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Head ST, Leslie EJ, Cutler DJ, Epstein MP. POIROT: a powerful test for parent-of-origin effects in unrelated samples leveraging multiple phenotypes. Bioinformatics 2023; 39:btad199. [PMID: 37067493 PMCID: PMC10148680 DOI: 10.1093/bioinformatics/btad199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/18/2023] Open
Abstract
MOTIVATION There is widespread interest in identifying genetic variants that exhibit parent-of-origin effects (POEs) wherein the effect of an allele on phenotype expression depends on its parental origin. POEs can arise from different phenomena including genomic imprinting and have been documented for many complex traits. Traditional tests for POEs require family data to determine parental origins of transmitted alleles. As most genome-wide association studies (GWAS) sample unrelated individuals (where allelic parental origin is unknown), the study of POEs in such datasets requires sophisticated statistical methods that exploit genetic patterns we anticipate observing when POEs exist. We propose a method to improve discovery of POE variants in large-scale GWAS samples that leverages potential pleiotropy among multiple correlated traits often collected in such studies. Our method compares the phenotypic covariance matrix of heterozygotes to homozygotes based on a Robust Omnibus Test. We refer to our method as the Parent of Origin Inference using Robust Omnibus Test (POIROT) of multiple quantitative traits. RESULTS Through simulation studies, we compared POIROT to a competing univariate variance-based method which considers separate analysis of each phenotype. We observed POIROT to be well-calibrated with improved power to detect POEs compared to univariate methods. POIROT is robust to non-normality of phenotypes and can adjust for population stratification and other confounders. Finally, we applied POIROT to GWAS data from the UK Biobank using BMI and two cholesterol phenotypes. We identified 338 genome-wide significant loci for follow-up investigation. AVAILABILITY AND IMPLEMENTATION The code for this method is available at https://github.com/staylorhead/POIROT-POE.
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Affiliation(s)
- S Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, United States
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, United States
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2
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Feng YCA, Stanaway IB, Connolly JJ, Denny JC, Luo Y, Weng C, Wei WQ, Weiss ST, Karlson EW, Smoller JW. Psychiatric manifestations of rare variation in medically actionable genes: a PheWAS approach. BMC Genomics 2022; 23:385. [PMID: 35590255 PMCID: PMC9121574 DOI: 10.1186/s12864-022-08600-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As genomic sequencing moves closer to clinical implementation, there has been an increasing acceptance of returning incidental findings to research participants and patients for mutations in highly penetrant, medically actionable genes. A curated list of genes has been recommended by the American College of Medical Genetics and Genomics (ACMG) for return of incidental findings. However, the pleiotropic effects of these genes are not fully known. Such effects could complicate genetic counseling when returning incidental findings. In particular, there has been no systematic evaluation of psychiatric manifestations associated with rare variation in these genes. RESULTS Here, we leveraged a targeted sequence panel and real-world electronic health records from the eMERGE network to assess the burden of rare variation in the ACMG-56 genes and two psychiatric-associated genes (CACNA1C and TCF4) across common mental health conditions in 15,181 individuals of European descent. As a positive control, we showed that this approach replicated the established association between rare mutations in LDLR and hypercholesterolemia with no visible inflation from population stratification. However, we did not identify any genes significantly enriched with rare deleterious variants that confer risk for common psychiatric disorders after correction for multiple testing. Suggestive associations were observed between depression and rare coding variation in PTEN (P = 1.5 × 10-4), LDLR (P = 3.6 × 10-4), and CACNA1S (P = 5.8 × 10-4). We also observed nominal associations between rare variants in KCNQ1 and substance use disorders (P = 2.4 × 10-4), and APOB and tobacco use disorder (P = 1.1 × 10-3). CONCLUSIONS Our results do not support an association between psychiatric disorders and incidental findings in medically actionable gene mutations, but power was limited with the available sample sizes. Given the phenotypic and genetic complexity of psychiatric phenotypes, future work will require a much larger sequencing dataset to determine whether incidental findings in these genes have implications for risk of psychopathology.
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Affiliation(s)
- Yen-Chen A Feng
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, USA. .,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan. .,Master of Public Health Program, National Taiwan University, Taipei, Taiwan.
| | - Ian B Stanaway
- Division of Nephrology, School of Medicine, Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,All of Us Research Program, National Institutes of Health, Besthesda, MD, USA
| | - Yuan Luo
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott T Weiss
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth W Karlson
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Jordan W Smoller
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, USA. .,Center for Precision Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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3
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Tucker EJ, Grover SR, Robevska G, van den Bergen J, Hanna C, Sinclair AH. Identification of variants in pleiotropic genes causing "isolated" premature ovarian insufficiency: implications for medical practice. Eur J Hum Genet 2018; 26:1319-1328. [PMID: 29706645 PMCID: PMC6117257 DOI: 10.1038/s41431-018-0140-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/25/2018] [Accepted: 03/13/2018] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS) is increasingly being used in a clinical setting for the molecular diagnosis of patients with heterogeneous disorders, such as premature ovarian insufficiency (POI). We performed NGS of ~1000 candidate genes in four unrelated patients with POI. We discovered the genetic cause of "isolated" POI in two cases, both of which had causative variants in surprising genes. In the first case, a homozygous nonsense variant in NBN was causative. Recessive function-altering NBN variants typically cause Nijmegen breakage syndrome characterized by microcephaly, cancer predisposition, and immunodeficiency, none of which are evident in the patient. At a cellular level, we found evidence of chromosomal instability. In the second case, compound heterozygous variants in EIF2B2 were causative. Recessive EIF2B2 function-altering variants usually cause leukoencephalopathy with episodic decline. Subsequent MRI revealed subclinical neurological abnormalities. These cases demonstrate that variants in NBN and EIF2B2, which usually cause severe syndromes, can cause apparently isolated POI, and that (1) NGS can precede clinical diagnosis and guide patient management, (2) NGS can redefine the phenotypic spectrum of syndromes, and (3) NGS may make unanticipated diagnoses that must be sensitively communicated to patients. Although there is rigorous debate about the handling of secondary/incidental findings using NGS, there is little discussion of the management of causative pleiotropic gene variants that have broader implications than that for which genetic studies were sought.
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Affiliation(s)
- Elena J Tucker
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Sonia R Grover
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia
- Department of Paediatric and Adolescent Gynaecology, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Gorjana Robevska
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Jocelyn van den Bergen
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Chloe Hanna
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
- Department of Paediatric and Adolescent Gynaecology, Royal Children's Hospital, Melbourne, VIC, 3052, Australia
| | - Andrew H Sinclair
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, 3052, Australia.
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, 3052, Australia.
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4
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Fischer ST, Jiang Y, Broadaway KA, Conneely KN, Epstein MP. Powerful and robust cross-phenotype association test for case-parent trios. Genet Epidemiol 2018; 42:447-458. [PMID: 29460449 PMCID: PMC6013339 DOI: 10.1002/gepi.22116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 12/17/2022]
Abstract
There has been increasing interest in identifying genes within the human genome that influence multiple diverse phenotypes. In the presence of pleiotropy, joint testing of these phenotypes is not only biologically meaningful but also statistically more powerful than univariate analysis of each separate phenotype accounting for multiple testing. Although many cross-phenotype association tests exist, the majority of such methods assume samples composed of unrelated subjects and therefore are not applicable to family-based designs, including the valuable case-parent trio design. In this paper, we describe a robust gene-based association test of multiple phenotypes collected in a case-parent trio study. Our method is based on the kernel distance covariance (KDC) method, where we first construct a similarity matrix for multiple phenotypes and a similarity matrix for genetic variants in a gene; we then test the dependency between the two similarity matrices. The method is applicable to either common variants or rare variants in a gene, and resulting tests from the method are by design robust to confounding due to population stratification. We evaluated our method through simulation studies and observed that the method is substantially more powerful than standard univariate testing of each separate phenotype. We also applied our method to phenotypic and genotypic data collected in case-parent trios as part of the Genetics of Kidneys in Diabetes (GoKinD) study and identified a genome-wide significant gene demonstrating cross-phenotype effects that was not identified using standard univariate approaches.
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Affiliation(s)
- S. Taylor Fischer
- Department of Human Genetics and Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA
| | - Yunxuan Jiang
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA
| | - K. Alaine Broadaway
- Department of Human Genetics and Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA
| | - Karen N. Conneely
- Department of Human Genetics and Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA
| | - Michael P. Epstein
- Department of Human Genetics and Center for Computational and Quantitative Genetics, Emory University, Atlanta, GA
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5
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Lázaro-Muñoz G, Farrell MS, Crowley JJ, Filmyer DM, Shaughnessy RA, Josiassen RC, Sullivan PF. Improved ethical guidance for the return of results from psychiatric genomics research. Mol Psychiatry 2018; 23:15-23. [PMID: 29158581 PMCID: PMC5752587 DOI: 10.1038/mp.2017.228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/27/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022]
Abstract
There is an emerging consensus that genomic researchers should, at a minimum, offer to return to individual participants clinically valid, medically important and medically actionable genomic findings (for example, pathogenic variants in BRCA1) identified in the course of research. However, this is not a common practice in psychiatric genetics research. Furthermore, psychiatry researchers often generate findings that do not meet all of these criteria, yet there may be ethically compelling arguments to offer selected results. Here, we review the return of results debate in genomics research and propose that, as for genomic studies of other medical conditions, psychiatric genomics researchers should offer findings that meet the minimum criteria stated above. Additionally, if resources allow, psychiatry researchers could consider offering to return pre-specified 'clinically valuable' findings even if not medically actionable-for instance, findings that help corroborate a psychiatric diagnosis, and findings that indicate important health risks. Similarly, we propose offering 'likely clinically valuable' findings, specifically, variants of uncertain significance potentially related to a participant's symptoms. The goal of this Perspective is to initiate a discussion that can help identify optimal ways of managing the return of results from psychiatric genomics research.
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Affiliation(s)
- G Lázaro-Muñoz
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - M S Farrell
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - J J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweeden
| | - D M Filmyer
- Translational Neuroscience LLC, Conshohocken, PA, USA
| | - R A Shaughnessy
- Translational Neuroscience LLC, Conshohocken, PA, USA
- Department of Psychiatry, Drexel University College of Medicine, Philadelphia, PA, USA
| | - R C Josiassen
- Translational Neuroscience LLC, Conshohocken, PA, USA
| | - P F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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6
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Prince AER, Cadigan RJ, Henderson GE, Evans JP, Adams M, Coker-Schwimmer E, Penn DC, Van Riper M, Corbie-Smith G, Jonas DE. Is there evidence that we should screen the general population for Lynch syndrome with genetic testing? A systematic review. Pharmgenomics Pers Med 2017; 10:49-60. [PMID: 28260941 PMCID: PMC5325104 DOI: 10.2147/pgpm.s123808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The emerging dual imperatives of personalized medicine and technologic advances make population screening for preventable conditions resulting from genetic alterations a realistic possibility. Lynch syndrome is a potential screening target due to its prevalence, penetrance, and the availability of well-established, preventive interventions. However, while population screening may lower incidence of preventable conditions, implementation without evidence may lead to unintentional harms. We examined the literature to determine whether evidence exists that screening for Lynch-associated mismatch repair (MMR) gene mutations leads to improved overall survival, cancer-specific survival, or quality of life. Documenting evidence and gaps is critical to implementing genomic approaches in public health and guiding future research. MATERIALS AND METHODS Our 2014-2015 systematic review identified studies comparing screening with no screening in the general population, and controlled studies assessing analytic validity of targeted next-generation sequencing, and benefits or harms of interventions or screening. We conducted meta-analyses for the association between early or more frequent colonoscopies and health outcomes. RESULTS Twelve studies met our eligibility criteria. No adequate evidence directly addressed the main question or the harms of screening in the general population. Meta-analyses found relative reductions of 68% for colorectal cancer incidence (relative risk: 0.32, 95% confidence interval: 0.23-0.43, three cohort studies, 590 participants) and 78% for all-cause mortality (relative risk: 0.22, 95% confidence interval: 0.09-0.56, three cohort studies, 590 participants) for early or more frequent colonoscopies among family members of people with cancer who also had an associated MMR gene mutation. CONCLUSION Inadequate evidence exists examining harms and benefits of population-based screening for Lynch syndrome. Lack of evidence highlights the need for data that directly compare benefits and harms.
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Affiliation(s)
| | - R Jean Cadigan
- Center for Genomics and Society
- Department of Social Medicine
| | | | - James P Evans
- Center for Genomics and Society
- Department of Genetics
- Carolina Center for Genome Sciences
- Lineberger Comprehensive Cancer Center
- Department of Medicine
| | - Michael Adams
- Center for Genomics and Society
- Department of Genetics
| | | | | | - Marcia Van Riper
- Center for Genomics and Society
- School of Nursing, The University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Giselle Corbie-Smith
- Center for Genomics and Society
- Department of Social Medicine
- Department of Medicine
| | - Daniel E Jonas
- Center for Genomics and Society
- Department of Medicine
- Cecil G. Sheps Center for Health Services Research
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7
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Lázaro-Muñoz G, Conley JM, Davis AM, Prince AER, Cadigan RJ. Which Results to Return: Subjective Judgments in Selecting Medically Actionable Genes. Genet Test Mol Biomarkers 2017; 21:184-194. [PMID: 28146641 DOI: 10.1089/gtmb.2016.0397] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Advances in genomics have led to calls for returning information about medically actionable genes (MAGs) to patients, research subjects, biobank participants, and through screening programs, the general adult population. Which MAGs are returned affects the harms and benefits of every genetic testing endeavor. Despite published recommendations of selection criteria for MAGs to return, scant data exist regarding how decision makers actually apply such criteria. METHODS The process and criteria used by researchers when selecting MAGs for a preventive genomic sequencing program targeting the general adult population were examined. The authors observed and audio-recorded the gene selection meetings, and analyzed meeting transcripts, gene scoring sheets, and meeting handouts. RESULTS To select MAGs, the committee imported, from a preexisting project, "a semiquantitative metric" that scores genes on five criteria. Numerous subjective judgments and conceptual challenges in defining and applying the five criteria complicated the selection process. Criteria-related challenges also included the limited evidence available about facts fundamental to the scoring decisions and the emergence and application of criteria that were not part of the original metric. CONCLUSIONS When identifying MAGs appropriate for screening and return, decision makers must expect and prepare to address such issues as the inevitability of subjective judgments, limited evidence about fundamental decision-making elements, the conceptual complexity of defining criteria, and the emergence of unplanned criteria during the gene selection process.
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Affiliation(s)
- Gabriel Lázaro-Muñoz
- 1 Center for Genomics and Society, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,2 Center for Medical Ethics and Health Policy , Baylor College of Medicine, Houston, Texas
| | - John M Conley
- 1 Center for Genomics and Society, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,3 School of Law, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Arlene M Davis
- 1 Center for Genomics and Society, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,4 Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,5 Center for Bioethics, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Anya E R Prince
- 1 Center for Genomics and Society, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - R Jean Cadigan
- 1 Center for Genomics and Society, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,4 Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
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8
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Holm IA. Pediatric Issues in Return of Results and Incidental Findings: Weighing Autonomy and Best Interests. Genet Test Mol Biomarkers 2017; 21:155-158. [PMID: 28140662 DOI: 10.1089/gtmb.2016.0414] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nowhere are the ethical issues in genomic research more complex than in pediatrics. Balancing the sometime conflicting autonomy of the parent and the child, and the best interest of the family and the child, brings up many challenging issues. Addressing this balance, especially in the context of the child's developing maturity and comprehension, requires deep analysis and discussion. Issues discussed include the impact of genetic information on the family, parental versus the child's autonomy, the best interests of the child versus the family, potential limitations on the parents' right to know or not know information about their child, and changing role of the developing child in return of research results. Finally, a dynamic model will be proposed that takes into consideration the child's evolving role in consenting and return of results that can be adapted in different national contexts.
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Affiliation(s)
- Ingrid A Holm
- 1 Division of Genetics and Genomics, Boston Children's Hospital , Boston, Massachusetts.,2 The Manton Center for Orphan Disease Research , Boston Children's Hospital, Boston, Massachusetts.,3 Department of Pediatrics, Harvard Medical School , Boston, Massachusetts
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9
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Tucker EJ, Grover SR, Bachelot A, Touraine P, Sinclair AH. Premature Ovarian Insufficiency: New Perspectives on Genetic Cause and Phenotypic Spectrum. Endocr Rev 2016; 37:609-635. [PMID: 27690531 DOI: 10.1210/er.2016-1047] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Premature ovarian insufficiency (POI) is one form of female infertility, defined by loss of ovarian activity before the age of 40 and characterized by amenorrhea (primary or secondary) with raised gonadotropins and low estradiol. POI affects up to one in 100 females, including one in 1000 before the age of 30. Substantial evidence suggests a genetic basis for POI; however, the majority of cases remain unexplained, indicating that genes likely to be associated with this condition are yet to be discovered. This review discusses the current knowledge of the genetic basis of POI. We highlight genes typically known to cause syndromic POI that can be responsible for isolated POI. The role of mouse models in understanding POI pathogenesis is discussed, and a thorough list of candidate POI genes is provided. Identifying a genetic basis for POI has multiple advantages, such as enabling the identification of presymptomatic family members who can be offered counseling and cryopreservation of eggs before depletion, enabling personalized treatment based on the cause of an individual's condition, and providing better understanding of disease mechanisms that ultimately aid the development of improved treatments.
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Affiliation(s)
- Elena J Tucker
- Murdoch Children's Research Institute (E.J.T., S.R.G., A.H.S.), Royal Children's Hospital, Melbourne, VIC 3052 Australia; Department of Paediatrics (E.J.T., S.R.G., A.H.S.), University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatric and Adolescent Gynaecology (S.R.G.), Royal Children's Hospital, Melbourne, VIC 3052, Australia; Assistance Publique Hôpitaux de Paris, (A.B., P.T.), IE3M, Université Pierre et Marie Curie, Paris 6 University, Department of Endocrinology and Reproductive Medicine, Centre de Référence des Maladies Endocriniennes Rares de la Croissance et des Pathologies Gynécologiques Rares, Pitié-Salpêtrière Hospital, Université Pierre et Marie Curie, 75013 Paris, France; Institut National de la Santé et de la Recherche Médicale (A.B., P.T.), 75654 Paris, France
| | - Sonia R Grover
- Murdoch Children's Research Institute (E.J.T., S.R.G., A.H.S.), Royal Children's Hospital, Melbourne, VIC 3052 Australia; Department of Paediatrics (E.J.T., S.R.G., A.H.S.), University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatric and Adolescent Gynaecology (S.R.G.), Royal Children's Hospital, Melbourne, VIC 3052, Australia; Assistance Publique Hôpitaux de Paris, (A.B., P.T.), IE3M, Université Pierre et Marie Curie, Paris 6 University, Department of Endocrinology and Reproductive Medicine, Centre de Référence des Maladies Endocriniennes Rares de la Croissance et des Pathologies Gynécologiques Rares, Pitié-Salpêtrière Hospital, Université Pierre et Marie Curie, 75013 Paris, France; Institut National de la Santé et de la Recherche Médicale (A.B., P.T.), 75654 Paris, France
| | - Anne Bachelot
- Murdoch Children's Research Institute (E.J.T., S.R.G., A.H.S.), Royal Children's Hospital, Melbourne, VIC 3052 Australia; Department of Paediatrics (E.J.T., S.R.G., A.H.S.), University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatric and Adolescent Gynaecology (S.R.G.), Royal Children's Hospital, Melbourne, VIC 3052, Australia; Assistance Publique Hôpitaux de Paris, (A.B., P.T.), IE3M, Université Pierre et Marie Curie, Paris 6 University, Department of Endocrinology and Reproductive Medicine, Centre de Référence des Maladies Endocriniennes Rares de la Croissance et des Pathologies Gynécologiques Rares, Pitié-Salpêtrière Hospital, Université Pierre et Marie Curie, 75013 Paris, France; Institut National de la Santé et de la Recherche Médicale (A.B., P.T.), 75654 Paris, France
| | - Philippe Touraine
- Murdoch Children's Research Institute (E.J.T., S.R.G., A.H.S.), Royal Children's Hospital, Melbourne, VIC 3052 Australia; Department of Paediatrics (E.J.T., S.R.G., A.H.S.), University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatric and Adolescent Gynaecology (S.R.G.), Royal Children's Hospital, Melbourne, VIC 3052, Australia; Assistance Publique Hôpitaux de Paris, (A.B., P.T.), IE3M, Université Pierre et Marie Curie, Paris 6 University, Department of Endocrinology and Reproductive Medicine, Centre de Référence des Maladies Endocriniennes Rares de la Croissance et des Pathologies Gynécologiques Rares, Pitié-Salpêtrière Hospital, Université Pierre et Marie Curie, 75013 Paris, France; Institut National de la Santé et de la Recherche Médicale (A.B., P.T.), 75654 Paris, France
| | - Andrew H Sinclair
- Murdoch Children's Research Institute (E.J.T., S.R.G., A.H.S.), Royal Children's Hospital, Melbourne, VIC 3052 Australia; Department of Paediatrics (E.J.T., S.R.G., A.H.S.), University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatric and Adolescent Gynaecology (S.R.G.), Royal Children's Hospital, Melbourne, VIC 3052, Australia; Assistance Publique Hôpitaux de Paris, (A.B., P.T.), IE3M, Université Pierre et Marie Curie, Paris 6 University, Department of Endocrinology and Reproductive Medicine, Centre de Référence des Maladies Endocriniennes Rares de la Croissance et des Pathologies Gynécologiques Rares, Pitié-Salpêtrière Hospital, Université Pierre et Marie Curie, 75013 Paris, France; Institut National de la Santé et de la Recherche Médicale (A.B., P.T.), 75654 Paris, France
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10
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Hurlimann T, Robitaille J, Vohl MC, Godard B. Ethical considerations in the implementation of nutrigenetics/nutrigenomics. Per Med 2016; 14:75-83. [PMID: 29749825 DOI: 10.2217/pme-2016-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Awareness of ethical issues that may be raised by the implementation of nutrigenetic/nutrigenomic (NGx) testing and personalized nutrition, at an individual or a public health level, is crucial to ensure the latter's sound and effective implementation. NGx tests that are currently offered or developed have different natures and scopes. We provide an example of NGx testing on the MTHFR gene to illustrate the current challenges when it comes to grasp the meaning of the results of such testing. In addition, NGx testing is developed within an evolving landscape of new genomic technologies and occurs at a time when public health policies mainly focus on preventive and predictive healthcare, with an emphasis on increased individual responsibility. The ethical issues raised by such a context and the genetic nature of NGx testing both should be carefully evaluated.
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Affiliation(s)
- Thierry Hurlimann
- Public Health Research Institute - University of Montreal (IRSPUM), PO Box 6128, Station Centre-ville, Montreal, QC, H3C 3J7, Canada
| | - Julie Robitaille
- Institute of Nutrition & Functional Foods (INAF) & School of Nutrition, Université Laval, 2440 Hochelaga Blvd, Room 2729-N, Quebec City, QC, Canada
| | - Marie-Claude Vohl
- Institute of Nutrition & Functional Foods (INAF) & School of Nutrition, Université Laval, 2440 Hochelaga Blvd, Room 2729-N, Quebec City, QC, Canada
| | - Béatrice Godard
- Public Health Research Institute - University of Montreal (IRSPUM), PO Box 6128, Station Centre-ville, Montreal, QC, H3C 3J7, Canada
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11
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Fawcett GL, Karina Eterovic A. Identification of Genomic Somatic Variants in Cancer: From Discovery to Actionability. Adv Clin Chem 2016; 78:123-162. [PMID: 28057186 DOI: 10.1016/bs.acc.2016.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The perfect method to discover and validate actionable somatic variants in cancer has not yet been developed, yet significant progress has been made toward this goal. There have been huge increases in the throughput and cost of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) sequencing technologies that have led to the burgeoning possibility of using sequencing data in clinical settings. Discovery of somatic mutations is relatively simple and has been improved recently due to laboratory methods optimization, bioinformatics algorithms development, and the expansion of various databases of population genomic information. Tiered systems of evidence evaluation are currently being used to classify genomic variants for clinicians to more rapidly and accurately determine actionability of these aberrations. These efforts are complicated by the intricacies of communicating sequencing results to physicians and supporting its biological relevance, emphasizing the need for increasing education of clinicians and administrators, and the ongoing development of ethical standards for dealing with incidental results. This chapter will focus on general aspects of DNA and RNA tumor sequencing technologies, data analysis and interpretation, assessment of biological and clinical relevance of genomic aberrations, ethical aspects of germline sequencing, and how these factors impact cancer personalized care.
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Affiliation(s)
- G L Fawcett
- Institute for Personalized Cancer Therapy (IPCT) at University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - A Karina Eterovic
- Institute for Personalized Cancer Therapy (IPCT) at University of Texas M.D. Anderson Cancer Center, Houston, TX, United States.
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12
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Oetjens MT, Bush WS, Denny JC, Birdwell K, Kodaman N, Verma A, Dilks HH, Pendergrass SA, Ritchie MD, Crawford DC. Evidence for extensive pleiotropy among pharmacogenes. Pharmacogenomics 2016; 17:853-66. [PMID: 27249515 DOI: 10.2217/pgs-2015-0007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
AIM We sought to identify potential pleiotropy involving pharmacogenes. METHODS We tested 184 functional variants in 34 pharmacogenes for associations using a custom grouping of International Classification and Disease, Ninth Revision billing codes extracted from deidentified electronic health records of 6892 patients. RESULTS We replicated several associations including ABCG2 (rs2231142) and gout (p = 1.73 × 10(-7); odds ratio [OR]: 1.73; 95% CI: 1.40-2.12); and SLCO1B1 (rs4149056) and jaundice (p = 2.50 × 10(-4); OR: 1.67; 95% CI: 1.27-2.20). CONCLUSION In this systematic screen for phenotypic associations with functional variants, several novel genotype-phenotype combinations also achieved phenome-wide significance, including SLC15A2 rs1143672 and renal osteodystrophy (p = 2.67 × 10(-) (6); OR: 0.61; 95% CI: 0.49-0.75).
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Affiliation(s)
- Matthew T Oetjens
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - William S Bush
- Department of Epidemiology & Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37203, USA
| | - Kelly Birdwell
- Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Nuri Kodaman
- Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
| | - Anurag Verma
- Center for Systems Genomics, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holli H Dilks
- Sarah Cannon Research Institute, Nashville, TN 37203 USA
| | - Sarah A Pendergrass
- Center for Systems Genomics, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Marylyn D Ritchie
- Center for Systems Genomics, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dana C Crawford
- Department of Epidemiology & Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
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13
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Christensen KD, Roberts JS, Whitehouse PJ, Royal CD, Obisesan TO, Cupples LA, Vernarelli JA, Bhatt DL, Linnenbringer E, Butson MB, Fasaye GA, Uhlmann WR, Hiraki S, Wang N, Cook-Deegan R, Green RC. Disclosing Pleiotropic Effects During Genetic Risk Assessment for Alzheimer Disease: A Randomized Trial. Ann Intern Med 2016; 164:155-63. [PMID: 26810768 PMCID: PMC4979546 DOI: 10.7326/m15-0187] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Increasing use of genetic testing raises questions about disclosing secondary findings, including pleiotropic information. OBJECTIVE To determine the safety and behavioral effect of disclosing modest associations between apolipoprotein E (APOE) genotype and coronary artery disease (CAD) risk during APOE-based genetic risk assessments for Alzheimer disease (AD). DESIGN Randomized, multicenter equivalence clinical trial. (ClinicalTrials.gov: NCT00462917). SETTING 4 teaching hospitals. PARTICIPANTS 257 asymptomatic adults were enrolled, 69% of whom had 1 AD-affected first-degree relative. INTERVENTION Disclosure of genetic risk information about AD and CAD (AD+CAD) or AD only (AD-only). MEASUREMENTS Primary outcomes were Beck Anxiety Inventory (BAI) and Center for Epidemiologic Studies Depression Scale (CES-D) scores at 12 months. Secondary outcomes were all measures at 6 weeks and 6 months and test-related distress and health behavior changes at 12 months. RESULTS At 12 months, mean BAI scores were 3.5 in both the AD-only and AD+CAD groups (difference, 0.0 [95% CI, -1.0 to 1.0]), and mean CES-D scores were 6.4 and 7.1 in the AD-only and AD+CAD groups, respectively (difference, 0.7 [CI, -1.0 to 2.4]). Both confidence bounds fell within the equivalence margin of ±5 points. Among carriers of the APOE ε4 allele, distress was lower in the AD+CAD groups (difference, -4.8 [CI, -8.6 to -1.0]) (P = 0.031 for the interaction between group and APOE genotype). Participants in the AD+CAD groups also reported more health behavior changes, regardless of APOE genotype. LIMITATIONS Outcomes were self-reported by volunteers without severe anxiety, severe depression, or cognitive problems. Analyses omitted 33 randomly assigned participants. CONCLUSION Disclosure of pleiotropic information did not increase anxiety or depression and may have decreased distress among persons at increased risk for 2 conditions. Providing risk modification information about CAD improved health behaviors. Findings highlight the potential benefits of disclosure of secondary genetic findings when options exist for decreasing risk. PRIMARY FUNDING SOURCE National Human Genome Research Institute.
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Affiliation(s)
- Kurt D. Christensen
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - J. Scott Roberts
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Peter J. Whitehouse
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Charmaine D.M. Royal
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Thomas O. Obisesan
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - L. Adrienne Cupples
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Jacqueline A. Vernarelli
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Deepak L. Bhatt
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Erin Linnenbringer
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Melissa B. Butson
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Grace-Ann Fasaye
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Wendy R. Uhlmann
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Susan Hiraki
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Na Wang
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Robert Cook-Deegan
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
| | - Robert C. Green
- From Brigham and Women's Hospital and Boston University School of Public Health, Boston, Massachusetts; University of Michigan School of Public Health and University of Michigan Medical School, Ann Arbor, Michigan; Case Western Reserve University, Cleveland, Ohio; Duke University and Sanford School of Public Policy, Durham, North Carolina; Howard University Hospital, Washington, DC; Fairfield University, Fairfield, Connecticut; Washington University School of Medicine, St. Louis, Missouri
- Walter Reed National Military Medical Center, Bethesda, Maryland; and GeneDx, Gaithersburg, Maryland
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Ratbi I, Falkenberg KD, Sommen M, Al-Sheqaih N, Guaoua S, Vandeweyer G, Urquhart JE, Chandler KE, Williams SG, Roberts NA, El Alloussi M, Black GC, Ferdinandusse S, Ramdi H, Heimler A, Fryer A, Lynch SA, Cooper N, Ong KR, Smith CEL, Inglehearn CF, Mighell AJ, Elcock C, Poulter JA, Tischkowitz M, Davies SJ, Sefiani A, Mironov AA, Newman WG, Waterham HR, Van Camp G. Heimler Syndrome Is Caused by Hypomorphic Mutations in the Peroxisome-Biogenesis Genes PEX1 and PEX6. Am J Hum Genet 2015; 97:535-45. [PMID: 26387595 PMCID: PMC4596894 DOI: 10.1016/j.ajhg.2015.08.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/21/2015] [Indexed: 11/17/2022] Open
Abstract
Heimler syndrome (HS) is a rare recessive disorder characterized by sensorineural hearing loss (SNHL), amelogenesis imperfecta, nail abnormalities, and occasional or late-onset retinal pigmentation. We ascertained eight families affected by HS and, by using a whole-exome sequencing approach, identified biallelic mutations in PEX1 or PEX6 in six of them. Loss-of-function mutations in both genes are known causes of a spectrum of autosomal-recessive peroxisome-biogenesis disorders (PBDs), including Zellweger syndrome. PBDs are characterized by leukodystrophy, hypotonia, SNHL, retinopathy, and skeletal, craniofacial, and liver abnormalities. We demonstrate that each HS-affected family has at least one hypomorphic allele that results in extremely mild peroxisomal dysfunction. Although individuals with HS share some subtle clinical features found in PBDs, the diagnosis was not suggested by routine blood and skin fibroblast analyses used to detect PBDs. In conclusion, our findings define HS as a mild PBD, expanding the pleiotropy of mutations in PEX1 and PEX6.
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Affiliation(s)
- Ilham Ratbi
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Kim D Falkenberg
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Manou Sommen
- Department of Medical Genetics, University of Antwerp, Antwerp 2610, Belgium
| | - Nada Al-Sheqaih
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Soukaina Guaoua
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp 2610, Belgium
| | - Jill E Urquhart
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Simon G Williams
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Neil A Roberts
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Mustapha El Alloussi
- Département de Pédodontie-Prévention, Faculté de Médecine Dentaire, Université Mohammed V, BP 6212 Madinat Al Irfane, 10100 Rabat, Morocco; Service d'Odontologie, Hôpital Militaire d'Instruction Mohamed V, Avenue des Far, Hay Riad, 10100 Rabat, Morocco
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Hind Ramdi
- Département de Pédodontie-Prévention, Faculté de Médecine Dentaire, Université Mohammed V, BP 6212 Madinat Al Irfane, 10100 Rabat, Morocco
| | - Audrey Heimler
- Division of Human Genetics, Schneider Children's Hospital of Long Island Jewish Medical Center, New Hyde Park, NY 11042, USA
| | - Alan Fryer
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool L8 7SS, UK
| | - Sally-Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland; Department of Genetics, Children's University Hospital, Dublin 12, Ireland
| | - Nicola Cooper
- West Midlands Regional Genetics Service, Birmingham Women's Hospital NHS Trust, Birmingham B15 2TG, UK
| | - Kai Ren Ong
- West Midlands Regional Genetics Service, Birmingham Women's Hospital NHS Trust, Birmingham B15 2TG, UK
| | - Claire E L Smith
- Leeds Institute of Biomedical and Clinical Sciences, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Christopher F Inglehearn
- Leeds Institute of Biomedical and Clinical Sciences, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Alan J Mighell
- Leeds Institute of Biomedical and Clinical Sciences, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, UK; School of Dentistry, University of Leeds, Leeds LS2 9JT, UK
| | - Claire Elcock
- Academic Unit of Oral Health and Development, School of Clinical Dentistry, University of Sheffield, S10 2TA, UK
| | - James A Poulter
- Leeds Institute of Biomedical and Clinical Sciences, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Marc Tischkowitz
- Department of Medical Genetics and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Clinical Genetics, East Anglian Regional Genetics Service, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Sally J Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Abdelaziz Sefiani
- Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V, 10100 Rabat, Morocco; Département de Génétique Médicale, Institut National d'Hygiène, BP 769 Agdal, 10090 Rabat, Morocco
| | | | - William G Newman
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, Antwerp 2610, Belgium.
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15
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Roche MI, Berg JS. Incidental Findings with Genomic Testing: Implications for Genetic Counseling Practice. CURRENT GENETIC MEDICINE REPORTS 2015; 3:166-176. [PMID: 26566463 PMCID: PMC4633435 DOI: 10.1007/s40142-015-0075-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This paper summarizes the current controversies surrounding the identification and disclosure of "incidental" or "secondary" findings from genomic sequencing and the implications for genetic counseling practice. The rapid expansion of clinical sequencing has influenced the ascertainment and return of incidental findings, while empiric data to inform best practices are still being generated. Using the North Carolina Clinical Genomic Evaluation by Next Generation Exome Sequencing (NCGENES) research project as an example, we discuss the implications of different models of consent and their impact on patient decisions.
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Affiliation(s)
- Myra I. Roche
- />Department of Pediatrics and Genetics, School of Medicine, The University of North Carolina at Chapel Hill, 326A MacNider, Chapel Hill, NC 27599-7240 USA
| | - Jonathan S. Berg
- />Department of Genetics, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599-7264 USA
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16
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Christenhusz GM, Devriendt K, Van Esch H, Dierickx K. Ethical signposts for clinical geneticists in secondary variant and incidental finding disclosure discussions. MEDICINE, HEALTH CARE, AND PHILOSOPHY 2015; 18:361-370. [PMID: 25407129 DOI: 10.1007/s11019-014-9611-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
While ethical and empirical interest in so-called secondary variants and incidental findings in clinical genetics contexts is growing, critical reflection on the ethical foundations of the various recommendations proposed is thus far largely lacking. We examine and critique the ethical justifications of the three most prominent disclosure positions: briefly, the clinical geneticist decides, a joint decision, and the patient decides. Subsequently, instead of immediately developing a new disclosure option, we explore relevant foundational ethical values and norms, drawing on the normative and empirical ethical literature. Four ethical signposts are thereby developed to help guide disclosure discussions. These are: respectful sharing of the clinician's expertise; transparent communication; epistemic modesty; and respect for the embedded nature of the patient. We conclude by considering the most common current disclosure positions in the light of the four ethical signposts.
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Crawford DC, Goodloe R, Farber-Eger E, Boston J, Pendergrass SA, Haines JL, Ritchie MD, Bush WS. Leveraging Epidemiologic and Clinical Collections for Genomic Studies of Complex Traits. Hum Hered 2015. [PMID: 26201699 DOI: 10.1159/000381805] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND/AIMS Present-day limited resources demand DNA and phenotyping alternatives to the traditional prospective population-based epidemiologic collections. METHODS To accelerate genomic discovery with an emphasis on diverse populations, we--as part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study--accessed all non-European American samples (n = 15,863) available in BioVU, the Vanderbilt University biorepository linked to de-identified electronic medical records, for genomic studies as part of the larger Population Architecture using Genomics and Epidemiology (PAGE) I study. Given previous studies have cautioned against the secondary use of clinically collected data compared with epidemiologically collected data, we present here a characterization of EAGLE BioVU, including the billing and diagnostic (ICD-9) code distributions for adult and pediatric patients as well as comparisons made for select health metrics (body mass index, glucose, HbA1c, HDL-C, LDL-C, and triglycerides) with the population-based National Health and Nutrition Examination Surveys (NHANES) linked to DNA samples (NHANES III, n = 7,159; NHANES 1999-2002, n = 7,839). RESULTS Overall, the distributions of billing and diagnostic codes suggest this clinical sample is a mixture of healthy and sick patients like that expected for a contemporary American population. CONCLUSION Little bias is observed among health metrics, suggesting this clinical collection is suitable for genomic studies along with traditional epidemiologic cohorts.
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Affiliation(s)
- Dana C Crawford
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
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18
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Compare and contrast: a cross-national study across UK, USA and Greek experts regarding return of incidental findings from clinical sequencing. Eur J Hum Genet 2015; 24:344-9. [PMID: 26059844 DOI: 10.1038/ejhg.2015.132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 11/09/2022] Open
Abstract
Return of incidental findings (IFs) from clinical sequencing has become a hotly debated topic over the past year. Efforts are being made by several bodies to provide guidance at both national and international levels; however, no studies comparing attitudes of experts across different countries have been published so far. Our goal was to investigate attitudes towards return of IFs from clinical sequencing across UK, USA and Greek experts. Thirty in-depth interviews were conducted with genetics and genomic experts with different backgrounds. Our study revealed more differences when experts were compared according to their professional background than their country. General principles guiding the decision-making and the feedback process were common across all experts but the details of integrating these tests might vary as different professionals reported different needs and attitudes.
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Wang Y, Liu A, Mills JL, Boehnke M, Wilson AF, Bailey-Wilson JE, Xiong M, Wu CO, Fan R. Pleiotropy analysis of quantitative traits at gene level by multivariate functional linear models. Genet Epidemiol 2015; 39:259-75. [PMID: 25809955 PMCID: PMC4443751 DOI: 10.1002/gepi.21895] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 01/28/2015] [Accepted: 01/28/2015] [Indexed: 10/23/2022]
Abstract
In genetics, pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. A common approach is to analyze the phenotypic traits separately using univariate analyses and combine the test results through multiple comparisons. This approach may lead to low power. Multivariate functional linear models are developed to connect genetic variant data to multiple quantitative traits adjusting for covariates for a unified analysis. Three types of approximate F-distribution tests based on Pillai-Bartlett trace, Hotelling-Lawley trace, and Wilks's Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants in one genetic region. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and optimal sequence kernel association test (SKAT-O). Extensive simulations were performed to evaluate the false positive rates and power performance of the proposed models and tests. We show that the approximate F-distribution tests control the type I error rates very well. Overall, simultaneous analysis of multiple traits can increase power performance compared to an individual test of each trait. The proposed methods were applied to analyze (1) four lipid traits in eight European cohorts, and (2) three biochemical traits in the Trinity Students Study. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and SKAT-O for the three biochemical traits. The approximate F-distribution tests of the proposed functional linear models are more sensitive than those of the traditional multivariate linear models that in turn are more sensitive than SKAT-O in the univariate case. The analysis of the four lipid traits and the three biochemical traits detects more association than SKAT-O in the univariate case.
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Affiliation(s)
- Yifan Wang
- Biostatistics and Bioinformatics Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Aiyi Liu
- Biostatistics and Bioinformatics Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James L. Mills
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alexander F. Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Momiao Xiong
- Human Genetics Center, University of Texas - Houston, Houston, Texas, United States of America
| | - Colin O. Wu
- Office of Biostatistics Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ruzong Fan
- Biostatistics and Bioinformatics Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
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20
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Sorace J, Rogers M, Millman M, Rogers D, Price K, Queen S, Worrall C, Kelman J. A Comparison of Disease Burden Between Twins and Control Pairs in Medicare: Quantification of Heredity's Role in Human Health. Popul Health Manag 2015; 18:383-91. [PMID: 25658666 DOI: 10.1089/pop.2014.0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To quantify heredity's effects on the burden of illness in the Medicare population, this study linked information between participants in a research twin registry to a comprehensive set of Medicare claims. To calculate disease categories, the authors used the Centers for Medicare & Medicaid Services Hierarchical Conditions Categories (HCC) model that was developed to risk adjust Medicare's capitation payments to private health care plans based on the health expenditure risk of their enrollees. Using the Medicare database, 2 sets of unrelated but demographically matched control pairs (MCPs) were generated, one specific for the monozygotic twin population and the second specific for the dizygotic twin population. The concordance and correlation rates of the 70 HCC categories for the 2 twin populations, in comparison to their corresponding MCP, was then calculated using Medicare claims data from 1991 through 2011. When indicated, HCCs for which there was a statistically significant difference between the twin and corresponding MCP control group were analyzed by calculating concordance and correlation rates of the International Classification of Diseases, Ninth Revision codes that compose the HCC. Findings reveal that monozygotic twins share 6.5% more HCC disease categories than their MCP while dizygotic twins share 3.8% more HCC disease categories than their MCP. Atrial fibrillation is a highly heritable disease category, a finding consistent with prior literature describing the heritability of the cardiac arrhythmias. These findings are consistent with qualitative assessments of heredity's role found in previous models of population health, and provide both novel methods and quantitative evidence to support future model development.
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Affiliation(s)
- James Sorace
- 1 Office of Science and Data Policy , Washington, D.C
| | | | | | | | | | - Susan Queen
- 1 Office of Science and Data Policy , Washington, D.C
| | - Chris Worrall
- 3 Centers for Medicare & Medicaid Services , Washington, D.C
| | - Jeffrey Kelman
- 3 Centers for Medicare & Medicaid Services , Washington, D.C
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21
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Newman WG, Black GC. Delivery of a clinical genomics service. Genes (Basel) 2014; 5:1001-17. [PMID: 25383561 PMCID: PMC4276923 DOI: 10.3390/genes5041001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 01/30/2023] Open
Abstract
Over the past five years, next generation sequencing has revolutionised the discovery of genes responsible for rare inherited diseases previously resistant to traditional discovery techniques. This review considers how this new technology is being introduced into clinical practice to aid diagnosis and improve the clinical management of individuals and families affected by rare diseases where access to genetic testing was previously limited. We compare and contrast the different approaches that have been adopted including panel based tests, exome and genome sequencing. We provide insights from our own clinical practice demonstrating the challenges and benefits of this new technology.
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Affiliation(s)
- William G Newman
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, M13 9WL, UK.
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, M13 9WL, UK.
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22
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Prince AER, Berg JS, Evans JP, Jonas DE, Henderson G. Genomic screening of the general adult population: key concepts for assessing net benefit with systematic evidence reviews. Genet Med 2014; 17:441-3. [PMID: 25232850 PMCID: PMC4387105 DOI: 10.1038/gim.2014.129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/13/2014] [Indexed: 11/09/2022] Open
Affiliation(s)
- Anya E R Prince
- Center for Genomics and Society, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- 1] Center for Genomics and Society, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [2] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [4] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James P Evans
- 1] Center for Genomics and Society, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [2] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [4] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel E Jonas
- 1] Center for Genomics and Society, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [2] Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [3] Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gail Henderson
- 1] Center for Genomics and Society, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA [2] Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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23
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Prince AER, Roche MI. Genetic information, non-discrimination, and privacy protections in genetic counseling practice. J Genet Couns 2014; 23:891-902. [PMID: 25063358 DOI: 10.1007/s10897-014-9743-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/04/2014] [Indexed: 11/29/2022]
Abstract
The passage of the Genetic Information Non Discrimination Act (GINA) was hailed as a pivotal achievement that was expected to calm the fears of both patients and research participants about the potential misuse of genetic information. However, 6 years later, patient and provider awareness of legal protections at both the federal and state level remains discouragingly low, thereby, limiting their potential effectiveness. The increasing demand for genetic testing will expand the number of individuals and families who could benefit from obtaining accurate information about the privacy and anti-discriminatory protections that GINA and other laws extend. In this paper we describe legal protections that are applicable to individuals seeking genetic counseling, review the literature on patient and provider fears of genetic discrimination and examine their awareness and understandings of existing laws, and summarize how genetic counselors currently discuss genetic discrimination. We then present three genetic counseling cases to illustrate issues of genetic discrimination and provide relevant information on applicable legal protections. Genetic counselors have an unprecedented opportunity, as well as the professional responsibility, to disseminate accurate knowledge about existing legal protections to their patients. They can strengthen their effectiveness in this role by achieving a greater knowledge of current protections including being able to identify specific steps that can help protect genetic information.
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Affiliation(s)
- Anya E R Prince
- Center for Genomics and Society, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
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24
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Pharmacogenomics: Current State-of-the-Art. Genes (Basel) 2014; 5:430-43. [PMID: 24865298 PMCID: PMC4094941 DOI: 10.3390/genes5020430] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 05/05/2014] [Accepted: 05/08/2014] [Indexed: 02/04/2023] Open
Abstract
The completion of the human genome project 10 years ago was met with great optimism for improving drug therapy through personalized medicine approaches, with the anticipation that an era of genotype-guided patient prescribing was imminent. To some extent this has come to pass and a number of key pharmacogenomics markers of inter-individual drug response, for both safety and efficacy, have been identified and subsequently been adopted in clinical practice as pre-treatment genetic tests. However, the universal application of genetics in treatment guidance is still a long way off. This review will highlight important pharmacogenomic discoveries which have been facilitated by the human genome project and other milestone projects such as the International HapMap and 1000 genomes, and by the continued development of genotyping and sequencing technologies, including rapid point of care pre-treatment genetic testing. However, there are still many challenges to implementation for the many other reported biomarkers which continue to languish within the discovery phase. As technology advances over the next 10 years, and the costs fall, the field will see larger genetic data sets, including affordable whole genome sequences, which will, it is hoped, improve patient outcomes through better diagnostic, prognostic and predictive biomarkers.
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25
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Li A, Meyre D. Jumping on the Train of Personalized Medicine: A Primer for Non- Geneticist Clinicians: Part 3. Clinical Applications in the Personalized Medicine Area. CURRENT PSYCHIATRY REVIEWS 2014; 10:118-132. [PMID: 25598768 PMCID: PMC4287884 DOI: 10.2174/1573400510666140630170549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/27/2014] [Accepted: 05/29/2014] [Indexed: 12/17/2022]
Abstract
The rapid decline of sequencing costs brings hope that personal genome sequencing will become a common feature of medical practice. This series of three reviews aim to help non-geneticist clinicians to jump into the fast-moving field of personalized genetic medicine. In the first two articles, we covered the fundamental concepts of molecular genetics and the methodologies used in genetic epidemiology. In this third article, we discuss the evolution of personalized medicine and illustrate the most recent success in the fields of Mendelian and complex human diseases. We also address the challenges that currently limit the use of personalized medicine to its full potential.
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Affiliation(s)
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON L8N 3Z5, Canada
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26
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Olson JE, Bielinski SJ, Ryu E, Winkler EM, Takahashi PY, Pathak J, Cerhan JR. Biobanks and personalized medicine. Clin Genet 2014; 86:50-5. [PMID: 24588254 DOI: 10.1111/cge.12370] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/27/2014] [Accepted: 02/27/2014] [Indexed: 12/21/2022]
Abstract
We provide a mini-review of how biobanks can support clinical genetics in the era of personalized medicine. We discuss types of biobanks, including disease specific and general biobanks not focused on one disease. We present considerations in setting up a biobank, including consenting and governance, biospecimens, risk factor and related data, informatics, and linkage to electronic health records for phenotyping. We also discuss the uses of biobanks and ongoing considerations, including genotype-driven recruitment, investigations of gene-environment associations, and the re-use of data generated from studies. Finally, we present a brief discussion of some of the unresolved issues, such as return of research results and sustaining biobanks over time. In summary, carefully designed biobanks can provide critical research and infrastructure support for clinical genetics in the era of personalized medicine.
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Affiliation(s)
- J E Olson
- Department of Health Sciences Research, Rochester, MN, USA
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