401
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Abstract
Genetics has been revolutionised by recent technologies. The latest addition to these advances is next-generation sequencing, which is set to transform clinical diagnostics in every branch of medicine. In the research arena this has already been instrumental in identifying hundreds of novel genetic syndromes, making a molecular diagnosis possible for the first time in numerous refractory cases. However, the pace of change has left many clinicians bewildered by new terminology and the implications of next-generation sequencing for their clinical practice. The rapid developments have also left many diagnostic laboratories struggling to implement these new technologies with limited resources. This review explains the basic concepts of next-generation sequencing, gives examples of its role in clinically applied research and examines the challenges of its introduction into clinical practice.
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402
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Freeze HH, Chong JX, Bamshad MJ, Ng BG. Solving glycosylation disorders: fundamental approaches reveal complicated pathways. Am J Hum Genet 2014; 94:161-75. [PMID: 24507773 DOI: 10.1016/j.ajhg.2013.10.024] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Indexed: 11/30/2022] Open
Abstract
Over 100 human genetic disorders result from mutations in glycosylation-related genes. In 2013, a new glycosylation disorder was reported every 17 days. This trend will probably continue given that at least 2% of the human genome encodes glycan-biosynthesis and -recognition proteins. Established biosynthetic pathways provide many candidate genes, but finding unanticipated mutated genes will offer new insights into glycosylation. Simple glycobiomarkers can be used in narrowing the candidates identified by exome and genome sequencing, and those can be validated by glycosylation analysis of serum or cells from affected individuals. Model organisms will expand the understanding of these mutations' impact on glycosylation and pathology. Here, we highlight some recently discovered glycosylation disorders and the barriers, breakthroughs, and surprises they presented. We predict that some glycosylation disorders might occur with greater frequency than current estimates of their prevalence. Moreover, the prevalence of some disorders differs substantially between European and African Americans.
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Affiliation(s)
- Hudson H Freeze
- Human Genetics Program, Sanford Children's Health Research Center, Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA.
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Bobby G Ng
- Human Genetics Program, Sanford Children's Health Research Center, Sanford Burnham Medical Research Institute, La Jolla, CA 92037, USA
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403
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Affiliation(s)
- Raffaele Badolato
- Department of Experimental and Clinical Sciences, Institute of Molecular Medicine "Angelo Nocivelli", University of Brescia, Brescia, Italy.
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404
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van Zelst-Stams WA, Scheffer H, Veltman JA. Clinical exome sequencing in daily practice: 1,000 patients and beyond. Genome Med 2014; 6:2. [PMID: 24456652 PMCID: PMC3978472 DOI: 10.1186/gm521] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Wendy A van Zelst-Stams
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, 6500 HC, Nijmegen, The Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, 6500 HC, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, 6500 HC, Nijmegen, The Netherlands
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405
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Swanson A, Ramos E, Snyder H. Next Generation Sequencing is the Impetus for the Next Generation of Laboratory-Based Genetic Counselors. J Genet Couns 2014; 23:647-54. [DOI: 10.1007/s10897-013-9684-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/12/2013] [Indexed: 02/04/2023]
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406
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Boycott KM, Dyment DA, Sawyer SL, Vanstone MR, Beaulieu CL. Identification of Genes for Childhood Heritable Diseases. Annu Rev Med 2014; 65:19-31. [DOI: 10.1146/annurev-med-101712-122108] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kym M. Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1 Canada; , , , , ,
| | - David A. Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1 Canada; , , , , ,
| | - Sarah L. Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1 Canada; , , , , ,
| | - Megan R. Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1 Canada; , , , , ,
| | - Chandree L. Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, K1H 8L1 Canada; , , , , ,
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407
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Landau YE, Lichter-Konecki U, Levy HL. Genomics in newborn screening. J Pediatr 2014; 164:14-9. [PMID: 23992678 DOI: 10.1016/j.jpeds.2013.07.028] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/28/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Yuval E Landau
- Division of Genetics, Boston Children's Hospital and the Department of Pediatrics, Harvard Medical School, Boston, MA; Pediatric Neurology Unit, Dana Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Uta Lichter-Konecki
- Division of Genetics and Metabolism, Children's National Medical Center and the Department of Pediatrics, The George Washington University School of Medicine, Washington, DC
| | - Harvey L Levy
- Division of Genetics, Boston Children's Hospital and the Department of Pediatrics, Harvard Medical School, Boston, MA.
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408
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Feero WG, Guttmacher AE. Genomics, personalized medicine, and pediatrics. Acad Pediatr 2014; 14:14-22. [PMID: 24369865 PMCID: PMC4227880 DOI: 10.1016/j.acap.2013.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 06/17/2013] [Accepted: 06/27/2013] [Indexed: 12/22/2022]
Abstract
Genomic discoveries are advancing biomedicine at an ever-increasing pace. Pediatrics is near the epicenter of these discoveries, which are revising our understanding of the genome and its function. Since the completion of the Human Genome Project in 2003, dramatic reductions in the cost of genotyping, and more recently sequencing, have permitted the study of the genomes of a great number of species as well as humans. These studies have led to insights on gene regulation and the complex interplay of factors responsible for normal development and biology. Study of single-gene disorders has greatly benefited from the genomics revolution and tests are now available for well over 2000 Mendelian conditions; availability of these tests are changing screening and diagnosis paradigms for rare conditions. Genomics is also yielding an increased understanding of common conditions such as diabetes, obesity, asthma, cancers, and mental health conditions. Personalized medicine, an approach to care in which an individual's genomic information is used to help tailor interventions to maximize health outcomes, is rapidly becoming a reality for a variety of conditions. Though challenges remain in translating new genomic insights into improved patient health, today's pediatricians and their patients will increasingly benefit from this watershed moment in the biological sciences.
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Affiliation(s)
| | - Alan E Guttmacher
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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409
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Borry P, Shabani M, Howard HC. Is There a Right Time to Know? The Right Not to Know and Genetic Testing in Children. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2014; 42:19-27. [PMID: 26767473 DOI: 10.1111/jlme.12115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The increasing implementation of next-generation sequencing technologies in the clinical context and the expanding commercial offer of genetic tests directly-toconsumers has increased the availability of previously inaccessible genetic information. A particular concern in both situations is how the volume of novel information will affect the processing of genetic and genomic information from minors. For minors, it is argued that in the provision of genetic testing, their "right not to know" should be respected as much as possible. Testing a minor early in life eliminates the possibility for the minor to make use of his or her "right not to know." The article discusses the theoretical underpinnings of the right not know, analyzes reasons why various direct-to-consumer companies process samples from minors, and discusses the right not to know in relation to common complex disorders in a pediatric population.
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Affiliation(s)
- Pascal Borry
- Assistant Professor of Bioethics at the Centre for Biomedical Ethics and Law (University of Leuven, Belgium)
| | - Mahsa Shabani
- Ph.D. researcher at the Center for Biomedical Ethics and Law (University of Leuven, Belgium)
| | - Heidi Carmen Howard
- Assistant Professor at Radboud University Medical Centre in Nijmegen, the Netherlands
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410
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Abstract
Structural genomics efforts focused on the human proteome have had three aims: to understand the structural and functional variations within protein families; to understand the structural basis of disease and genetic variation; and to determine the structures of human integral membrane proteins. The overarching theme is to advance the understanding of human health and to provide a structural platform to aid in the development of therapeutics. A decade or more of work in this field has identified optimal experimental strategies that can be used to expedite expression and crystallization of human proteins-and we provide some guidance to this end.
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Affiliation(s)
- Khan Tanjid Osman
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 706, Toronto, ON, Canada, M5G 1L7
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411
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Ormond KE, Cho MK. Translating personalized medicine using new genetic technologies in clinical practice: the ethical issues. Per Med 2014; 11:211-222. [PMID: 25221608 PMCID: PMC4160120 DOI: 10.2217/pme.13.104] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The integration of new genetic technologies into clinical practice holds great promise for the personalization of medical care, particularly the use of large-scale DNA sequencing for genome-wide genetic testing. However, these technologies also yield unprecedented amounts of information whose clinical implications are not fully understood, and we are still developing technical standards for measuring sequence accuracy. These technical and clinical challenges raise ethical issues that are similar to but qualitatively different from those that we are accustomed to dealing with for traditional medical genetics. The sheer amount of information afforded by genome sequencing requires rethinking of how to implement core ethical principles including, but not limited to: informed consent, privacy and data ownership and sharing, technology regulation, issues of access, particularly as new technology is integrated into clinical practice, and issues of potential stigma and impact on perceptions of disability. In this article, we will review the issues of informed consent, privacy, data ownership and technology regulation as they relate to the emerging field of personalized medicine and genomics.
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Affiliation(s)
- Kelly E Ormond
- Department of Genetics, Mail Stop-5208, Stanford University, Stanford, CA 94305-5208, USA
- Stanford Center for Biomedical Ethics, 1215 Welch Road, Modular A, Stanford, CA 94305-5417, USA
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics, 1215 Welch Road, Modular A, Stanford, CA 94305-5417, USA
- Department of Pediatrics, 300 Pasteur Drive, Stanford, CA 94305-5208, USA
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412
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George AL. Recent genetic discoveries implicating ion channels in human cardiovascular diseases. Curr Opin Pharmacol 2013; 15:47-52. [PMID: 24721653 DOI: 10.1016/j.coph.2013.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 12/19/2022]
Abstract
The term 'channelopathy' refers to human genetic disorders caused by mutations in genes encoding ion channels or their interacting proteins. Recent advances in this field have been enabled by next-generation DNA sequencing strategies such as whole exome sequencing with several intriguing and unexpected discoveries. This review highlights important discoveries implicating ion channels or ion channel modulators in cardiovascular disorders including cardiac arrhythmia susceptibility, cardiac conduction phenotypes, pulmonary and systemic hypertension. These recent discoveries further emphasize the importance of ion channels in the pathophysiology of human disease and as important druggable targets.
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Affiliation(s)
- Alfred L George
- Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA.
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413
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Paria N, Copley LA, Herring JA, Kim HKW, Richards BS, Sucato DJ, Wise CA, Rios JJ. Whole-exome sequencing: discovering genetic causes of orthopaedic disorders. J Bone Joint Surg Am 2013; 95:e1851-8. [PMID: 24306708 DOI: 10.2106/jbjs.l.01620] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Nandina Paria
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research (N.P., H.K.W.K., C.A.W., and J.J.R.), Department of Orthopaedics (L.A.C., J.A.H, B.S.R., and D.J.S.), Texas Scottish Rite Hospital for Children, 2222 Welborn Street, Dallas, TX 75219. E-mail address for J.J. Rios:
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414
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Kim ES, Ahn EH, Chung E, Kim DH. Recent advances in nanobiotechnology and high-throughput molecular techniques for systems biomedicine. Mol Cells 2013; 36:477-84. [PMID: 24258011 PMCID: PMC3887963 DOI: 10.1007/s10059-013-0304-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 10/20/2013] [Indexed: 01/29/2023] Open
Abstract
Nanotechnology-based tools are beginning to emerge as promising platforms for quantitative high-throughput analysis of live cells and tissues. Despite unprecedented progress made over the last decade, a challenge still lies in integrating emerging nanotechnology-based tools into macroscopic biomedical apparatuses for practical purposes in biomedical sciences. In this review, we discuss the recent advances and limitations in the analysis and control of mechanical, biochemical, fluidic, and optical interactions in the interface areas of nanotechnologybased materials and living cells in both in vitro and in vivo settings.
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Affiliation(s)
- Eung-Sam Kim
- Department of Bioengineering, University of Washington, Seattle, WA 98195,
USA
- Department of Medical System Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Eun Hyun Ahn
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA 98195,
USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109,
USA
| | - Euiheon Chung
- Department of Medical System Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
- School of Mechatronics, Gwangju Institute of Science and Technology, Gwangju 500-712,
Korea
| | - Deok-Ho Kim
- Department of Bioengineering, University of Washington, Seattle, WA 98195,
USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109,
USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA 98109,
USA
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415
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Takeichi T, Nanda A, Liu L, Salam A, Campbell P, Fong K, Akiyama M, Ozoemena L, Stone KL, Al-Ajmi H, Simpson MA, McGrath JA. Impact of next generation sequencing on diagnostics in a genetic skin disease clinic. Exp Dermatol 2013; 22:825-31. [DOI: 10.1111/exd.12276] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Takuya Takeichi
- St John's Institute of Dermatology; King's College London; Guy's Hospital; London UK
- Department of Dermatology; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Arti Nanda
- As'ad Al-Hamad Dermatology Center; Al-Sabah Hospital; Kuwait City Kuwait
| | - Lu Liu
- The National Diagnostic EB Laboratory GSTS Pathology St Thomas' Hospital; London UK
| | - Amr Salam
- St John's Institute of Dermatology; King's College London; Guy's Hospital; London UK
| | - Patrick Campbell
- St John's Institute of Dermatology; King's College London; Guy's Hospital; London UK
| | - Kenneth Fong
- St John's Institute of Dermatology; King's College London; Guy's Hospital; London UK
| | - Masashi Akiyama
- Department of Dermatology; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Linda Ozoemena
- The National Diagnostic EB Laboratory GSTS Pathology St Thomas' Hospital; London UK
| | - Kristina L. Stone
- Department of Genetics and Molecular Medicine; King's College London; Guy's Hospital; London UK
| | - Hejab Al-Ajmi
- As'ad Al-Hamad Dermatology Center; Al-Sabah Hospital; Kuwait City Kuwait
| | - Michael A. Simpson
- Department of Genetics and Molecular Medicine; King's College London; Guy's Hospital; London UK
| | - John A. McGrath
- St John's Institute of Dermatology; King's College London; Guy's Hospital; London UK
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416
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Klugman S, Suskin B, Spencer BL, Dar P, Bajaj K, Powers J, Reichling J, Wasserman D, Dolan SM, Merkatz IR. Clinical utility of chromosomal microarray analysis in prenatal diagnosis: report of first 6 months in clinical practice. J Matern Fetal Neonatal Med 2013; 27:1333-8. [PMID: 24147763 DOI: 10.3109/14767058.2013.858243] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE We studied the clinical utility of chromosomal microarray analysis (CMA) in prenatal diagnosis in a clinical setting in New York City. METHODS Our center began offering CMA to pregnant women undergoing invasive diagnostic procedures for an abnormal structural finding on ultrasound, maternal age of 35 years or older, or elevated risk on aneuploidy screening, beginning March 2012. Our first six months experience is reported. RESULTS Benign familial variants were the most common finding (16/22 fetuses). Variants of uncertain significance were frequent, especially when fathers were not available for testing (4/22 fetuses). Most patients undertook CMA as part of evaluation of an ultrasound anomaly (52%). One patient terminated a pregnancy based on an ultrasound finding in the setting of a benign familial variant on CMA, and a second terminated a pregnancy based on a copy number variant identified on CMA. CONCLUSION For CMA to be maximally useful in prenatal diagnosis, parental DNA samples as well as robust datasets to provide predictive phenotypic information are required. The most common reason for undertaking CMA was to evaluate an ultrasound anomaly, and benign familial variants were a common finding. Genetic services are required to provide pre- and post-test genetic counseling and help families interpret results.
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Affiliation(s)
- Susan Klugman
- Department of Obstetrics & Gynecology and Women's Health , Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY , USA
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417
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Chrystoja CC, Diamandis EP. Whole genome sequencing as a diagnostic test: challenges and opportunities. Clin Chem 2013; 60:724-33. [PMID: 24227285 DOI: 10.1373/clinchem.2013.209213] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Extraordinary technological advances and decreases in the cost of DNA sequencing have made the possibility of whole genome sequencing (WGS) as a highly accessible clinical test for numerous indications feasible. There have been many recent, successful applications of WGS in establishing the etiology of complex diseases and guiding therapeutic decision-making in neoplastic and nonneoplastic diseases and in various aspects of reproductive health. However, there are major, but not insurmountable, obstacles to the increased clinical implementation of WGS, such as hidden costs, issues surrounding sequencing and analysis, quality assurance and standardization protocols, ethical dilemmas, and difficulties with interpretation of the results. CONTENT The widespread use of WGS in routine clinical practice remains a distant proposition. Prospective trials will be needed to establish if, and for whom, the benefits of WGS will outweigh the likely substantial costs associated with follow-up tests, the risks of overdiagnosis and overtreatment, and the associated emotional distress. SUMMARY WGS should be carefully implemented in the clinic to allow the realization of its potential to improve patient health in specific indications. To minimize harm the use of WGS for all other reasons must be carefully evaluated before clinical implementation.
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Affiliation(s)
- Caitlin C Chrystoja
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
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418
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Whole-genome sequencing in health care: recommendations of the European Society of Human Genetics. Eur J Hum Genet 2013; 21:580-4. [PMID: 23676617 DOI: 10.1038/ejhg.2013.46] [Citation(s) in RCA: 258] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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419
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Worthey EA. Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis. CURRENT PROTOCOLS IN HUMAN GENETICS 2013; 79:9.24.1-9.24.24. [PMID: 24510652 DOI: 10.1002/0471142905.hg0924s79] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the last several years, next-generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing, and also in the systems required for analysis of these large volumes of data. This technology is now being used as a standard molecular diagnostic test under particular circumstances in some clinical settings. The advances in sequencing have come so rapidly that the major bottleneck in identification of causal variants is no longer the sequencing but rather the analysis and interpretation. Interpretation of genetic findings in a clinical setting is scarcely a new challenge, but the task is increasingly complex in clinical genome-wide sequencing given the dramatic increase in dataset size and complexity. This increase requires the development of novel or repositioned analysis tools, methodologies, and processes. This unit provides an overview of these items. Specific challenges related to implementation in a clinical setting are discussed.
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Affiliation(s)
- Elizabeth A Worthey
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin.,The Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin.,Department of Computer Science, University of Wisconsin, Milwaukee, Wisconsin
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420
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Dotta L, Parolini S, Prandini A, Tabellini G, Antolini M, Kingsmore SF, Badolato R. Clinical, laboratory and molecular signs of immunodeficiency in patients with partial oculo-cutaneous albinism. Orphanet J Rare Dis 2013; 8:168. [PMID: 24134793 PMCID: PMC3856608 DOI: 10.1186/1750-1172-8-168] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 10/11/2013] [Indexed: 01/04/2023] Open
Abstract
Hypopigmentation disorders that are associated with immunodeficiency feature both partial albinism of hair, skin and eyes together with leukocyte defects. These disorders include Chediak Higashi (CHS), Griscelli (GS), Hermansky-Pudlak (HPS) and MAPBP-interacting protein deficiency syndromes. These are heterogeneous autosomal recessive conditions in which the causal genes encode proteins with specific roles in the biogenesis, function and trafficking of secretory lysosomes. In certain specialized cells, these organelles serve as a storage compartment. Impaired secretion of specific effector proteins from that intracellular compartment affects biological activities. In particular, these intracellular granules are essential constituents of melanocytes, platelets, granulocytes, cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. Thus, abnormalities affect pigmentation, primary hemostasis, blood cell counts and lymphocyte cytotoxic activity against microbial pathogens. Among eight genetically distinct types of HPS, only type 2 is characterized by immunodeficiency. Recently, a new subtype, HPS9, was defined in patients presenting with immunodeficiency and oculocutaneous albinism, associated with mutations in the pallidin-encoding gene, PLDN.Hypopigmentation together with recurrent childhood bacterial or viral infections suggests syndromic albinism. T and NK cell cytotoxicity are generally impaired in patients with these disorders. Specific clinical and biochemical phenotypes can allow differential diagnoses among these disorders before molecular testing. Ocular symptoms, including nystagmus, that are usually evident at birth, are common in patients with HPS2 or CHS. Albinism with short stature is unique to MAPBP-interacting protein (MAPBPIP) deficiency, while hemophagocytic lymphohistiocytosis (HLH) mainly suggests a diagnosis of CHS or GS type 2 (GS2). Neurological disease is a long-term complication of CHS, but is uncommon in other syndromic albinism. Chronic neutropenia is a feature of HPS2 and MAPBPIP-deficiency syndrome, whereas it is usually transient in CHS and GS2. In every patient, an accurate diagnosis is required for prompt and appropriate treatment, particularly in patients who develop HLH or in whom bone marrow transplant is required. This review describes the molecular and pathogenetic mechanisms of these diseases, focusing on clinical and biochemical aspects that allow early differential diagnosis.
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Affiliation(s)
- Laura Dotta
- Department of Experimental and Clinical Sciences, Institute of Molecular Medicine “Angelo Nocivelli”, University of Brescia, Brescia, Italy
| | - Silvia Parolini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
| | - Alberto Prandini
- Department of Experimental and Clinical Sciences, Institute of Molecular Medicine “Angelo Nocivelli”, University of Brescia, Brescia, Italy
| | - Giovanna Tabellini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia 25123, Italy
| | - Maddalena Antolini
- Department of Experimental and Clinical Sciences, Institute of Molecular Medicine “Angelo Nocivelli”, University of Brescia, Brescia, Italy
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, MO 64108, USA
| | - Raffaele Badolato
- Department of Experimental and Clinical Sciences, Institute of Molecular Medicine “Angelo Nocivelli”, University of Brescia, Brescia, Italy
- Istituto di Medicina Molecolare “Angelo Nocivelli”, Universita' di Brescia, c/o Spedali Civili, Brescia 25123, Italy
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421
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Liu X, Ladias JAA. Structural basis for the BRCA1 BRCT interaction with the proteins ATRIP and BAAT1. Biochemistry 2013; 52:7618-27. [PMID: 24073851 DOI: 10.1021/bi400714v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The breast and ovarian cancer susceptibility protein 1 (BRCA1) plays a central role in DNA damage response (DDR). Two tandem BRCA1 C-terminal (BRCT) domains interact with several proteins that function in DDR and contain the generally accepted motif pS-X-X-F (pS denoting phosphoserine and X any amino acid), including the ATR-interacting protein (ATRIP) and the BRCA1-associated protein required for ATM activation-1 (BAAT1). The crystal structures of the BRCA1 BRCTs bound to the phosphopeptides ATRIP (235-PEACpSPQFG-243) and BAAT1 (266-VARpSPVFSS-274) were determined at 1.75 Å and 2.2 Å resolution, respectively. The pSer and Phe(+3) anchor the phosphopeptides into the BRCT binding groove, with adjacent peptide residues contributing to the interaction. In the BRCA1-ATRIP structure, Gln(+2) is accommodated through a conformational change of the BRCA1 E1698 side chain. Importantly, isothermal titration calorimetry experiments showed that the size and charge of the side chains at peptide positions +1 and +2 contribute significantly to the BRCA1 BRCT-peptide binding affinity. In particular, the Asp(+1) and Glu(+2) in the human CDC27 peptide 816-HAAEpSDEF-823 abrogate the interaction with the BRCA1 BRCTs due in large part to electrostatic repulsion between Glu(+2) and E1698, indicating a preference of these domains for specific side chains at positions +1 and +2. These results emphasize the need for a systematic assessment of the contribution of the peptide residues surrounding pSer and Phe(+3) to the binding affinity and specificity of the BRCA1 BRCTs in order to elucidate the molecular mechanisms underlying the hierarchy of target selection by these versatile domains during DDR and tumorigenesis.
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Affiliation(s)
- Xuying Liu
- Molecular Medicine Laboratory and Macromolecular Crystallography Unit, Department of Medicine, Harvard Medical School , Boston Massachusetts 02215, United States
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422
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Dinwiddie DL, Soden SE, Saunders CJ, Miller NA, Farrow EG, Smith LD, Kingsmore SF. De novo frameshift mutation in ASXL3 in a patient with global developmental delay, microcephaly, and craniofacial anomalies. BMC Med Genomics 2013; 6:32. [PMID: 24044690 PMCID: PMC3851682 DOI: 10.1186/1755-8794-6-32] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 09/11/2013] [Indexed: 12/23/2022] Open
Abstract
Background Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved despite extensive clinical investigation. The recent advent and use of genomic medicine has resulted in a paradigm shift in the clinical molecular genetics of rare diseases and has provided insight into the causes of numerous rare genetic conditions. In particular, whole exome and genome sequencing of families has been particularly useful in discovering de novo germline mutations as the cause of both rare diseases and complex disorders. Case presentation We present a six year old, nonverbal African American female with microcephaly, autism, global developmental delay, and metopic craniosynostosis. Exome sequencing of the patient and her two parents revealed a heterozygous two base pair de novo deletion, c.1897_1898delCA, p.Gln633ValfsX13 in ASXL3, predicted to result in a frameshift at codon 633 with substitution of a valine for a glutamine and introduction of a premature stop codon. Conclusions We provide additional evidence that, truncating and frameshifting mutations in the ASXL3 gene are the cause of a newly recognized disorder characterized by severe global developmental delay, short stature, microcephaly, and craniofacial anomalies. Furthermore, we expand the knowledge about disease causing mutations and the genotype-phenotype relationships in ASXL3 and provide evidence that rare, nonsynonymous, damaging mutations are not associated with developmental delay or microcephaly.
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Affiliation(s)
- Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
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423
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Ong FS, Lin JC, Das K, Grosu DS, Fan JB. Translational utility of next-generation sequencing. Genomics 2013; 102:137-9. [DOI: 10.1016/j.ygeno.2013.04.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 04/19/2013] [Indexed: 12/31/2022]
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424
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Molecular diagnosis of infantile onset inflammatory bowel disease by exome sequencing. Genomics 2013; 102:442-7. [PMID: 24001973 DOI: 10.1016/j.ygeno.2013.08.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/23/2013] [Accepted: 08/24/2013] [Indexed: 12/19/2022]
Abstract
Pediatric-onset inflammatory bowel disease (IBD) is known to be associated with severe disease, poor response to therapy, and increased morbidity and mortality. We conducted exome sequencing of two brothers from a non-consanguineous relationship who presented before the age of one with severe infantile-onset IBD, failure to thrive, skin rash, and perirectal abscesses refractory to medical management. We examined the variants discovered in all known IBD-associated and primary immunodeficiency genes in both siblings. The siblings were identified to harbor compound heterozygous mutations in IL10RA (c.784C>T, p.Arg262Cys; c.349C>T, p.Arg117Cys). Upon molecular diagnosis, the proband underwent successful hematopoietic stem cell transplantation and demonstrated marked clinical improvement of all IBD-associated clinical symptoms. Exome sequencing can be an effective tool to aid in the molecular diagnosis of pediatric-onset IBD. We provide additional evidence of the safety and benefit of HSCT for patients with IBD due to mutations in the IL10RA gene.
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425
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Tsukamoto A, Uchida N, Capela A, Gorba T, Huhn S. Clinical translation of human neural stem cells. Stem Cell Res Ther 2013; 4:102. [PMID: 23987648 PMCID: PMC3854682 DOI: 10.1186/scrt313] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Human neural stem cell transplants have potential as therapeutic candidates to treat a vast number of disorders of the central nervous system (CNS). StemCells, Inc. has purified human neural stem cells and developed culture conditions for expansion and banking that preserve their unique biological properties. The biological activity of these human central nervous system stem cells (HuCNS-SC®) has been analyzed extensively in vitro and in vivo. When formulated for transplantation, the expanded and cryopreserved banked cells maintain their stem cell phenotype, self-renew and generate mature oligodendrocytes, neurons and astrocytes, cells normally found in the CNS. In this overview, the rationale and supporting data for pursuing neuroprotective strategies and clinical translation in the three components of the CNS (brain, spinal cord and eye) are described. A phase I trial for a rare myelin disorder and phase I/II trial for spinal cord injury are providing intriguing data relevant to the biological properties of neural stem cells, and the early clinical outcomes compel further development.
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426
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Knoppers BM, Avard D, Sénécal K, Zawati MH. Return of whole-genome sequencing results in paediatric research: a statement of the P3G international paediatrics platform. Eur J Hum Genet 2013; 22:3-5. [PMID: 23921532 DOI: 10.1038/ejhg.2013.176] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
| | - Denise Avard
- Centre of Genomics and Policy, McGill University, Montreal, Quebec, Canada
| | - Karine Sénécal
- Centre of Genomics and Policy, McGill University, Montreal, Quebec, Canada
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427
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428
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Abstract
Genomic technologies are reaching the point of being able to detect genetic variation in patients at high accuracy and reduced cost, offering the promise of fundamentally altering medicine. Still, although scientists and policy advisers grapple with how to interpret and how to handle the onslaught and ambiguity of genome-wide data, established and well-validated molecular technologies continue to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities. Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics. In parallel, we outline implementation challenges that will be necessary to address to ensure the future of genetic medicine.
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429
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Abstract
The medical genomics community needs carefully considered guidelines for the reporting of incidental findings.
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Affiliation(s)
- Stephen F. Kingsmore
- Director of the Center for Pediatric Genomic Medicine, Children’s Mercy Hospitals and Clinics, Kansas City, MO 64108, USA
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430
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Wade CH, Tarini BA, Wilfond BS. Growing up in the genomic era: implications of whole-genome sequencing for children, families, and pediatric practice. Annu Rev Genomics Hum Genet 2013; 14:535-55. [PMID: 23875800 DOI: 10.1146/annurev-genom-091212-153425] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Whole-genome sequencing (WGS) has advanced to a point where it is beginning to be integrated into pediatric practice. With little consensus on how to maximize the benefits of WGS for children, there is a growing need for focused efforts that connect researchers, clinicians, and families to chart a path forward. To illustrate relevant concerns, two contrasting applications of pediatric WGS are explored: clinical use with children who have undiagnosed conditions, and population-based screening. Specific challenges for health care services, policy development, and the well-being of children are discussed in light of current research. In the interest of ensuring evidence-based pediatric WGS, strategies are identified for advancing our understanding of what it means for children to grow up with WGS results guiding their health care.
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Affiliation(s)
- Christopher H Wade
- Nursing and Health Studies Program, University of Washington Bothell, Bothell, Washington 98011;
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431
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Barnard JA. Recent advances in pediatric gastroenterology, hepatology and nutrition. F1000PRIME REPORTS 2013; 5:25. [PMID: 23864932 PMCID: PMC3702219 DOI: 10.12703/p5-25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Pediatric gastroenterology, hepatology and nutrition are rapidly evolving, exciting and diverse disciplines. Because the field is so expansive, this commentary highlights important trends, rather than narrowly focusing on specific advances. Examples of advances in the highest impact and rapidly moving areas of pediatric gastroenterology are reviewed, including the intestinal microbiome, biomedical genomics, the biology of unique gastrointestinal cell types, and microRNAs (miRNAs).
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432
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Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire A, Nussbaum RL, O’Daniel JM, Ormond KE, Rehm HL, Watson MS, Williams MS, Biesecker LG. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013; 15:565-74. [PMID: 23788249 PMCID: PMC3727274 DOI: 10.1038/gim.2013.73] [Citation(s) in RCA: 1783] [Impact Index Per Article: 162.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 04/11/2013] [Indexed: 12/11/2022] Open
Abstract
In clinical exome and genome sequencing, there is a potential for the recognition and reporting of incidental or secondary findings unrelated to the indication for ordering the sequencing but of medical value for patient care. The American College of Medical Genetics and Genomics (ACMG) recently published a policy statement on clinical sequencing that emphasized the importance of alerting the patient to the possibility of such results in pretest patient discussions, clinical testing, and reporting of results. The ACMG appointed a Working Group on Incidental Findings in Clinical Exome and Genome Sequencing to make recommendations about responsible management of incidental findings when patients undergo exome or genome sequencing. This Working Group conducted a year-long consensus process, including an open forum at the 2012 Annual Meeting and review by outside experts, and produced recommendations that have been approved by the ACMG Board. Specific and detailed recommendations, and the background and rationale for these recommendations, are described herein. The ACMG recommends that laboratories performing clinical sequencing seek and report mutations of the specified classes or types in the genes listed here. This evaluation and reporting should be performed for all clinical germline (constitutional) exome and genome sequencing, including the "normal" of tumor-normal subtractive analyses in all subjects, irrespective of age but excluding fetal samples. We recognize that there are insufficient data on penetrance and clinical utility to fully support these recommendations, and we encourage the creation of an ongoing process for updating these recommendations at least annually as further data are collected.
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Affiliation(s)
- Robert C. Green
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Wayne W. Grody
- Division of Medical Genetics, Department of Human Genetics, UCLA School of Medicine, Los Angeles, California, USA
- Division of Molecular Pathology, Department of Pathology & Laboratory Medicine, UCLA School of Medicine, Los Angeles, California, USA
- Division of Pediatric Genetics, Department of Pediatrics, UCLA School of Medicine, Los Angeles, California, USA
| | - Sarah S. Kalia
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama, Birmingham, Alabama, USA
| | - Christa L. Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Amy McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Robert L. Nussbaum
- Division of Genomic Medicine, Department of Medicine, and Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | | | - Kelly E. Ormond
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Heidi L. Rehm
- Partners Healthcare Center for Personalized Genetic Medicine, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael S. Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland, USA
| | - Marc S. Williams
- Genomic Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Leslie G. Biesecker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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433
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Krier JB, Green RC. Management of incidental findings in clinical genomic sequencing. ACTA ACUST UNITED AC 2013; Chapter 9:Unit9.23. [PMID: 23595601 DOI: 10.1002/0471142905.hg0923s77] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genomic sequencing is becoming accurate, fast, and inexpensive, and is rapidly being incorporated into clinical practice. Incidental findings, which result in large numbers from genomic sequencing, are a potential barrier to the utility of this new technology due to their high prevalence and the lack of evidence or guidelines available to guide their clinical interpretation. This unit reviews the definition, classification, and management of incidental findings from genomic sequencing. The unit focuses on the clinical aspects of handling incidental findings, with an emphasis on the key role of clinical context in defining incidental findings and determining their clinical relevance and utility.
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Affiliation(s)
- Joel B Krier
- Harvard Medical School Genetics Training Program, Boston, MA, USA
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434
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Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation. Nat Rev Genet 2013; 14:460-70. [PMID: 23752795 DOI: 10.1038/nrg3455] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Next-generation sequencing is becoming the primary discovery tool in human genetics. There have been many clear successes in identifying genes that are responsible for Mendelian diseases, and sequencing approaches are now poised to identify the mutations that cause undiagnosed childhood genetic diseases and those that predispose individuals to more common complex diseases. There are, however, growing concerns that the complexity and magnitude of complete sequence data could lead to an explosion of weakly justified claims of association between genetic variants and disease. Here, we provide an overview of the basic workflow in next-generation sequencing studies and emphasize, where possible, measures and considerations that facilitate accurate inferences from human sequencing studies.
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Affiliation(s)
- David B Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, 308 Research Drive, Box 91009, LSRC B Wing, Room 330, Durham, North Carolina 27708, USA.
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435
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Raczy C, Petrovski R, Saunders CT, Chorny I, Kruglyak S, Margulies EH, Chuang HY, Källberg M, Kumar SA, Liao A, Little KM, Strömberg MP, Tanner SW. Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. ACTA ACUST UNITED AC 2013; 29:2041-3. [PMID: 23736529 DOI: 10.1093/bioinformatics/btt314] [Citation(s) in RCA: 224] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
SUMMARY An ultrafast DNA sequence aligner (Isaac Genome Alignment Software) that takes advantage of high-memory hardware (>48 GB) and variant caller (Isaac Variant Caller) have been developed. We demonstrate that our combined pipeline (Isaac) is four to five times faster than BWA + GATK on equivalent hardware, with comparable accuracy as measured by trio conflict rates and sensitivity. We further show that Isaac is effective in the detection of disease-causing variants and can easily/economically be run on commodity hardware. AVAILABILITY Isaac has an open source license and can be obtained at https://github.com/sequencing.
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Affiliation(s)
- Come Raczy
- Illumina United Kingdom, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex, UK.
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436
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van El CG, Cornel MC, Borry P, Hastings RJ, Fellmann F, Hodgson SV, Howard HC, Cambon-Thomsen A, Knoppers BM, Meijers-Heijboer H, Scheffer H, Tranebjaerg L, Dondorp W, de Wert GMWR. Whole-genome sequencing in health care. Recommendations of the European Society of Human Genetics. Eur J Hum Genet 2013; 21 Suppl 1:S1-S5. [PMID: 23819146 PMCID: PMC3660957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Affiliation(s)
- Carla G van El
- Section Community Genetics, Department of Clinical Genetics and EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands.
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437
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Trujillano D, Ramos MD, González J, Tornador C, Sotillo F, Escaramis G, Ossowski S, Armengol L, Casals T, Estivill X. Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR. J Med Genet 2013; 50:455-62. [PMID: 23687349 DOI: 10.1136/jmedgenet-2013-101602] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Here we have developed a novel and much more efficient strategy for the complete molecular characterisation of the cystic fibrosis (CF) transmembrane regulator (CFTR) gene, based on multiplexed targeted resequencing. We have tested this approach in a cohort of 92 samples with previously characterised CFTR mutations and polymorphisms. METHODS After enrichment of the pooled barcoded DNA libraries with a custom NimbleGen SeqCap EZ Choice array (Roche) and sequencing with a HiSeq2000 (Illumina) sequencer, we applied several bioinformatics tools to call mutations and polymorphisms in CFTR. RESULTS The combination of several bioinformatics tools allowed us to detect all known pathogenic variants (point mutations, short insertions/deletions, and large genomic rearrangements) and polymorphisms (including the poly-T and poly-thymidine-guanine polymorphic tracts) in the 92 samples. In addition, we report the precise characterisation of the breakpoints of seven genomic rearrangements in CFTR, including those of a novel deletion of exon 22 and a complex 85 kb inversion which includes two large deletions affecting exons 4-8 and 12-21, respectively. CONCLUSIONS This work is a proof-of-principle that targeted resequencing is an accurate and cost-effective approach for the genetic testing of CF and CFTR-related disorders (ie, male infertility) amenable to the routine clinical practice, and ready to substitute classical molecular methods in medical genetics.
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Affiliation(s)
- D Trujillano
- Genetic Causes of Disease Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
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438
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Dinwiddie DL, Smith LD, Miller NA, Atherton AM, Farrow EG, Strenk ME, Soden SE, Saunders CJ, Kingsmore SF. Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome. Genomics 2013; 102:148-56. [PMID: 23631824 DOI: 10.1016/j.ygeno.2013.04.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 01/22/2023]
Abstract
Mitochondrial diseases are notoriously difficult to diagnose due to extreme locus and allelic heterogeneity, with both nuclear and mitochondrial genomes potentially liable. Using exome sequencing we demonstrate the ability to rapidly and cost effectively evaluate both the nuclear and mitochondrial genomes to obtain a molecular diagnosis for four patients with three distinct mitochondrial disorders. One patient was found to have Leigh syndrome due to a mutation in MT-ATP6, two affected siblings were discovered to be compound heterozygous for mutations in the NDUFV1 gene, which causes mitochondrial complex I deficiency, and one patient was found to have coenzyme Q10 deficiency due to compound heterozygous mutations in COQ2. In all cases conventional diagnostic testing failed to identify a molecular diagnosis. We suggest that additional studies should be conducted to evaluate exome sequencing as a primary diagnostic test for mitochondrial diseases, including those due to mtDNA mutations.
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Affiliation(s)
- Darrell L Dinwiddie
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA.
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439
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440
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Kilpivaara O, Aaltonen LA. Diagnostic cancer genome sequencing and the contribution of germline variants. Science 2013; 339:1559-62. [PMID: 23539595 DOI: 10.1126/science.1233899] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Whole-genome sequencing (WGS) is revolutionizing medical research and has the potential to serve as a powerful and cost-effective diagnostic tool in the management of cancer. We review the progress to date in the use of WGS to reveal how germline variants and mutations may be associated with cancer. We use colorectal cancer as an example of how the current level of knowledge can be translated into predictions of predisposition. We also address challenges in the clinical implementation of the variants in germline DNA identified through cancer genome sequencing. We call for the international development of standards to facilitate the clinical use of germline information arising from diagnostic cancer genome sequencing.
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Affiliation(s)
- O Kilpivaara
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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441
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Next-generation sequencing diagnostics for neurological diseases/disorders: from a clinical perspective. Hum Genet 2013; 132:721-34. [PMID: 23525706 DOI: 10.1007/s00439-013-1287-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/02/2013] [Indexed: 12/13/2022]
Abstract
Neurological diseases encompass a broad, heterogeneous group of disorders ranging from pediatric neurodevelopmental diseases to late-onset neurodegenerative diseases, most of which are poorly understood and few of which are curable. Most of these diseases have a genetic basis and thus are expected to be amenable to genetic or genomic analysis by next-generation sequencing (NGS). While the advancement of contemporary technologies (such as NGS) is exciting, translating this tool into actual benefit for patients and clinicians can be challenging. In a clinical setting, a sequencing test that is fast, non-invasive, cheap and with perfect specificity would be ideal. However, in practice, there are several hurdles and caveats to consider even before a NGS diagnostic testing can be optimally applied. Proper definition of clinical phenotype, selection of the most appropriate subjects and the clinical setting, optimization of both sensitivity and specificity of the test, evaluation of the availability of the infrastructure and expertise, and consideration of economic, ethical and legal issues are vital in the final application of NGS diagnostic screening in the clinics.
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442
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443
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Abstract
PURPOSE OF REVIEW To provide an updated overview of autism spectrum disorders (ASDs), with particular attention to the pediatrician's role in assessing and managing patients with ASDs. RECENT FINDINGS Clinical perspectives on ASDs continue to evolve. The prevalence of ASDs in the United States continues to rise, and pediatricians are being tasked with the responsibility for universal screening. Further changes in its epidemiology will undoubtedly result from anticipated changes in the diagnostic criteria put forth in the upcoming revision to the Diagnostic and Statistical Manual (5th edition). Although there have been considerable advances in identifying a genetic cause in many more cases, the cause remains elusive in most cases. Recent studies of concordant twins suggest there is a stronger environmental component than previously believed. Research suggests earlier diagnosis may be feasible in some cases, and a new treatment approach has been shown to be effective in very young children. Although there have not been any large-scale advances in the medical treatment, some isolated successes have been reported and other promising therapies are now being investigated. SUMMARY Clinical guidelines for ASDs are evolving, with updated diagnostic criteria expected and revised recommendations for evaluation also imminent. This article provides pediatricians with a clinical overview of ASD - with an emphasis on the clinical considerations relating to screening, evaluation, and management.
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444
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Fernandez CV, Strahlendorf C, Avard D, Knoppers BM, O'Connell C, Bouffet E, Malkin D, Jabado N, Boycott K, Sorensen PH. Attitudes of Canadian researchers toward the return to participants of incidental and targeted genomic findings obtained in a pediatric research setting. Genet Med 2013; 15:558-64. [PMID: 23370450 PMCID: PMC3910293 DOI: 10.1038/gim.2012.183] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 12/14/2012] [Indexed: 11/23/2022] Open
Abstract
Purpose: The purpose of this study was to explore the attitudes of genomics researchers in a pediatric setting in the context of regulatory guidance recommending the disclosure of clinically significant research findings. Methods: A validated 32-item questionnaire was sent to 107 researchers with two large-scale projects (the Canadian Pediatric Cancer Genome Consortium and the Finding of Rare Genes Canada Consortium). We examined researchers' attitudes toward obligations to offer genomic research results (including if the participant was deceased, a relative, or a child), influence of the certainty/severity of the condition on this obligation, and personal experiences. Results: Of the 107 researchers, 74 (69%) responded. Researchers did not feel a strong responsibility to look for meaningful incidental results in the research genomic data set (n = 27, 37%). However, once identified, they felt participants had a strong right to receive them, irrespective of being incidental (n = 50, 68%) or primary targets (n = 64, 87%). There was a high degree of support for informing siblings of genomic results (n = 46, 62%), especially for treatable conditions (n = 56, 76%). Less than half of the participants indicated that their research ethics board required an offer of results (n = 34, 46%) or provided a detailed process (n = 16, 22%). Conclusion: Researchers strongly support the offer of targeted and incidental genomic research results to participants. Greater regulatory guidance is needed for a consistent approach.
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Affiliation(s)
- Conrad V Fernandez
- Department of Pediatrics, IWK Health Centre and Dalhousie University, Halifax, Nova Scotia, Canada.
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445
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Freeze HH. Understanding human glycosylation disorders: biochemistry leads the charge. J Biol Chem 2013; 288:6936-45. [PMID: 23329837 DOI: 10.1074/jbc.r112.429274] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Nearly 70 inherited human glycosylation disorders span a breathtaking clinical spectrum, impacting nearly every organ system and launching a family-driven diagnostic odyssey. Advances in genetics, especially next generation sequencing, propelled discovery of many glycosylation disorders in single and multiple pathways. Interpretation of whole exome sequencing results, insights into pathological mechanisms, and possible therapies will hinge on biochemical analysis of patient-derived materials and animal models. Biochemical diagnostic markers and readouts offer a physiological context to confirm candidate genes. Recent discoveries suggest novel perspectives for textbook biochemistry and novel research opportunities. Basic science and patients are the immediate beneficiaries of this bidirectional collaboration.
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Affiliation(s)
- Hudson H Freeze
- Genetic Disease Program, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
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Whole-genome sequencing diagnostics for newborns. Nat Rev Genet 2012. [DOI: 10.1038/nrg3362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Two-day test diagnoses genetic diseases in newborns. Nature 2012. [DOI: 10.1038/nature.2012.11527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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