Holly Tabor

All Publications

• Rethinking the "open future" argument against predictive genetic testing of children GENETICS IN MEDICINE Garrett, J. R., Lantos, J. D., Biesecker, L. G., Childerhose, J. E., Chung, W. K., Holm, I. A., Koenig, B. A., McEwen, J. E., Wilfond, B. S., Brothers, K., Berkman, B., Bernhardt, B., Caga-Anan, C., Clayton, E., Goldenberg, A., Hull, S., Joffe, S., Krantz, I., Lewis, M., Liang, W., Lockhart, N., McCollum, S., McCullough, L., McGuire, A., Noorbaksh, A., Panchang, S., Parsons, D., Reiss, J., Roche, M., Rodriguez, L., Romasko, E., Ross, L., Sharp, R., Skinner, D., Slashinski, M., Tabor, H., Tomlinson, A., Wolf, S., Yu, J., CSER Consortium Pediat 2019; 21 (10): 2190–98

  Abstract

  Professional consensus has traditionally discouraged predictive genetic testing when no childhood interventions can reduce future morbidity or mortality. However, advances in genome sequencing and accumulating evidence that children and families cope adequately with predictive genetic information have weakened this consensus. The primary argument remaining against testing appeals to children's "right to an open future." It claims that the autonomy of the future adult is violated when others make an irreversible choice to obtain or disclose predictive genetic information during childhood. We evaluate this argument and conclude that children's interest in an open future should not be understood as a right. Rather an open future is one significant interest to weigh against other important interests when evaluating decisions. Thus, predictive genetic testing is ethically permissible in principle, as long as the interests promoted outweigh potential harms. We conclude by offering an expanded model of children's interests that might be considered in such circumstances, and present two case analyses to illustrate how this framework better guides decisions about predictive genetic testing in pediatrics.

  View details for DOI 10.1038/s41436-019-0483-4

  View details for Web of Science ID 000488530100006

  View details for PubMedID 30894702

  View details for PubMedCentralID PMC6754817

• "Before Facebook and before social media...we did not know anybody else that had this": parent perspectives on internet and social media use during the pediatric clinical genetic testing process JOURNAL OF COMMUNITY GENETICS Barton, K. S., Wingerson, A., Barzilay, J. R., Tabor, H. K. 2019; 10 (3): 375–83

  View details for DOI 10.1007/s12687-018-0400-6

  View details for Web of Science ID 000472908300006

• Assessing genetic counselors' experiences with physician aid-in-dying and practice implications. Journal of genetic counseling D'Angelo, A., Ormond, K. E., Magnus, D., Tabor, H. K. 2019

  Abstract

  Physician aid-in-dying (PAD) is now legalized in more than half a dozen states across the United States yet remains controversial among health care providers and the general public. Previous studies have described physicians' and nurses' experiences with and attitudes about PAD; however, there is no data about PAD in the context of genetic counseling. This study explores genetic counselors' experiences, understanding, training, and perspectives about PAD. Fifteen participants were recruited to complete semistructured telephone interviews. Five participants had received patient inquiries about PAD. Most participants (n=10) did not feel prepared to discuss PAD with patients and felt that they did not have adequate knowledge to answer patient questions about the practice. Participants described how the unique training, skills, and experiences of genetic counselors could be beneficial for discussing PAD with patients, in comparison to other providers. All participants supported training for genetic counselors about PAD, with many suggesting integration with education about palliative care and end-of-life planning. This is the first study to investigate PAD in the context of genetic counseling. Genetic counselors have had patients ask questions about PAD, want education and access to resources about PAD, and believe they can provide important support and guidance to patients considering PAD in some genetic counseling contexts.

  View details for PubMedID 30688387

• Consent insufficient for data release. Science (New York, N.Y.) Nicol, D., Eckstein, L., Bentzen, H. B., Borry, P., Burgess, M., Burke, W., Chalmers, D., Cho, M., Dove, E., Fullerton, S., Ida, R., Kato, K., Kaye, J., Koenig, B., Manson, S., McGrail, K., Meslin, E., O'Doherty, K., Prainsack, B., Shabani, M., Tabor, H., Thorogood, A., de Vries, J. 2019; 364 (6439): 445–46

  View details for DOI 10.1126/science.aax0892

  View details for PubMedID 31048483

• High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research An Official American Thoracic Society Workshop Report ANNALS OF THE AMERICAN THORACIC SOCIETY Hersh, C. P., Adcock, I. M., Celedon, J. C., Cho, M. H., Christiani, D. C., Himes, B. E., Kaminski, N., Mathias, R. A., Meyers, D. A., Quackenbush, J., Redline, S., Steiling, K. A., Tabor, H. K., Tobin, M. D., Wurfel, M. M., Yang, I. V., Koppelman, G. H., American Thoracic Soc Sect Genetic 2019; 16 (1): 1–16

  Abstract

  High-throughput, "next-generation" sequencing methods are now being broadly applied across all fields of biomedical research, including respiratory disease, critical care, and sleep medicine. Although there are numerous review articles and best practice guidelines related to sequencing methods and data analysis, there are fewer resources summarizing issues related to study design and interpretation, especially as applied to common, complex, nonmalignant diseases. To address these gaps, a single-day workshop was held at the American Thoracic Society meeting in May 2017, led by the American Thoracic Society Section on Genetics and Genomics. The aim of this workshop was to review the design, analysis, interpretation, and functional follow-up of high-throughput sequencing studies in respiratory, critical care, and sleep medicine research. This workshop brought together experts in multiple fields, including genetic epidemiology, biobanking, bioinformatics, and research ethics, along with physician-scientists with expertise in a range of relevant diseases. The workshop focused on application of DNA and RNA sequencing research in common chronic diseases and did not cover sequencing studies in lung cancer, monogenic diseases (e.g., cystic fibrosis), or microbiome sequencing. Participants reviewed and discussed study design, data analysis and presentation, interpretation, functional follow-up, and reporting of results. This report summarizes the main conclusions of the workshop, specifically addressing the application of these methods in respiratory, critical care, and sleep medicine research. This workshop report may serve as a resource for our research community as well as for journal editors and reviewers of sequencing-based manuscript submissions in our research field.

  View details for DOI 10.1513/AnnalsATS.201810-716WS

  View details for Web of Science ID 000454507300001

  View details for PubMedID 30592451

• Perspectives on Spinraza (Nusinersen) Treatment Study: Views of Individuals and Parents of Children Diagnosed with Spinal Muscular Atrophy. Journal of neuromuscular diseases Pacione, M., Siskind, C. E., Day, J. W., Tabor, H. K. 2018

  Abstract

  BACKGROUND: Spinal muscular atrophy (SMA) is a genetic disorder characterized by muscle loss. In December 2016 the FDA approved the first and only treatment drug for SMA: Spinraza (nusinersen). Despite excitement and optimism, there are no published data on the perceptions of individuals with SMA and their families about the benefits, risks, and challenges associated with treatment.OBJECTIVE: This qualitative interview study sought to characterize the perspectives of patients/families with SMA who did not want, or were unsure about, receiving this new innovative treatment for a previously untreatable and often fatal condition.METHODS: Individuals and families were recruited via advertisements on Facebook groups related to SMA and through the Stanford Neuromuscular Contact Registry. Participants completed a demographic questionnaire and participated in a semi-structured interview via voice conferencing. Interview questions focused on: 1) experiences with SMA, 2) opinions about Spinraza treatment, and 3) factors considered in decisions regarding treatment.RESULTS: Thirteen people were interviewed: ten adults with SMA (ages 27- 48, nine with Type II) and three parents of minor children with SMA (one each of Types I, II and III). Qualitative content analysis identified a range of opinions about Spinraza treatment: five were uninterested (2 adults, 3 parents), four adults were still deciding whether to pursue treatment, three adults were interested or in the process of pursuing treatment, and one adult was currently receiving the drug after overcoming significant reluctance. Participants described several key factors influencing their treatment decisions, including: concerns about risk factors and side effects, high cost, insurance coverage, time involvement, and lack of data about efficacy. Participants reported learning about most of these factors through parent/patient testimonials on SMA-specific social media groups.CONCLUSIONS: Participants reported basing decisions about pursuing Spinraza on a variety of practical and value-based considerations. They described carefully weighing the perceived potential benefits and risks of treatment through the lens of their current quality of life and prognosis. These findings suggest that providers should be aware that some patients and parents, especially those with Types II-IV, may approach treatment decisions differently than parents of children with SMA I. Informed treatment decisions can be supported through: 1) the collection and dissemination of better data on Spinraza treatment in these populations; 2) clear communication about risks, side effects and eligibility; 3) improved access to payment and treatment facilities; and 4) facilitation of discussions between providers and patients/families about identity and disability in the context of goals of care and other life and support challenges.

  View details for PubMedID 30594933

• "Before Facebook and before social mediawe did not know anybody else that had this": parent perspectives on internet and social media use during the pediatric clinical genetic testing process. Journal of community genetics Barton, K. S., Wingerson, A., Barzilay, J. R., Tabor, H. K. 2018

  Abstract

  Parents of children who undergo clinical genetic testing have significant informational and emotional support needs at different stages of the testing process. We analyzed parent views about use of both the internet and social media to help meet these needs. We interviewed 20 parents of children who underwent clinical genetic testing and analyzed transcripts to identify themes related to internet and social media use. Parents described using the internet to search for information at three stages of the genetic testing process: before testing, pending results return, and after results return. Each stage corresponded to different information vacuums and needs. Parents also described using condition-specific Facebook groups to learn more about their child's condition and to find support networks of families with similar experiences in ways that were challenging using non-social media approaches. Both the internet and social media play important roles in meeting informational and support needs in pediatric genetic testing, especially for rare conditions. Providers should consider engaging parents at different stages of the testing process about their use of the internet and social media, and consider directing them to vetted sites and groups as part of shared decision making and to improve satisfaction and outcomes.

  View details for PubMedID 30569339

• What Precision Medicine Can Learn from Rare Genetic Disease Research and Translation. AMA journal of ethics Tabor, H. K., Goldenberg, A. 2018; 20 (9): E834–840

  Abstract

  The goal of this article is to examine the intersections of precision health and rare diseases. Specifically, we propose 3 lessons from the last decade of applying genomics to rare diseases: (1) precision can end one odyssey and start another; (2) precise interventions can exacerbate health disparities and create other ethical dilemmas; and (3) democratization of data will transform research and translation. By studying experiences of patients with rare diseases, researchers, clinicians, and policymakers can anticipate similar challenges in precision medicine and hopefully mitigate potential harms or injustices.

  View details for PubMedID 30242814

• Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience. Molecular genetics & genomic medicine Porter, K. M., Kauffman, T. L., Koenig, B. A., Lewis, K. L., Rehm, H. L., Richards, C. S., Strande, N. T., Tabor, H. K., Wolf, S. M., Yang, Y., Amendola, L. M., Azzariti, D. R., Berg, J. S., Bergstrom, K., Biesecker, L. G., Biswas, S., Bowling, K. M., Chung, W. K., Clayton, E. W., Conlin, L. K., Cooper, G. M., Dulik, M. C., Garraway, L. A., Ghazani, A. A., Green, R. C., Hiatt, S. M., Jamal, S. M., Jarvik, G. P., Goddard, K. A., Wilfond, B. S., members of the CSER Actionability and Return of Results Working Group 2018

  Abstract

  BACKGROUND: Clinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X-linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed.METHODS: Representatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project-specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects.RESULTS: The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results.CONCLUSION: Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.

  View details for PubMedID 30133189

• Ethical Challenges Confronted When Providing Nusinersen Treatment for Spinal Muscular Atrophy. JAMA pediatrics Burgart, A. M., Magnus, D., Tabor, H. K., Paquette, E. D., Frader, J., Glover, J. J., Jackson, B. M., Harrison, C. H., Urion, D. K., Graham, R. J., Brandsema, J. F., Feudtner, C. 2018; 172 (2): 188–92

  Abstract

  The US Food and Drug Administration's December 2016 approval of nusinersen for the treatment of patients with all subtypes of spinal muscular atrophy ushered in a new era for patients with spinal muscular atrophy, their families, and all those involved in their care. The extreme cost of the medication and the complicated logistical requirements for administering nusinersen via lumbar puncture have created practical challenges that raise important ethical considerations. We discuss 6 challenges faced at the institutional level in the United States: cost, limited evidence, informed consent, treatment allocation, fair distribution of responsibilities, and transparency with stakeholders. These challenges must be understood to ensure that patients with spinal muscular atrophy benefit from treatment, are protected from harm, and are treated fairly.

  View details for PubMedID 29228163

• Pathways from autism spectrum disorder diagnosis to genetic testing. Genetics in medicine : official journal of the American College of Medical Genetics Barton, K. S., Tabor, H. K., Starks, H., Garrison, N. A., Laurino, M., Burke, W. 2017

  Abstract

  PurposeThis study examined challenges faced by families and health providers related to genetic testing for autism spectrum disorder (ASD).MethodsThis qualitative study of 14 parents and 15 health providers identified an unstandardized three-step process for families who pursue ASD genetic testing.ResultsStep 1 is the clinical diagnosis of ASD, confirmed by providers practicing alone or in a team. Step 2 is the offer of genetic testing to find an etiology. For those offered testing, step 3 involves the parents' decision whether to pursue testing. Despite professional guidelines and recommendations, interviews describe considerable variability in approaches to genetic testing for ASD, a lack of consensus among providers, and questions about clinical utility. Many families in our study were unaware of the option for genetic testing; testing decisions by parents appear to be influenced by both provider recommendations and insurance coverage.ConclusionConsideration of genetic testing for ASD should take into account different views about the clinical utility of testing and variability in insurance coverage. Ideally, policy makers from the range of clinical specialties involved in ASD care should revisit policies to clarify the purpose of genetic testing for ASD and promote consensus about its appropriate use.GENETICS in MEDICINE advance online publication, 19 October 2017. doi:10.1038/gim.2017.166.

  View details for PubMedID 29048417

• My46: a Web-based tool for self-guided management of genomic test results in research and clinical settings. Genetics in medicine Tabor, H. K., Jamal, S. M., Yu, J., Crouch, J. M., Shankar, A. G., Dent, K. M., Anderson, N., Miller, D. A., Futral, B. T., Bamshad, M. J. 2016

  Abstract

  A major challenge to implementing precision medicine is the need for an efficient and cost-effective strategy for returning individual genomic test results that is easily scalable and can be incorporated into multiple models of clinical practice. My46 is a Web-based tool for managing the return of genetic results that was designed and developed to support a wide range of approaches to disclosing results, ranging from traditional face-to-face disclosure to self-guided models. My46 has five key functions: set and modify results-return preferences, return results, educate, manage the return of results, and assess the return of results. These key functions are supported by six distinct modules and a suite of features that enhance the user experience, ease site navigation, facilitate knowledge sharing, and enable results-return tracking. My46 is a potentially effective solution for returning results and supports current trends toward shared decision making between patients and providers and patient-driven health management.Genet Med advance online publication 15 September 2016Genetics in Medicine (2016); doi:10.1038/gim.2016.133.

  View details for DOI 10.1038/gim.2016.133

  View details for PubMedID 27632689

• Use of metaphors about exome and whole genome sequencing. American journal of medical genetics. Part A Nelson, S. C., Crouch, J. M., Bamshad, M. J., Tabor, H. K., Yu, J. 2016; 170A (5): 1127-1133

  Abstract

  Clinical and research uses of exome and whole genome sequencing (ES/WGS) are growing rapidly. An enhanced understanding of how individuals conceptualize and communicate about sequencing results is needed to ensure effective, mutual exchange of information between care providers and patients and between researchers and participants. Focus groups and interviews participants were recruited to discuss their attitudes and preferences for receiving hypothetical results from ES/WGS. African Americans were intentionally oversampled. We qualitatively analyzed participants' speech to identify unsolicited metaphorical language pertaining to genes and health, and grouped these occurrences into metaphorical concepts. Participants compared genetic information to physical objects including tools, weapons, contents of boxes, and formal documents or reports. These metaphorical concepts centered on several key themes, including locus of control; containment versus release of information; and desirability, usability, interpretability, and ownership of genetic results. Metaphorical language is often used intentionally or unintentionally in discussions about receiving results from ES/WGS in both clinical and research settings. Awareness of the use of metaphorical language and attention to its varied meanings facilitates effective communication about return of ES/WGS results. In turn, both should foster shared and informed decision-making and improve the translation of genetic information by clinicians and researchers.

  View details for DOI 10.1002/ajmg.a.37571

  View details for PubMedID 26822973

• Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features. Genetics in medicine : official journal of the American College of Medical Genetics Chong, J. X., Yu, J. H., Lorentzen, P., Park, K. M., Jamal, S. M., Tabor, H. K., Rauch, A., Saenz, M. S., Boltshauser, E., Patterson, K. E., Nickerson, D. A., Bamshad, M. J. 2016; 18 (8): 788–95

  Abstract

  The pace of Mendelian gene discovery is slowed by the "n-of-1 problem"-the difficulty of establishing the causality of a putatively pathogenic variant in a single person or family. Identification of an unrelated person with an overlapping phenotype and suspected pathogenic variant in the same gene can overcome this barrier, but it is often impeded by lack of a convenient or widely available way to share data on candidate variants/genes among families, clinicians, and researchers.Social networking among families, clinicians, and researchers was used to identify three children with variants of unknown significance in KDM1A and similar phenotypes.De novo variants in KDM1A underlie a new syndrome characterized by developmental delay and distinctive facial features.Social networking is a potentially powerful strategy to discover genes for rare Mendelian conditions, particularly those with nonspecific phenotypic features. To facilitate the efforts of families to share phenotypic and genomic information with each other, clinicians, and researchers, we developed the Repository for Mendelian Genomics Family Portal (RMD-FP; http://uwcmg.org/#/family). Design and development of MyGene2 (http://www.mygene2.org), a Web-based tool that enables families, clinicians, and researchers to search for gene matches based on analysis of phenotype and exome data deposited into the RMD-FP, is under way.Genet Med 18 8, 788-795.

  View details for PubMedID 26656649

  View details for PubMedCentralID PMC4902791

• The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. American journal of human genetics Chong, J. X., Buckingham, K. J., Jhangiani, S. N., Boehm, C., Sobreira, N., Smith, J. D., Harrell, T. M., McMillin, M. J., Wiszniewski, W., Gambin, T., Coban Akdemir, Z. H., Doheny, K., Scott, A. F., Avramopoulos, D., Chakravarti, A., Hoover-Fong, J., Mathews, D., Witmer, P. D., Ling, H., Hetrick, K., Watkins, L., Patterson, K. E., Reinier, F., Blue, E., Muzny, D., Kircher, M., Bilguvar, K., López-Giráldez, F., Sutton, V. R., Tabor, H. K., Leal, S. M., Gunel, M., Mane, S., Gibbs, R. A., Boerwinkle, E., Hamosh, A., Shendure, J., Lupski, J. R., Lifton, R. P., Valle, D., Nickerson, D. A., Bamshad, M. J. 2015; 97 (2): 199-215

  Abstract

  Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families.

  View details for DOI 10.1016/j.ajhg.2015.06.009

  View details for PubMedID 26166479

  View details for PubMedCentralID PMC4573249

• Actionable exomic incidental findings in 6503 participants: challenges of variant classification GENOME RESEARCH Amendola, L. M., Dorschner, M. O., Robertson, P. D., Salama, J. S., Hart, R., Shirts, B. H., Murray, M. L., Tokita, M. J., Gallego, C. J., Kim, D. S., Bennett, J. T., Crosslin, D. R., Ranchalis, J., Jones, K. L., Rosenthal, E. A., Jarvik, E. R., Itsara, A., Turner, E. H., Herman, D. S., Schleit, J., Burt, A., Jamal, S. M., Abrudan, J. L., Johnson, A. D., Conlin, L. K., Dulik, M. C., Santani, A., Metterville, D. R., Kelly, M., Foreman, A. K., Lee, K., Taylor, K. D., Guo, X., Crooks, K., Kiedrowski, L. A., Raffe, L. J., Gordon, O., Machini, K., Desnick, R., Biesecker, L. G., Lubitz, S. A., Mulchandani, S., Cooper, G. M., Joffe, S., Richards, C. S., Yang, Y., Rotter, J. I., Rich, S. S., O'Donne, C. J., Berg, J. S., Spinner, N. B., Evans, J. P., Fullerton, S. M., Leppig, K. A., Bennett, R. L., Bird, T., Sybert, V. P., Grady, W. M., Tabor, H. K., Kim, J. H., Bamshad, M. J., Wilfond, B., Motulsky, A. G., Scott, R., Pritchard, C. C., Walsh, T. D., Burke, W., Raskind, W. H., Byers, P., Hisama, F. M., Rehm, H., Nickerson, D. A., Jarvik, G. P. 2015; 25 (3): 305-315

  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.

  View details for DOI 10.1101/gr.183483.114

  View details for Web of Science ID 000350526700001

  View details for PubMedID 25637381

  View details for PubMedCentralID PMC4352885

• "We Don't Know Her History, Her Background": Adoptive Parents' Perspectives on Whole Genome Sequencing Results JOURNAL OF GENETIC COUNSELING Crouch, J., Yu, J., Shankar, A. G., Tabor, H. K. 2015; 24 (1): 67-77

  Abstract

  Exome sequencing and whole genome sequencing (ES/WGS) can provide parents with a wide range of genetic information about their children, and adoptive parents may have unique issues to consider regarding possible access to this information. The few papers published on adoption and genetics have focused on targeted genetic testing of children in the pre-adoption context. There are no data on adoptive parents' perspectives about pediatric ES/WGS, including their preferences about different kinds of results, and the potential benefits and risks of receiving results. To explore these issues, we conducted four exploratory focus groups with adoptive parents (N = 26). The majority lacked information about their children's biological family health history and ancestry, and many viewed WGS results as a way to fill in these gaps in knowledge. Some expressed concerns about protecting their children's future privacy and autonomy, but at the same time stated that WGS results could possibly help them be proactive about their children's health. A few parents expressed concerns about the risks of WGS in a pre-adoption context, specifically about decreasing a child's chance of adoption. These results suggest that issues surrounding genetic information in the post-adoption and ES/WGS contexts need to be considered, as well as concerns about risks in the pre-adoption context. A critical challenge for ES/WGS in the context of adoption will be balancing the right to know different kinds of genetic information with the right not to know. Specific guidance for geneticists and genetic counselors may be needed to maximize benefits of WGS while minimizing harms and prohibiting misuse of the information in the adoption process.

  View details for DOI 10.1007/s10897-014-9738-z

  View details for Web of Science ID 000348131000008

  View details for PubMedID 25011977

  View details for PubMedCentralID PMC4291307

• Exome Sequencing of Phenotypic Extremes Identifies CAV2 and TMC6 as Interacting Modifiers of Chronic Pseudomonas aeruginosa Infection in Cystic Fibrosis. PLoS genetics Emond, M. J., Louie, T., Emerson, J., Chong, J. X., Mathias, R. A., Knowles, M. R., Rieder, M. J., Tabor, H. K., Nickerson, D. A., Barnes, K. C., Go, L., Gibson, R. L., Bamshad, M. J. 2015; 11 (6): e1005273

  Abstract

  Discovery of rare or low frequency variants in exome or genome data that are associated with complex traits often will require use of very large sample sizes to achieve adequate statistical power. For a fixed sample size, sequencing of individuals sampled from the tails of a phenotype distribution (i.e., extreme phenotypes design) maximizes power and this approach was recently validated empirically with the discovery of variants in DCTN4 that influence the natural history of P. aeruginosa airway infection in persons with cystic fibrosis (CF; MIM219700). The increasing availability of large exome/genome sequence datasets that serve as proxies for population-based controls affords the opportunity to test an alternative, potentially more powerful and generalizable strategy, in which the frequency of rare variants in a single extreme phenotypic group is compared to a control group (i.e., extreme phenotype vs. control population design). As proof-of-principle, we applied this approach to search for variants associated with risk for age-of-onset of chronic P. aeruginosa airway infection among individuals with CF and identified variants in CAV2 and TMC6 that were significantly associated with group status. These results were validated using a large, prospective, longitudinal CF cohort and confirmed a significant association of a variant in CAV2 with increased age-of-onset of P. aeruginosa airway infection (hazard ratio = 0.48, 95% CI=[0.32, 0.88]) and variants in TMC6 with diminished age-of-onset of P. aeruginosa airway infection (HR = 5.4, 95% CI=[2.2, 13.5]) A strong interaction between CAV2 and TMC6 variants was observed (HR=12.1, 95% CI=[3.8, 39]) for children with the deleterious TMC6 variant and without the CAV2 protective variant. Neither gene showed a significant association using an extreme phenotypes design, and conditions for which the power of an extreme phenotype vs. control population design was greater than that for the extreme phenotypes design were explored.

  View details for PubMedID 26047157

  View details for PubMedCentralID PMC4457883

• Single-nucleotide polymorphism arrays and unexpected consanguinity: considerations for clinicians when returning results to families. Genetics in medicine : official journal of the American College of Medical Genetics Delgado, F., Tabor, H. K., Chow, P. M., Conta, J. H., Feldman, K. W., Tsuchiya, K. D., Beck, A. E. 2015; 17 (5): 400–404

  Abstract

  The broad use of single-nucleotide polymorphism microarrays has increased identification of unexpected consanguinity. Therefore, guidelines to address reporting of consanguinity have been published for clinical laboratories. Because no such guidelines for clinicians exist, we describe a case and present recommendations for clinicians to disclose unexpected consanguinity to families.In a boy with multiple endocrine abnormalities and structural birth defects, single-nucleotide polymorphism array analysis revealed ~23% autosomal homozygosity suggestive of a first-degree parental relationship. We assembled an interdisciplinary health-care team, planned the most appropriate way to discuss results of the single-nucleotide polymorphism array with the adult mother, including the possibility of multiple autosomal recessive disorders in her child, and finally met with her as a team.From these discussions, we developed four major considerations for clinicians returning results of unexpected consanguinity, all guided by the child's best interests: (i) ethical and legal obligations for reporting possible abuse, (ii) preservation of the clinical relationship, (iii) attention to justice and psychosocial challenges, and (iv) utilization of the single-nucleotide polymorphism array results to guide further testing.As single-nucleotide polymorphism arrays become a common clinical diagnostic tool, clinicians can use this framework to return results of unexpected consanguinity to families in a supportive and productive manner.

  View details for PubMedID 25232848

  View details for PubMedCentralID PMC4404161

• De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay. American journal of human genetics Chong, J. X., McMillin, M. J., Shively, K. M., Beck, A. E., Marvin, C. T., Armenteros, J. R., Buckingham, K. J., Nkinsi, N. T., Boyle, E. A., Berry, M. N., Bocian, M., Foulds, N., Uzielli, M. L., Haldeman-Englert, C., Hennekam, R. C., Kaplan, P., Kline, A. D., Mercer, C. L., Nowaczyk, M. J., Klein Wassink-Ruiter, J. S., McPherson, E. W., Moreno, R. A., Scheuerle, A. E., Shashi, V., Stevens, C. A., Carey, J. C., Monteil, A., Lory, P., Tabor, H. K., Smith, J. D., Shendure, J., Nickerson, D. A., Bamshad, M. J. 2015; 96 (3): 462–73

  Abstract

  Freeman-Sheldon syndrome, or distal arthrogryposis type 2A (DA2A), is an autosomal-dominant condition caused by mutations in MYH3 and characterized by multiple congenital contractures of the face and limbs and normal cognitive development. We identified a subset of five individuals who had been putatively diagnosed with "DA2A with severe neurological abnormalities" and for whom congenital contractures of the limbs and face, hypotonia, and global developmental delay had resulted in early death in three cases; this is a unique condition that we now refer to as CLIFAHDD syndrome. Exome sequencing identified missense mutations in the sodium leak channel, non-selective (NALCN) in four families affected by CLIFAHDD syndrome. We used molecular-inversion probes to screen for NALCN in a cohort of 202 distal arthrogryposis (DA)-affected individuals as well as concurrent exome sequencing of six other DA-affected individuals, thus revealing NALCN mutations in ten additional families with "atypical" forms of DA. All 14 mutations were missense variants predicted to alter amino acid residues in or near the S5 and S6 pore-forming segments of NALCN, highlighting the functional importance of these segments. In vitro functional studies demonstrated that NALCN alterations nearly abolished the expression of wild-type NALCN, suggesting that alterations that cause CLIFAHDD syndrome have a dominant-negative effect. In contrast, homozygosity for mutations in other regions of NALCN has been reported in three families affected by an autosomal-recessive condition characterized mainly by hypotonia and severe intellectual disability. Accordingly, mutations in NALCN can cause either a recessive or dominant condition characterized by varied though overlapping phenotypic features, perhaps based on the type of mutation and affected protein domain(s).

  View details for PubMedID 25683120

  View details for PubMedCentralID PMC4375444

• Pathogenic Variants for Mendelian and Complex Traits in Exomes of 6,517 European and African Americans: Implications for the Return of Incidental Results AMERICAN JOURNAL OF HUMAN GENETICS Tabor, H. K., Auer, P. L., Jamal, S. M., Chong, J. X., Yu, J., Gordon, A. S., Graubert, T. A., O'Donnell, C. J., Rich, S. S., Nickerson, D. A., Bamshad, M. J. 2014; 95 (2): 183-193

  Abstract

  Exome sequencing (ES) is rapidly being deployed for use in clinical settings despite limited empirical data about the number and types of incidental results (with potential clinical utility) that could be offered for return to an individual. We analyzed deidentified ES data from 6,517 participants (2,204 African Americans and 4,313 European Americans) from the National Heart, Lung, and Blood Institute Exome Sequencing Project. We characterized the frequencies of pathogenic alleles in genes underlying Mendelian conditions commonly assessed by newborn-screening (NBS, n = 39) programs, genes associated with age-related macular degeneration (ARMD, n = 17), and genes known to influence drug response (PGx, n = 14). From these 70 genes, we identified 10,789 variants and curated them by manual review of OMIM, HGMD, locus-specific databases, or primary literature to a total of 399 validated pathogenic variants. The mean number of risk alleles per individual was 15.3. Every individual had at least five known PGx alleles, 99% of individuals had at least one ARMD risk allele, and 45% of individuals were carriers for at least one pathogenic NBS allele. The carrier burden for severe recessive childhood disorders was 0.57. Our results demonstrate that risk alleles of potential clinical utility for both Mendelian and complex traits are detectable in every individual. These findings highlight the necessity of developing guidelines and policies that consider the return of results to all individuals and underscore the need to develop innovative approaches and tools that enable individuals to exercise their choice about the return of incidental results.

  View details for DOI 10.1016/j.ajhg.2014.07.006

  View details for Web of Science ID 000340076000005

  View details for PubMedID 25087612

  View details for PubMedCentralID PMC4129409

• Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset HUMAN MOLECULAR GENETICS Gordon, A. S., Tabor, H. K., Johnson, A. D., Snively, B. M., Assimes, T. L., Auer, P. L., Ioannidis, J. P., Peters, U., Robinson, J. G., Sucheston, L. E., Wang, D., Sotoodehnia, N., Rotter, J. I., Psaty, B. M., Jackson, R. D., Herrington, D. M., ODonnell, C. J., Reiner, A. P., Rich, S. S., Rieder, M. J., Bamshad, M. J., Nickerson, D. A. 2014; 23 (8): 1957-1963

  Abstract

  The study of genetic influences on drug response and efficacy ('pharmacogenetics') has existed for over 50 years. Yet, we still lack a complete picture of how genetic variation, both common and rare, affects each individual's responses to medications. Exome sequencing is a promising alternative method for pharmacogenetic discovery as it provides information on both common and rare variation in large numbers of individuals. Using exome data from 2203 AA and 4300 Caucasian individuals through the NHLBI Exome Sequencing Project, we conducted a survey of coding variation within 12 Cytochrome P450 (CYP) genes that are collectively responsible for catalyzing nearly 75% of all known Phase I drug oxidation reactions. In addition to identifying many polymorphisms with known pharmacogenetic effects, we discovered over 730 novel nonsynonymous alleles across the 12 CYP genes of interest. These alleles include many with diverse functional effects such as premature stop codons, aberrant splicesites and mutations at conserved active site residues. Our analysis considering both novel, predicted functional alleles as well as known, actionable CYP alleles reveals that rare, deleterious variation contributes markedly to the overall burden of pharmacogenetic alleles within the populations considered, and that the contribution of rare variation to this burden is over three times greater in AA individuals as compared with Caucasians. While most of these impactful alleles are individually rare, 7.6-11.7% of individuals interrogated in the study carry at least one newly described potentially deleterious alleles in a major drug-metabolizing CYP.

  View details for DOI 10.1093/hmg/ddt588

  View details for Web of Science ID 000333269400001

• Attitudes of genetics professionals toward the return of incidental results from exome and whole-genome sequencing. American journal of human genetics Yu, J. H., Harrell, T. M., Jamal, S. M., Tabor, H. K., Bamshad, M. J. 2014; 95 (1): 77–84

  Abstract

  Professional recommendations for the return of results from exome and whole-genome sequencing (ES/WGS) have been controversial. The lack of clear guidance about whether and, if so, how to return ES/WGS incidental results limits the extent to which individuals and families might benefit from ES/WGS. The perspectives of genetics professionals, particularly those at the forefront of using ES/WGS in clinics, are largely unknown. Data on stakeholder perspectives could help clarify how to weigh expert positions and recommendations. We conducted an online survey of 9,857 genetics professionals to learn their attitudes on the return of incidental results from ES/WGS and the recent American College of Medical Genetic and Genomics Recommendations for Reporting of Incidental Findings in Clinical Exome and Genome Sequencing. Of the 847 respondents, 760 completed the survey. The overwhelming majority of respondents thought that incidental ES/WGS results should be offered to adult patients (85%), healthy adults (75%), and the parents of a child with a medical condition (74%). The majority thought that incidental results about adult-onset conditions (62%) and carrier status (62%) should be offered to the parents of a child with a medical condition. About half thought that offered results should not be limited to those deemed clinically actionable. The vast majority (81%) thought that individual preferences should guide return. Genetics professionals' perspectives on the return of ES/WGS results differed substantially from current recommendations, underscoring the need to establish clear purpose for recommendations on the return of incidental ES/WGS results as professional societies grapple with developing and updating recommendations.

  View details for PubMedID 24975944

  View details for PubMedCentralID PMC4085580

• Mutations in PIEZO2 cause Gordon syndrome, Marden-Walker syndrome, and distal arthrogryposis type 5. American journal of human genetics McMillin, M. J., Beck, A. E., Chong, J. X., Shively, K. M., Buckingham, K. J., Gildersleeve, H. I., Aracena, M. I., Aylsworth, A. S., Bitoun, P., Carey, J. C., Clericuzio, C. L., Crow, Y. J., Curry, C. J., Devriendt, K., Everman, D. B., Fryer, A., Gibson, K., Giovannucci Uzielli, M. L., Graham, J. M., Hall, J. G., Hecht, J. T., Heidenreich, R. A., Hurst, J. A., Irani, S., Krapels, I. P., Leroy, J. G., Mowat, D., Plant, G. T., Robertson, S. P., Schorry, E. K., Scott, R. H., Seaver, L. H., Sherr, E., Splitt, M., Stewart, H., Stumpel, C., Temel, S. G., Weaver, D. D., Whiteford, M., Williams, M. S., Tabor, H. K., Smith, J. D., Shendure, J., Nickerson, D. A., Bamshad, M. J. 2014; 94 (5): 734–44

  Abstract

  Gordon syndrome (GS), or distal arthrogryposis type 3, is a rare, autosomal-dominant disorder characterized by cleft palate and congenital contractures of the hands and feet. Exome sequencing of five GS-affected families identified mutations in piezo-type mechanosensitive ion channel component 2 (PIEZO2) in each family. Sanger sequencing revealed PIEZO2 mutations in five of seven additional families studied (for a total of 10/12 [83%] individuals), and nine families had an identical c.8057G>A (p.Arg2686His) mutation. The phenotype of GS overlaps with distal arthrogryposis type 5 (DA5) and Marden-Walker syndrome (MWS). Using molecular inversion probes for targeted sequencing to screen PIEZO2, we found mutations in 24/29 (82%) DA5-affected families and one of two MWS-affected families. The presence of cleft palate was significantly associated with c.8057G>A (Fisher's exact test, adjusted p value < 0.0001). Collectively, although GS, DA5, and MWS have traditionally been considered separate disorders, our findings indicate that they are etiologically related and perhaps represent variable expressivity of the same condition.

  View details for PubMedID 24726473

  View details for PubMedCentralID PMC4067551

• Parent perspectives on pediatric genetic research and implications for genotype-driven research recruitment. Journal of empirical research on human research ethics : JERHRE Tabor, H. K., Brazg, T., Crouch, J., Namey, E. E., Fullerton, S. M., Beskow, L. M., Wilfond, B. S. 2011; 6 (4): 41–52

  Abstract

  As genetic research is increasingly conducted in children, it is important to understand how parents make decisions about enrolling their children and what they think about receiving their children's genetic research results. We conducted semi-structured phone interviews with 23 parents of children enrolled in genetic studies of autism or diabetes. Qualitative thematic analysis focused on two important components of genetic research and genotype-driven recruitment: participation in genetic research and return of results. Our findings suggest that parents' preferences and perspectives may be specific to their child's disease and the needs of the family as a whole. Assessing the expectations of target research populations will be beneficial for developing best practices for pediatric genetic research, return of results, and genotype-driven recruitment.

  View details for PubMedID 22228059

  View details for PubMedCentralID PMC3426316

• Challenges in the use of direct-to-consumer personal genome testing in children. The American journal of bioethics : AJOB Tabor, H. K., Kelley, M. 2009; 9 (6-7): 32–34

  View details for PubMedID 19998111

  View details for PubMedCentralID PMC2792567

• Ethical implications of array comparative genomic hybridization in complex phenotypes: points to consider in research GENETICS IN MEDICINE Tabor, H. K., Cho, M. K. 2007; 9 (9): 626-631

  Abstract

  As with many new diagnostic technologies, the recent rapid emergence of array comparative genome hybridization in clinical genetics provides the power to observe new biological phenomena before their clinical significance is well understood. This raises ethical issues for clinicians when applying the technologies. However, at this early stage of research and development on array comparative genome hybridization, the ethical implications of the conduct of research, as well as how research findings are presented and interpreted, should also be considered by the research, clinical, and ethics communities. These considerations are especially important in the use of array comparative genome hybridization to study complex and common traits. We examined recent publications on autism as an example of the application of array comparative genome hybridization to a complex phenotype. Our goal was to identify points to consider for researchers, clinicians, and patients/families to ensure responsible and ethical design, presentation, and interpretation of these kinds of studies.

  View details for DOI 10.1097/GIM.0b013e3181485688

  View details for Web of Science ID 000249640800010

  View details for PubMedID 17873651

  View details for PubMedCentralID PMC2220022

• Candidate-gene approaches for studying complex genetic traits: practical considerations NATURE REVIEWS GENETICS Tabor, H. K., Risch, N. J., Myers, R. M. 2002; 3 (5): 391-A396

  Abstract

  Association studies with candidate genes have been widely used for the study of complex diseases. However, this approach has been criticized because of non-replication of results and limits on its ability to include all possible causative genes and polymorphisms. These challenges have led to pessimism about the candidate-gene approach and about the genetic analysis of complex diseases in general. We believe that these criticisms can be usefully countered with an appeal to the principles of epidemiological investigation.

  View details for DOI 10.1038/nrg796

  View details for Web of Science ID 000175350000016

  View details for PubMedID 11988764