertainment for developmental disorders.
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Affiliation(s)
- Andres Moreno-De-Luca
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania2Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania3Department of Radiology, Geisinger Health System, Danville, Pennsylvania4Program in N
| | - David W Evans
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania4Program in Neuroscience, Bucknell University, Lewisburg, Pennsylvania5Department of Psychology, Bucknell University, Lewisburg, Pennsylvania
| | - K B Boomer
- Department of Mathematics, Bucknell University, Lewisburg, Pennsylvania
| | - Ellen Hanson
- Division of Developmental Medicine, Children's Hospital Boston, Boston, Massachusetts8Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle
| | | | - Scott M Myers
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania4Program in Neuroscience, Bucknell University, Lewisburg, Pennsylvania11Department of Pediatrics, Geisinger Health System, Danville, Pennsylvania
| | - Thomas D Challman
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania4Program in Neuroscience, Bucknell University, Lewisburg, Pennsylvania11Department of Pediatrics, Geisinger Health System, Danville, Pennsylvania
| | | | - Mylissa M Slane
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania
| | - Abby E Hare
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania
| | - Wendy K Chung
- Simons Foundation, New York, New York14Department of Pediatrics, Columbia University, New York, New York15Department of Medicine, Columbia University, New York, New York
| | | | - W Andrew Faucett
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania2Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - Christa L Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania2Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - David H Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Lewisburg, Pennsylvania2Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania4Program in Neuroscience, Bucknell University, Lewisburg, Pennsylvania
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17
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Bernhardt BA, Kellom K, Barbarese A, Faucett WA, Wapner RJ. An exploration of genetic counselors' needs and experiences with prenatal chromosomal microarray testing. J Genet Couns 2014; 23:938-47. [PMID: 24569858 DOI: 10.1007/s10897-014-9702-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/05/2014] [Indexed: 11/28/2022]
Abstract
Because of the higher yield over traditional chromosomal analysis, chromosomal microarray analysis (CMA) is being used increasingly in prenatal diagnosis. Unfortunately, the clinical implication of many copy number variants found on prenatal CMA is uncertain, complicating genetic counseling. Recognizing that uncertain results will be encountered frequently as more of the genome is assayed prenatally, we set out to understand the experiences and needs of genetic counselors when counseling patients about uncertain prenatal microarray results, their comfort with various aspects of prenatal genetic counseling, and their interest in additional education and training about prenatal microarray testing. We first interviewed 10 genetic counselors about their experiences of providing pre- and post-test genetic counseling about prenatal CMA. Based on the findings from the counselor interviews, we developed items for a survey to assess the prevalence of genetic counselors' attitudes towards, experience and comfort with, and educational needs regarding prenatal CMA. Based on surveys completed by 193 prenatal genetic counselors, we found that when there is an uncertain CMA result, only 59% would be comfortable providing genetic counseling and only 43% would be comfortable helping a patient make a decision about pregnancy termination. Being less comfortable was associated with seeing fewer patients having prenatal CMA testing. Respondents expressed a high degree of interest in additional education about prenatal CMA and counseling about uncertain results. Further genetic counselor education and training aimed at improving counselors' personal comfort with uncertain results and communicating about them with patients is needed.
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18
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Williams JL, Faucett WA, Smith-Packard B, Wagner M, Williams MS. An assessment of time involved in pre-test case review and counseling for a whole genome sequencing clinical research program. J Genet Couns 2014; 23:516-21. [PMID: 24573557 PMCID: PMC4090811 DOI: 10.1007/s10897-014-9697-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 06/30/2013] [Accepted: 01/05/2014] [Indexed: 12/25/2022]
Abstract
Whole genome sequencing (WGS) is being used for evaluation of individuals with undiagnosed disease of suspected genetic origin. Implementing WGS into clinical practice will place an increased burden upon care teams with regard to pre-test patient education and counseling about results. To quantitate the time needed for appropriate pre-test evaluation of participants in WGS testing, we documented the time spent by our clinical research group on various activities related to program preparation, participant screening, and consent prior to WGS. Participants were children or young adults with autism, intellectual or developmental disability, and/or congenital anomalies, who have remained undiagnosed despite previous evaluation, and their biologic parents. Results showed that significant time was spent in securing allocation of clinical research space to counsel participants and families, and in acquisition and review of participant’s medical records. Pre-enrollment chart review identified two individuals with existing diagnoses resulting in savings of $30,000 for the genome sequencing alone, as well as saving hours of personnel time for genome interpretation and communication of WGS results. New WGS programs should plan for costs associated with additional pre-test administrative planning and patient evaluation time that will be required to provide high quality care.
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Affiliation(s)
- Janet L Williams
- Genomic Medicine Institute, Geisinger Health System, 100 N Academy Ave., Danville, PA, 17822, USA,
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19
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Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, Sanderson SC, Kannry J, Zinberg R, Basford MA, Brilliant M, Carey DJ, Chisholm RL, Chute CG, Connolly JJ, Crosslin D, Denny JC, Gallego CJ, Haines JL, Hakonarson H, Harley J, Jarvik GP, Kohane I, Kullo IJ, Larson EB, McCarty C, Ritchie MD, Roden DM, Smith ME, Böttinger EP, Williams MS. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med 2013; 15:761-71. [PMID: 23743551 PMCID: PMC3795928 DOI: 10.1038/gim.2013.72] [Citation(s) in RCA: 489] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/18/2013] [Indexed: 12/13/2022] Open
Abstract
The Electronic Medical Records and Genomics Network is a National Human Genome Research Institute–funded consortium engaged in the development of methods and best practices for using the electronic medical record as a tool for genomic research. Now in its sixth year and second funding cycle, and comprising nine research groups and a coordinating center, the network has played a major role in validating the concept that clinical data derived from electronic medical records can be used successfully for genomic research. Current work is advancing knowledge in multiple disciplines at the intersection of genomics and health-care informatics, particularly for electronic phenotyping, genome-wide association studies, genomic medicine implementation, and the ethical and regulatory issues associated with genomics research and returning results to study participants. Here, we describe the evolution, accomplishments, opportunities, and challenges of the network from its inception as a five-group consortium focused on genotype–phenotype associations for genomic discovery to its current form as a nine-group consortium pivoting toward the implementation of genomic medicine. Genet Med15 10, 761–771.
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20
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Riggs ER, Wain KE, Riethmaier D, Savage M, Smith-Packard B, Kaminsky EB, Rehm HL, Martin CL, Ledbetter DH, Faucett WA. Towards a Universal Clinical Genomics Database: the 2012 International Standards for Cytogenomic Arrays Consortium Meeting. Hum Mutat 2013; 34:915-9. [PMID: 23463607 DOI: 10.1002/humu.22306] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 02/27/2013] [Indexed: 11/05/2022]
Abstract
The 2012 International Standards for Cytogenomic Arrays (ISCA) Consortium Meeting, "Towards a Universal Clinical Genomic Database," was held in Bethesda, Maryland, May 21-22, 2012, and was attended by over 200 individuals from around the world representing clinical genetic testing laboratories, clinicians, academia, industry, research, and regulatory agencies. The scientific program centered on expanding the current focus of the ISCA Consortium to include the collection and curation of both structural and sequence-level variation into a unified clinical genomics database, available to the public through resources such as the National Center for Biotechnology Information's ClinVar database. Here, we provide an overview of the conference, with summaries of the topics presented for discussion by over 25 different speakers. Presentations are available online at www.iscaconsortium.org.
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Affiliation(s)
- Erin Rooney Riggs
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA.
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21
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Zufferey F, Sherr EH, Beckmann ND, Hanson E, Maillard AM, Hippolyte L, Macé A, Ferrari C, Kutalik Z, Andrieux J, Aylward E, Barker M, Bernier R, Bouquillon S, Conus P, Delobel B, Faucett WA, Goin-Kochel RP, Grant E, Harewood L, Hunter JV, Lebon S, Ledbetter DH, Martin CL, Männik K, Martinet D, Mukherjee P, Ramocki MB, Spence SJ, Steinman KJ, Tjernagel J, Spiro JE, Reymond A, Beckmann JS, Chung WK, Jacquemont S. A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders. J Med Genet 2013; 49:660-8. [PMID: 23054248 PMCID: PMC3494011 DOI: 10.1136/jmedgenet-2012-101203] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [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: 12/29/2022]
Abstract
Background The recurrent ∼600 kb 16p11.2 BP4-BP5 deletion is among the most frequent known genetic aetiologies of autism spectrum disorder (ASD) and related neurodevelopmental disorders. Objective To define the medical, neuropsychological, and behavioural phenotypes in carriers of this deletion. Methods We collected clinical data on 285 deletion carriers and performed detailed evaluations on 72 carriers and 68 intrafamilial non-carrier controls. Results When compared to intrafamilial controls, full scale intelligence quotient (FSIQ) is two standard deviations lower in carriers, and there is no difference between carriers referred for neurodevelopmental disorders and carriers identified through cascade family testing. Verbal IQ (mean 74) is lower than non-verbal IQ (mean 83) and a majority of carriers require speech therapy. Over 80% of individuals exhibit psychiatric disorders including ASD, which is present in 15% of the paediatric carriers. Increase in head circumference (HC) during infancy is similar to the HC and brain growth patterns observed in idiopathic ASD. Obesity, a major comorbidity present in 50% of the carriers by the age of 7 years, does not correlate with FSIQ or any behavioural trait. Seizures are present in 24% of carriers and occur independently of other symptoms. Malformations are infrequently found, confirming only a few of the previously reported associations. Conclusions The 16p11.2 deletion impacts in a quantitative and independent manner FSIQ, behaviour and body mass index, possibly through direct influences on neural circuitry. Although non-specific, these features are clinically significant and reproducible. Lastly, this study demonstrates the necessity of studying large patient cohorts ascertained through multiple methods to characterise the clinical consequences of rare variants involved in common diseases.
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Affiliation(s)
- Flore Zufferey
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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22
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Wain KE, Riggs E, Hanson K, Savage M, Riethmaier D, Muirhead A, Mitchell E, Packard BS, Faucett WA. The laboratory-clinician team: a professional call to action to improve communication and collaboration for optimal patient care in chromosomal microarray testing. J Genet Couns 2012; 21:631-7. [PMID: 22610653 DOI: 10.1007/s10897-012-9507-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 04/24/2012] [Indexed: 11/25/2022]
Abstract
The International Standards for Cytogenomic Arrays (ISCA) Consortium is a worldwide collaborative effort dedicated to optimizing patient care by improving the quality of chromosomal microarray testing. The primary effort of the ISCA Consortium has been the development of a database of copy number variants (CNVs) identified during the course of clinical microarray testing. This database is a powerful resource for clinicians, laboratories, and researchers, and can be utilized for a variety of applications, such as facilitating standardized interpretations of certain CNVs across laboratories or providing phenotypic information for counseling purposes when published data is sparse. A recognized limitation to the clinical utility of this database, however, is the quality of clinical information available for each patient. Clinical genetic counselors are uniquely suited to facilitate the communication of this information to the laboratory by virtue of their existing clinical responsibilities, case management skills, and appreciation of the evolving nature of scientific knowledge. We intend to highlight the critical role that genetic counselors play in ensuring optimal patient care through contributing to the clinical utility of the ISCA Consortium's database, as well as the quality of individual patient microarray reports provided by contributing laboratories. Current tools, paper and electronic forms, created to maximize this collaboration are shared. In addition to making a professional commitment to providing complete clinical information, genetic counselors are invited to become ISCA members and to become involved in the discussions and initiatives within the Consortium.
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24
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Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010; 86:749-64. [PMID: 20466091 PMCID: PMC2869000 DOI: 10.1016/j.ajhg.2010.04.006] [Citation(s) in RCA: 1791] [Impact Index Per Article: 127.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/12/2010] [Accepted: 04/19/2010] [Indexed: 12/11/2022] Open
Abstract
Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype ( approximately 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.
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Affiliation(s)
- David T. Miller
- Division of Genetics and Department of Laboratory Medicine, Children's Hospital Boston and Harvard Medical School, Boston, MA, USA
| | - Margaret P. Adam
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Leslie G. Biesecker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arthur R. Brothman
- Department of Pediatrics, Human Genetics, Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Deanna M. Church
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - John A. Crolla
- National Genetics Reference Laboratory (Wessex), Salisbury UK
| | - Evan E. Eichler
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Charles J. Epstein
- Institute for Human Genetics and Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - W. Andrew Faucett
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lars Feuk
- Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, and Child & Family Research Institute, Vancouver, British Columbia, Canada
| | - Ada Hamosh
- Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laird Jackson
- Department of Obstetrics and Gynecology, Drexel University College of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erin B. Kaminsky
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Klaas Kok
- Department of Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands
| | - Ian D. Krantz
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Robert M. Kuhn
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James M. Ostell
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, University Sao Paulo, Brazil
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genetic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Nancy B. Spinner
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Dimitri J. Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Erik C. Thorland
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Darrel J. Waggoner
- Department of Human Genetics and Pediatrics, University of Chicago, Chicago, IL, USA
| | | | - Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David H. Ledbetter
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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25
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Myers MF, Chang MH, Jorgensen C, Whitworth W, Kassim S, Litch JA, Armstrong L, Bernhardt B, Faucett WA, Irwin D, Mouchawar J, Bradley LA. Genetic testing for susceptibility to breast and ovarian cancer: evaluating the impact of a direct-to-consumer marketing campaign on physicians' knowledge and practices. Genet Med 2006; 8:361-70. [PMID: 16778598 DOI: 10.1097/01.gim.0000223544.68475.6c] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE To assess the impact of direct-to-consumer marketing of genetic testing for risk of breast and ovarian cancer by a biotechnology company on: 1) physicians' knowledge; 2) reasons given when asking questions about the test; and 3) physicians' practice patterns in two pilot cities where the campaign took place and two control cities. METHODS Survey of randomly selected family physicians, internists, obstetrician-gynecologists, and oncologists from May 1-May 21, 2003. RESULTS Physicians' knowledge did not differ between pilot and control cities. Significant differences (pilot versus control cities) were seen in the reasons patients gave for asking questions about testing. More physicians in pilot cities (14%) than control cities (7%) reported an increase in the number of times they ordered genetic testing for breast and ovarian cancer risk in the previous 6 months (adjusted odds ratio 1.9, 95% confidence interval, 1.2-3.1). Awareness of professional guidelines and being in a practice with a policy on genetic testing for risk of breast and ovarian cancer were associated with physicians' behaviors and interest among patients in testing. CONCLUSIONS Given the complexity and limitations of genetic testing for risk of breast and ovarian cancer, the development and broad dissemination of clinical guidelines and education of physicians are needed.
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Affiliation(s)
- Melanie F Myers
- Office of Genomics and Disease Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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26
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Affiliation(s)
- Suzanne M Cox
- Association of Schools of Public Health, Washington DC, USA
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27
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Faucett WA. Book Review: The Limits and Lies of Human Genetic Research, Dangers for Social Policy.
By Jonathan Michael Kaplan. Routledge, New York, 2000, 224 pp., $22.99 (paperback). J Genet Couns 2003. [DOI: 10.1023/a:1022667424914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- W. Andrew Faucett
- ; Division of Laboratory Systems; Association of Teachers of Preventive Medicine CDA, Centers for Disease Control and Prevention (CDC), Public Health Practice Program Office -; Mailstop G-25, 4770 Buford Highway Atlanta Georgia 30341
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28
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Greenberg F, Del Junco D, Weyland B, Faucett WA, Schmidt D, Rose E, Alpert E. The effect of gestational age on the detection rate of Down's syndrome by maternal serum alpha-fetoprotein screening. Am J Obstet Gynecol 1991; 165:1391-3. [PMID: 1720281 DOI: 10.1016/0002-9378(91)90375-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Low levels of maternal serum alpha-fetoprotein are currently being used to screen for Down's syndrome in midpregnancy. Because of the possibility that gestational age may affect the detection rate of Down's syndrome, we analyzed maternal serum AFP levels and gestational age in 51 Down's syndrome pregnancies that had been confirmed by amniocentesis or at birth, and we compared these pregnancies with 3239 screened singleton pregnancies with known normal outcomes. The highest yield of a low risk for Down's syndrome associated with maternal serum alpha-fetoprotein occurred at 16.5 to 17.5 weeks' gestation. Our data suggest that maternal serum alpha-fetoprotein screening for Down's syndrome should be done between 16 and 18 weeks' gestation, which is the gestational age currently recommended for neural tube defect screening.
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Affiliation(s)
- F Greenberg
- Institute for Molecular Genetics, Baylor College of Medicine, Houston, TX 77030
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