301
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Abstract
Across the span of the last 75+ years, technological and conceptual advances in genetics have found rapid implementation at the beginning of human life. From karyotype testing, to molecular cytogenetics, to gene panel testing, and now to whole exome and whole genome sequencing, each iterative expansion of our capability to acquire genetic data on the next generation has been implemented quickly in the clinical setting. In tandem, our continuously expanding ability to acquire large volumes of genetic data has generated its own challenges in terms of interpretation, clinical utility of the information, and concerns over privacy and discrimination; for the first time, we are faced with the possibility of having complete access to our genetic data from birth, if not shortly after conception. Here, we discuss the evolution of the field toward this new reality and we consider the potentially far-reaching consequences and, at present, an unclear path toward developing best practices for implementation.
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Affiliation(s)
- Ludmila Francescatto
- Center for Human Disease Modeling, Duke University School of Medicine, 300 N Duke St, Durham, NC 27701
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University School of Medicine, 300 N Duke St, Durham, NC 27701.
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302
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Abstract
Traditionally, genetic testing has been too slow or perceived to be impractical to initial management of the critically ill neonate. Technological advances have led to the ability to sequence and interpret the entire genome of a neonate in as little as 26 h. As the cost and speed of testing decreases, the utility of whole genome sequencing (WGS) of neonates for acute and latent genetic illness increases. Analyzing the entire genome allows for concomitant evaluation of the currently identified 5588 single gene diseases. When applied to a select population of ill infants in a level IV neonatal intensive care unit, WGS yielded a diagnosis of a causative genetic disease in 57% of patients. These diagnoses may lead to clinical management changes ranging from transition to palliative care for uniformly lethal conditions for alteration or initiation of medical or surgical therapy to improve outcomes in others. Thus, institution of 2-day WGS at time of acute presentation opens the possibility of early implementation of precision medicine. This implementation may create opportunities for early interventional, frequently novel or off-label therapies that may alter disease trajectory in infants with what would otherwise be fatal disease. Widespread deployment of rapid WGS and precision medicine will raise ethical issues pertaining to interpretation of variants of unknown significance, discovery of incidental findings related to adult onset conditions and carrier status, and implementation of medical therapies for which little is known in terms of risks and benefits. Despite these challenges, precision neonatology has significant potential both to decrease infant mortality related to genetic diseases with onset in newborns and to facilitate parental decision making regarding transition to palliative care.
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Affiliation(s)
- Joshua E. Petrikin
- The University of Missouri Kansas City School of Medicine, Department of Pediatrics, Division of Neonatal and Perinatal Medicine, Director of Neonatal Genomics, Center for Pediatric Genomic Medicine, Children's Mercy Hospital Kansas City, Kansas City, Missouri 64108, Phone: 816-701-4806, Fax: 816-802-1111,
| | - Laurel K. Willig
- The University of Missouri, Kansas City School of Medicine, Department of Pediatrics, Division of Pediatric Nephrology, Center for Pediatric Genomic Medicine, Children's Mercy Hospital Kansas City, Kansas City, Missouri 64108 USA, Phone: 816-701-4806, Fax: 816-802-1111,
| | - Laurie D. Smith
- The University of Missouri Kansas City School of Medicine, Department of Pediatrics, Center for Pediatric Genomic Medicine, Children's Mercy Hospital Kansas City, Kansas City, Missouri 64108 USA, Phone: 816-701-4806, Fax: 816-802-111,
| | - Stephen F. Kingsmore
- Dee Lyons/Missouri Endowed Chair in Pediatric Genomic Medicine, Department of Pediatrics, Department of Pathology and Laboratory Medicine, Director, Center for Pediatric Genomic Medicine, Children's Mercy Hospital Kansas City, Kansas City, Missouri, 64108 USA, Phone: 816-701-4806, Fax: 816-802-1111,
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303
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Giardino G, Gallo V, Somma D, Farrow EG, Thiffault I, D'Assante R, Donofrio V, Paciolla M, Ursini MV, Leonardi A, Saunders CJ, Pignata C. Targeted next-generation sequencing revealed MYD88 deficiency in a child with chronic yersiniosis and granulomatous lymphadenitis. J Allergy Clin Immunol 2015; 137:1591-1595.e4. [PMID: 26632527 DOI: 10.1016/j.jaci.2015.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 09/07/2015] [Accepted: 09/16/2015] [Indexed: 10/22/2022]
Affiliation(s)
- Giuliana Giardino
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Vera Gallo
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | - Domenico Somma
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Naples, Italy
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pathology, Children's Mercy-Kansas City, Kansas City, Mo; School of Medicine, University of Missouri-Kansas City, Kansas City, Mo
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pathology, Children's Mercy-Kansas City, Kansas City, Mo; School of Medicine, University of Missouri-Kansas City, Kansas City, Mo
| | - Roberta D'Assante
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy
| | | | | | | | - Antonio Leonardi
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Naples, Italy
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, Mo; Department of Pathology, Children's Mercy-Kansas City, Kansas City, Mo; School of Medicine, University of Missouri-Kansas City, Kansas City, Mo
| | - Claudio Pignata
- Department of Translational Medical Sciences, Federico II University of Naples, Naples, Italy.
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304
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Saunders CJ, Moon SH, Liu X, Thiffault I, Coffman K, LePichon JB, Taboada E, Smith LD, Farrow EG, Miller N, Gibson M, Patterson M, Kingsmore SF, Gross RW. Loss of function variants in human PNPLA8 encoding calcium-independent phospholipase A2 γ recapitulate the mitochondriopathy of the homologous null mouse. Hum Mutat 2015; 36:301-6. [PMID: 25512002 DOI: 10.1002/humu.22743] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/09/2014] [Indexed: 12/13/2022]
Abstract
Mitochondriopathies are a group of clinically heterogeneous genetic diseases caused by defects in mitochondrial metabolism, bioenergetic efficiency, and/or signaling functions. The large majority of proteins involved in mitochondrial function are encoded by nuclear genes, with many yet to be associated with human disease. We performed exome sequencing on a young girl with a suspected mitochondrial myopathy that manifested as progressive muscle weakness, hypotonia, seizures, poor weight gain, and lactic acidosis. She was compound heterozygous for two frameshift mutations, p.Asn112HisfsX29 and p.Leu659AlafsX4, in the PNPLA8 gene, which encodes mitochondrial calcium-independent phospholipase A2 γ (iPLA2 γ). Western blot analysis of affected muscle displayed the absence of PNPLA8 protein. iPLA2 s are critical mediators of a variety of cellular processes including growth, metabolism, and lipid second messenger generation, exerting their functions through catalyzing the cleavage of the acyl groups in glycerophospholipids. The clinical presentation, muscle histology and the mitochondrial ultrastructural abnormalities of this proband are highly reminiscent of Pnpla8 null mice. Although other iPLA2 -related diseases have been identified, namely, infantile neuroaxonal dystrophy and neutral lipid storage disease with myopathy, this is the first report of PNPLA8-related disease in a human. We suggest PNPLA8 join the increasing list of human genes involved in lipid metabolism associated with neuromuscular diseases due to mitochondrial dysfunction.
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Affiliation(s)
- Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospitals, Kansas City, Missouri
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305
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Beckmann JS. Can we afford to sequence every newborn baby's genome? Hum Mutat 2015; 36:283-6. [PMID: 25546530 DOI: 10.1002/humu.22748] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 12/17/2014] [Indexed: 01/19/2023]
Abstract
Whole-exome sequencing and whole-genome sequencing are gradually entering into the clinical arena. Drops in sequencing prices have led some to suggest that these analyses could be extended to the screening of whole populations or subsets thereof. Herein, we argue that this optimism is presently still unfounded. While cost estimates take into account the generation of sequence data, they fail to properly evaluate both the price of accurate and efficient interpretation and of the proper return of genomic information to the consulting individuals. Thus, short of inventing new, cost-effective ways of achieving these goals, the latter are likely to ruin our healthcare systems. We posit that due to lack of available resources, generalization of this practice remains, for the time being, unrealistic.
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Affiliation(s)
- Jacques S Beckmann
- Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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306
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Chitty LS, Friedman JM, Langlois S. Current controversies in prenatal diagnosis 2: should a fetal exome be used in the assessment of a dysmorphic or malformed fetus? Prenat Diagn 2015; 36:15-9. [PMID: 26525746 DOI: 10.1002/pd.4718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/21/2015] [Accepted: 10/27/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Lyn S Chitty
- Genetics and Genomic Medicine, UCL Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, England
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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307
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Hope S, Johannessen CH, Aanonsen NO, Strømme P. The investigation of inborn errors of metabolism as an underlying cause of idiopathic intellectual disability in adults in Norway. Eur J Neurol 2015; 23 Suppl 1:36-44. [DOI: 10.1111/ene.12884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2015] [Indexed: 12/17/2022]
Affiliation(s)
- S. Hope
- Department of Neuro Habilitation; Oslo University Hospital, Ullevål; Oslo Norway
- NORMENT; KG Jebsen Centre for Psychosis Research; Institute of Clinical Medicine; University of Oslo; Oslo Norway
| | - C. H. Johannessen
- Department of Neuro Habilitation; Oslo University Hospital, Ullevål; Oslo Norway
| | - N. O. Aanonsen
- Department of Neuro Habilitation; Oslo University Hospital, Ullevål; Oslo Norway
| | - P. Strømme
- Department of Clinical Neurosciences for Children; Women and Children′s Division; Oslo University Hospital, Ullevål; Oslo Norway
- University of Oslo; Oslo Norway
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308
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Human genotype–phenotype databases: aims, challenges and opportunities. Nat Rev Genet 2015; 16:702-15. [DOI: 10.1038/nrg3932] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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309
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Abstract
Whole-genome and whole-exome sequencing for clinical applications is now an integral part of medical genetics practice. The term newborn screening refers to public health programs designed to screen newborns for various treatable metabolic conditions, by measuring levels of circulating blood metabolites. The availability and significant decrease in sequencing costs has raised the question of whether metabolic newborn screening should be replaced by whole-genome or whole-exome sequencing. While newborn genome sequencing can potentially increase the number of disorders identified by newborn screening, the generalization of its practice raises a number of important ethical issues. This short article argues that there are medical, psychological, ethical and economic reasons why widespread dissemination of newborn screening is still premature.
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310
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Guimier A, Gabriel GC, Bajolle F, Tsang M, Liu H, Noll A, Schwartz M, El Malti R, Smith LD, Klena NT, Jimenez G, Miller NA, Oufadem M, Moreau de Bellaing A, Yagi H, Saunders CJ, Baker CN, Di Filippo S, Peterson KA, Thiffault I, Bole-Feysot C, Cooley LD, Farrow EG, Masson C, Schoen P, Deleuze JF, Nitschké P, Lyonnet S, de Pontual L, Murray SA, Bonnet D, Kingsmore SF, Amiel J, Bouvagnet P, Lo CW, Gordon CT. MMP21 is mutated in human heterotaxy and is required for normal left-right asymmetry in vertebrates. Nat Genet 2015; 47:1260-3. [PMID: 26437028 PMCID: PMC5620017 DOI: 10.1038/ng.3376] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/10/2015] [Indexed: 12/26/2022]
Abstract
Heterotaxy results from a failure to establish normal left-right asymmetry early in embryonic development. By whole-exome sequencing, whole-genome sequencing and high-throughput cohort resequencing, we identified recessive mutations in MMP21 (encoding matrix metallopeptidase 21) in nine index cases with heterotaxy. In addition, Mmp21-mutant mice and mmp21-morphant zebrafish displayed heterotaxy and abnormal cardiac looping, respectively, suggesting a new role for extracellular matrix remodeling in the establishment of laterality in vertebrates.
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Affiliation(s)
- Anne Guimier
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Fanny Bajolle
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de Référence Malformations Cardiaques Congénitales Complexes (M3C), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hui Liu
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Molly Schwartz
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rajae El Malti
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Nikolai T Klena
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Gina Jimenez
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Myriam Oufadem
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Anne Moreau de Bellaing
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Hisato Yagi
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | | | - Sylvie Di Filippo
- Service de Cardiologie Pédiatrique, Hospices Civils de Lyon, Lyon, France
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Christine Bole-Feysot
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Linda D Cooley
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Cécile Masson
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Patric Schoen
- Department of Pediatric Cardiology and Congenital Heart Disease, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Jean-François Deleuze
- Centre National de Génotypage, Institut de Génomique, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Evry, France
| | - Patrick Nitschké
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
- Service de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Loic de Pontual
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | | | - Damien Bonnet
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
- Unité Médico-Chirurgicale de Cardiologie Congénitale et Pédiatrique, Centre de Référence Malformations Cardiaques Congénitales Complexes (M3C), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Departments of Pediatrics and Pathology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
- Service de Génétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Patrice Bouvagnet
- Laboratoire Cardiogénétique, Hospices Civils de Lyon, Bron, France
- EA 4173, Université Lyon 1 and Hôpital Nord Ouest, Lyon, France
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations, INSERM U1163, Institut Imagine, Paris, France
- Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
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311
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Mundy SA, Krock BL, Mao R, Shen JJ. BRAT1-related disease--identification of a patient without early lethality. Am J Med Genet A 2015; 170:699-702. [PMID: 26494257 DOI: 10.1002/ajmg.a.37434] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/03/2015] [Indexed: 01/22/2023]
Abstract
We present a patient with neonatal onset of hypertonia and seizures identified through whole exome sequencing to have compound heterozygous variants, c.294dupA (p.Leu99fs) and c.1925C>A (p.Ala642Glu), in the BRCA1-associated protein required for ATM activation-1 (BRAT1) gene. Variants in BRAT1 have been identified to cause lethal neonatal rigidity and multifocal seizure syndrome (OMIM# 614498), which consistently manifests a severe neurological phenotype that includes neonatal presentation of rigidity and hypertonia, microcephaly and arrested head growth, intractable seizures, absence of developmental progress, apneic episodes, and death usually by 6 months of age. Our patient initially had a similarly severe neurological picture but remains alive at 6 years of age, expanding the phenotype to include longer term survival and providing further insights into genotype-phenotype correlations and the natural history of this disease.
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Affiliation(s)
- Sheraden A Mundy
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California.,Natera Inc., San Carlos, California
| | - Bryan L Krock
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Salt Lake City, Utah
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Laboratories, Salt Lake City, Utah
| | - Joseph J Shen
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California
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312
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Constantinou P, D'Alessandro M, Lochhead P, Samant S, Bisset WM, Hauptfleisch C, Dean J. A New, Atypical Case of Cobalamin F Disorder Diagnosed by Whole Exome Sequencing. Mol Syndromol 2015; 6:254-8. [PMID: 26997947 PMCID: PMC4772619 DOI: 10.1159/000441134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2015] [Indexed: 12/16/2022] Open
Abstract
Cobalamin F (cblF) disorder, caused by homozygous or compound heterozygous mutations in the LMBRD1 gene, is a recognised cause of developmental delay, pancytopaenia and failure to thrive which may present in the neonatal period. A handful of cases have been reported in the medical literature. We report a new case, diagnosed at the age of 6 years through whole exome sequencing, with atypical features including prominent metopic suture, cleft palate, unilateral renal agenesis and liver abnormalities, which broaden the phenotypic spectrum.
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Affiliation(s)
| | | | | | - Paul Lochhead
- North of Scotland Regional Genetics Service, Ashgrove House, Foresterhill, UK
| | - Shalaka Samant
- Molecular Genetics Department, University of Aberdeen, Foresterhill, UK
| | - W Michael Bisset
- Department of Paediatric Gastroenterology, Royal Aberdeen Children's Hospital, Foresterhill, UK
| | | | - John Dean
- North of Scotland Regional Genetics Service, Ashgrove House, Foresterhill, UK
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313
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Abstract
Hearing loss (HL) is one of the most common birth defects in developed countries and is a diverse pathologic condition with different classifications. One of these is based on the association with other clinical features, defined as syndromic hearing loss (SHL). Determining the cause of the HL in these patients is extremely beneficial as it enables a personalized approach to caring for the individual. Early screening can further aid in optimal rehabilitation for a child's development and growth. The advancement of high-throughput sequencing technology is facilitating rapid and low-cost diagnostics for patients with SHL.
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Affiliation(s)
- Tal Koffler
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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314
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Krier JB, Green RC. Management of Incidental Findings in Clinical Genomic Sequencing. ACTA ACUST UNITED AC 2015; 87:9.23.1-9.23.16. [PMID: 26439717 DOI: 10.1002/0471142905.hg0923s87] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genomic sequencing is becoming accurate, fast, and increasingly inexpensive, and is rapidly being incorporated into clinical practice. Incidental or secondary findings, which can occur in large numbers from genomic sequencing, are a potential barrier to the utility of this new technology due to their relatively 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
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert C Green
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Broad Institute, Boston, Massachusetts
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315
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Miller NA, Farrow EG, Gibson M, Willig LK, Twist G, Yoo B, Marrs T, Corder S, Krivohlavek L, Walter A, Petrikin JE, Saunders CJ, Thiffault I, Soden SE, Smith LD, Dinwiddie DL, Herd S, Cakici JA, Catreux S, Ruehle M, Kingsmore SF. A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases. Genome Med 2015; 7:100. [PMID: 26419432 PMCID: PMC4588251 DOI: 10.1186/s13073-015-0221-8] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/10/2015] [Indexed: 12/14/2022] Open
Abstract
While the cost of whole genome sequencing (WGS) is approaching the realm of routine medical tests, it remains too tardy to help guide the management of many acute medical conditions. Rapid WGS is imperative in light of growing evidence of its utility in acute care, such as in diagnosis of genetic diseases in very ill infants, and genotype-guided choice of chemotherapy at cancer relapse. In such situations, delayed, empiric, or phenotype-based clinical decisions may meet with substantial morbidity or mortality. We previously described a rapid WGS method, STATseq, with a sensitivity of >96 % for nucleotide variants that allowed a provisional diagnosis of a genetic disease in 50 h. Here improvements in sequencing run time, read alignment, and variant calling are described that enable 26-h time to provisional molecular diagnosis with >99.5 % sensitivity and specificity of genotypes. STATseq appears to be an appropriate strategy for acutely ill patients with potentially actionable genetic diseases.
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Affiliation(s)
- Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Margaret Gibson
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Byunggil Yoo
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Tyler Marrs
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Shane Corder
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Lisa Krivohlavek
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Adam Walter
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA
| | - Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA.,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA.,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA
| | - Darrell L Dinwiddie
- Deparment of Pediatrics, and Clinical Translational Science Center, University of New Mexico Health Science Center, Albuquerque, NM, 87131, USA
| | - Suzanne Herd
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Julie A Cakici
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Severine Catreux
- Edico Genome, Inc., 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA, 92037, USA
| | - Mike Ruehle
- Edico Genome, Inc., 3344 North Torrey Pines Court, Plaza Level, La Jolla, CA, 92037, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy, 2401 Gilham Road, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy, Kansas City, MO, 64108, USA. .,Department of Pathology, Children's Mercy, Kansas City, MO, 64108, USA. .,School of Medicine, University of Missouri-Kansas City, Kansas City, MO, 64108, USA. .,Rady Pediatric Genomics and Systems Medicine Institute, Rady Chlildren's Hospital, 3020 Children's Way, San Diego, CA, 92123, USA.
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316
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FRIEDMAN EITAN. Next generation sequencing for newborn screening: are we there yet? Genet Res (Camb) 2015; 97:e17. [PMID: 26392239 PMCID: PMC6863637 DOI: 10.1017/s001667231500018x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 11/07/2022] Open
Abstract
Screening programs for asymptomatic newborns (newborn screening - NBS) have increasingly been implemented in many westernized countries since the end of the 20th century (Wilson et al., 2010). The major goal of these programs is to unselectively screen all newborns for a well defined group of severe, rare, clearly identifiable and actionable conditions. These conditions should be diagnosed and treated in a timely fashion to ensure short and long term health of the newborn as an infant and an adult. As such, NBS programs are one of the pivotal public health achievements of the past decade (Centers for Disease Control and Prevention, 2011) that have led to the saving of lives and improving quality of life as well as posing less financial burden on the health care system. Technically the currently practiced screening process is performed 48 hours after birth, using a minute amount of blood collected on a dried blood spot card, which is subsequently subjected to biochemical analysis predominantly using mass spectrometry assays.
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Affiliation(s)
- EITAN FRIEDMAN
- Director, Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Tel-Hashomer, Israel
- Departments of Internal Medicine and Genetics and Biochemistry, Sackler School of Medicine, Tel-Aviv University Tel-Aviv, Israel
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317
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Drury S, Williams H, Trump N, Boustred C, Lench N, Scott RH, Chitty LS. Exome sequencing for prenatal diagnosis of fetuses with sonographic abnormalities. Prenat Diagn 2015; 35:1010-7. [DOI: 10.1002/pd.4675] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/21/2015] [Accepted: 08/08/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Suzanne Drury
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Hywel Williams
- Genetics and Genomic Medicine; UCL Institute of Child Health; London UK
| | - Natalie Trump
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Christopher Boustred
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Nicholas Lench
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Richard H. Scott
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Lyn S. Chitty
- North-East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
- Genetics and Genomic Medicine; UCL Institute of Child Health; London UK
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318
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Utility of whole-genome sequencing for detection of newborn screening disorders in a population cohort of 1,696 neonates. Genet Med 2015; 18:221-30. [PMID: 26334177 DOI: 10.1038/gim.2015.111] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/26/2015] [Indexed: 01/29/2023] Open
Abstract
PURPOSE To assess the potential of whole-genome sequencing (WGS) to replicate and augment results from conventional blood-based newborn screening (NBS). METHODS Research-generated WGS data from an ancestrally diverse cohort of 1,696 infants and both parents of each infant were analyzed for variants in 163 genes involved in disorders included or under discussion for inclusion in US NBS programs. WGS results were compared with results from state NBS and related follow-up testing. RESULTS NBS genes are generally well covered by WGS. There is a median of one (range: 0-6) database-annotated pathogenic variant in the NBS genes per infant. Results of WGS and NBS in detecting 28 state-screened disorders and four hemoglobin traits were concordant for 88.6% of true positives (n = 35) and 98.9% of true negatives (n = 45,757). Of the five infants affected with a state-screened disorder, WGS identified two whereas NBS detected four. WGS yielded fewer false positives than NBS (0.037 vs. 0.17%) but more results of uncertain significance (0.90 vs. 0.013%). CONCLUSION WGS may help rule in and rule out NBS disorders, pinpoint molecular diagnoses, and detect conditions not amenable to current NBS assays.
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319
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Yang H, Robinson PN, Wang K. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nat Methods 2015; 12:841-3. [PMID: 26192085 PMCID: PMC4718403 DOI: 10.1038/nmeth.3484] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/18/2015] [Indexed: 12/21/2022]
Abstract
Prior biological knowledge and phenotype information may help to identify disease genes from human whole-genome and whole-exome sequencing studies. We developed Phenolyzer (http://phenolyzer.usc.edu), a tool that uses prior information to implicate genes involved in diseases. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease genes, based on disease or phenotype terms entered as free text.
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Affiliation(s)
- Hui Yang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, California, USA
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
- Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California, USA
- Department of Psychiatry, University of Southern California, Los Angeles, California, USA
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
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320
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Abstract
Genetic testing based on whole-genome sequencing (WGS) often returns results that are not directly clinically actionable as well as raising the possibility of incidental (secondary) findings. In this article, we first survey the laws and policies guiding both researchers and clinicians in the return of results for WGS-based genetic testing. We then provide an overview of the landscape of international legislation and policies for return of these results, including considerations for return of incidental findings. Finally, we consider a range of approaches for the return of results.
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321
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Lay-Son RG, León PL. [Current perspectives on genome-based diagnostic tests in Pediatrics]. REVISTA CHILENA DE PEDIATRIA 2015. [PMID: 26223391 DOI: 10.1016/j.rchipe.2015.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Etiological diagnosis is essential in the clinical management of individual patients. Some children with complex medical conditions are subjected to numerous testing, known as "diagnostic odyssey", which often gives no conclusive results. In recent years, a revolution in genomic medicine is underway with the use of technologies that promise to increase the ability to make a diagnosis and reduce the time involved. The main advantages and limitations of genomic diagnosis, as opposed to usual methodologies are reviewed with an emphasis on Pediatrics.
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Affiliation(s)
- R Guillermo Lay-Son
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile; Hospital Padre Hurtado, San Ramón, Santiago, Chile.
| | - P Luis León
- Centro de Genética y Genómica, Clínica Alemana-Universidad del Desarrollo, Santiago, Chile
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322
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Kingsmore SF, Petrikin J, Willig LK, Guest E. Emergency medical genomes: a breakthrough application of precision medicine. Genome Med 2015; 7:82. [PMID: 26229553 PMCID: PMC4520148 DOI: 10.1186/s13073-015-0201-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Today there exist two medical applications where relatively strong evidence exists to support the broad adoption of genome-informed precision medicine. These are the differential diagnosis of single gene diseases and genotype-based selection of patients for targeted cancer therapies. However, despite the availability of the $1000 genome and $700 exome for research, there is as yet little broad uptake of genomic medicine, even in these applications. Significant impediments to mainstream adoption exist, including unavailability in many institutions, lack of scalability in others, a dearth of physician understanding of interpreted genome or exome results or knowledge of how to translate consequent precision medicine care plans, and a lack of test reimbursement. In short, genomic medicine lacks a breakthrough application. Rapid genome sequencing of acutely ill infants with suspected genetic diseases (STATseq) may become that application when scaled to dozens of trios per day without loss of timeliness or accuracy. Also critical for broad adoption is embedding STATseq in software for timely patient ascertainment, augmented intelligence for interpretation, explanation of results for generalist physicians, and dynamic precision medicine decision support.
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Affiliation(s)
- Stephen F. Kingsmore
- />Center for Pediatric Genomic Medicine, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />Department of Pediatrics, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />School of Medicine, University of Missouri — Kansas City, Kansas City, MO 64108 USA
| | - Josh Petrikin
- />Center for Pediatric Genomic Medicine, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />Department of Pediatrics, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />School of Medicine, University of Missouri — Kansas City, Kansas City, MO 64108 USA
- />Division of Neonatology, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
| | - Laurel K. Willig
- />Center for Pediatric Genomic Medicine, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />Department of Pediatrics, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />School of Medicine, University of Missouri — Kansas City, Kansas City, MO 64108 USA
- />Division of Nephrology, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
| | - Erin Guest
- />Center for Pediatric Genomic Medicine, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />Department of Pediatrics, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
- />School of Medicine, University of Missouri — Kansas City, Kansas City, MO 64108 USA
- />Division of Hematology and Oncology, Children’s Mercy — Kansas City, Kansas City, MO 64108 USA
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323
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Abstract
Next-generation sequencing is revolutionizing medical genetics and in the near future will pervade all medical fields. To maximize the potential clinical utility of this approach, global data sharing and phenotyping are needed, and the role of the geneticist in the interpretation of variation is vital.
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Affiliation(s)
- Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands ; Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - James R Lupski
- Department of Molecular and Human Genetics, Department of Pediatrics, and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza Room 604B, Houston, TX 77030 USA ; Texas Children's Hospital, Houston, TX 77030 USA
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324
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Soden SE, Saunders CJ, Willig LK, Farrow EG, Smith LD, Petrikin JE, LePichon JB, Miller NA, Thiffault I, Dinwiddie DL, Twist G, Noll A, Heese BA, Zellmer L, Atherton AM, Abdelmoity AT, Safina N, Nyp SS, Zuccarelli B, Larson IA, Modrcin A, Herd S, Creed M, Ye Z, Yuan X, Brodsky RA, Kingsmore SF. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med 2015; 6:265ra168. [PMID: 25473036 DOI: 10.1126/scitranslmed.3010076] [Citation(s) in RCA: 386] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurodevelopmental disorders (NDDs) affect more than 3% of children and are attributable to single-gene mutations at more than 1000 loci. Traditional methods yield molecular diagnoses in less than one-half of children with NDD. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can enable diagnosis of NDD, but their clinical and cost-effectiveness are unknown. One hundred families with 119 children affected by NDD received diagnostic WGS and/or WES of parent-child trios, wherein the sequencing approach was guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with nonacute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. The cost of prior negative tests in the nonacute patients was $19,100 per family, suggesting sequencing to be cost-effective at up to $7640 per family. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. If WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier than occurred in this study. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients.
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Affiliation(s)
- Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA.
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Jean-Baptiste LePichon
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA. Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Bryce A Heese
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Andrea M Atherton
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Ahmed T Abdelmoity
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Nicole Safina
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Sarah S Nyp
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Britton Zuccarelli
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ingrid A Larson
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Suzanne Herd
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Mitchell Creed
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
| | - Zhaohui Ye
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Xuan Yuan
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert A Brodsky
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO 64108, USA. School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA. Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO 64108, USA
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325
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Draft Genome Sequence of Lactobacillus panis DSM 6035T, First Isolated from Sourdough. GENOME ANNOUNCEMENTS 2015. [PMID: 26205855 PMCID: PMC4513149 DOI: 10.1128/genomea.00778-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We report a draft genome sequence of Lactobacillus panis DSM 6035T, isolated from sourdough. The genome of this strain is 2,082,789 bp long, with 47.9% G+C content. A total of 2,047 protein-coding genes were predicted.
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326
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Christensen KD, Vassy JL, Jamal L, Lehmann LS, Slashinski MJ, Perry DL, Robinson JO, Blumenthal-Barby J, Feuerman LZ, Murray MF, Green RC, McGuire AL. Are physicians prepared for whole genome sequencing? a qualitative analysis. Clin Genet 2015; 89:228-34. [PMID: 26080898 DOI: 10.1111/cge.12626] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 12/19/2022]
Abstract
Although the integration of whole genome sequencing (WGS) into standard medical practice is rapidly becoming feasible, physicians may be unprepared to use it. Primary care physicians (PCPs) and cardiologists enrolled in a randomized clinical trial of WGS received genomics education before completing semi-structured interviews. Themes about preparedness were identified in transcripts through team-based consensus-coding. Data from 11 PCPs and 9 cardiologists suggested that physicians enrolled in the trial primarily to prepare themselves for widespread use of WGS in the future. PCPs were concerned about their general genomic knowledge, while cardiologists were concerned about how to interpret specific types of results and secondary findings. Both cohorts anticipated preparing extensively before disclosing results to patients by using educational resources with which they were already familiar, and both cohorts anticipated making referrals to genetics specialists as needed. A lack of laboratory guidance, time pressures, and a lack of standards contributed to feeling unprepared. Physicians had specialty-specific concerns about their preparedness to use WGS. Findings identify specific policy changes that could help physicians feel more prepared, and highlight how providers of all types will need to become familiar with interpreting WGS results.
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Affiliation(s)
- K D Christensen
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - J L Vassy
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Section of General Internal Medicine, VA Boston Healthcare System, Boston, MA, USA
| | - L Jamal
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - L S Lehmann
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - M J Slashinski
- School of Public Health & Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - D L Perry
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - J O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - J Blumenthal-Barby
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - L Z Feuerman
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - M F Murray
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA
| | - R C Green
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Partners Personalized Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - A L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
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327
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Kalynchuk EJ, Althouse A, Parker LS, Saller DN, Rajkovic A. Prenatal whole-exome sequencing: parental attitudes. Prenat Diagn 2015; 35:1030-6. [PMID: 26151551 DOI: 10.1002/pd.4635] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The aim of this study was to survey the opinions of expectant parents regarding prenatal whole-exome sequencing. METHODS The study used a questionnaire that focused on acceptability of prenatal whole-exome sequencing to individuals who pursued first-trimester prenatal screening in a tertiary academic medical center. A total of 186 expectant individuals completed the questionnaire. The results of the questionnaire were analyzed using descriptive statistics and logistic regression models. RESULTS Eighty-three percent of the participants answered that prenatal whole-exome sequencing should be offered, 14.8% were neutral, and only 2.2% disagreed. Fifty-four percent of the participants were interested in having prenatal whole-exome sequencing for their fetus, 40.1% were neutral, and 6.6% disagreed. The majority of participants expressed a desire to know about treatable (96.2%) and non-treatable (86.3%) childhood conditions, and most said the same for treatable (76.0%) and non-treatable (74.3%) adult-onset conditions. Over half of the participants (59.7%) indicated a maximum acceptable turnaround time of 3 weeks or less for prenatal whole-exome sequencing. CONCLUSIONS The majority of respondents felt prenatal whole-exome sequencing should be offered. Moreover, the majority wanted to know prenatally about treatable and non-treatable childhood and adult conditions.
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Affiliation(s)
- Eve J Kalynchuk
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andrew Althouse
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lisa S Parker
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Devereux N Saller
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aleksandar Rajkovic
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
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328
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Khromykh A, Solomon BD, Bodian DL, Leon EL, Iyer RK, Baker RL, Ascher DP, Baveja R, Vockley JG, Niederhuber JE. Diagnosis of D-Bifunctional Protein Deficiency through Whole-Genome Sequencing: Implications for Cost-Effective Care. Mol Syndromol 2015; 6:141-6. [PMID: 26733776 DOI: 10.1159/000433621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 01/07/2023] Open
Abstract
D-Bifunctional protein deficiency, caused by recessive mutations in HSD17B4, is a severe disorder of peroxisomal fatty acid oxidation. Nonspecific clinical features may contribute to diagnostic challenges. We describe a newborn female with infantile-onset seizures and nonspecific mild dysmorphisms who underwent extensive genetic workup that resulted in the detection of a novel homozygous mutation (c.302+1_4delGTGA) in the HSD17B4 gene, consistent with a diagnosis of D-bifunctional protein deficiency. By comparing the standard clinical workup to diagnostic analysis performed through research-based whole-genome sequencing (WGS), which independently identified the causative mutation, we demonstrated the ability of genomic sequencing to serve as a timely and cost-effective diagnostic tool for the molecular diagnosis of apparent and occult newborn diseases. As genomic sequencing becomes more available and affordable, we anticipate that WGS and related omics technologies will eventually replace the traditional tiered approach to newborn diagnostic workup.
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Affiliation(s)
- Alina Khromykh
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Va., USA
| | - Benjamin D Solomon
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Va., USA; Inova Children's Hospital, Inova Health System, Falls Church, Va., USA; Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Va., USA
| | - Dale L Bodian
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Va., USA
| | - Eyby L Leon
- Division of Genetics and Metabolism, Children's National Medical Center, Washington, D.C., USA
| | - Ramaswamy K Iyer
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Va., USA; Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, Va., USA
| | - Robin L Baker
- Inova Children's Hospital, Inova Health System, Falls Church, Va., USA; Fairfax Neonatal Associates, Falls Church, Va., USA
| | - David P Ascher
- Inova Children's Hospital, Inova Health System, Falls Church, Va., USA; Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, Va., USA
| | - Rajiv Baveja
- Inova Children's Hospital, Inova Health System, Falls Church, Va., USA; Fairfax Neonatal Associates, Falls Church, Va., USA
| | - Joseph G Vockley
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Va., USA; Fairfax Neonatal Associates, Falls Church, Va., USA
| | - John E Niederhuber
- Inova Translational Medicine Institute, Inova Health System, Falls Church, Va., USA
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329
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Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet 2015; 97:111-24. [PMID: 26119816 PMCID: PMC4572507 DOI: 10.1016/j.ajhg.2015.05.020] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/22/2015] [Indexed: 12/24/2022] Open
Abstract
The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.
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Affiliation(s)
- Tudor Groza
- School of Information Technology and Electrical Engineering, University of Queensland, St. Lucia, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dawid Moldenhauer
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; University of Applied Sciences, Wiesenstrasse 14, 35390 Giessen, Germany
| | - Nicole Vasilevsky
- Library, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gareth Baynam
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6840, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Office of Population Health Genomics, Public Health and Clinical Services Division, Department of Health, Perth, WA 6004, Australia; Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; Telethon Kids Institute, Perth, WA 6008, Australia
| | - Tomasz Zemojtel
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Lynn Marie Schriml
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Warren Alden Kibbe
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Tim Beck
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Drashtti Vasant
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Andreas Zankl
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Academic Department of Medical Genetics, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2145, Australia
| | - Nicole L Washington
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Christopher J Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa A Haendel
- Library, Oregon Health & Science University, Portland, OR 97239, USA
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany.
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330
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van der Velde KJ, Kuiper J, Thompson BA, Plazzer J, van Valkenhoef G, de Haan M, Jongbloed JD, Wijmenga C, de Koning TJ, Abbott KM, Sinke R, Spurdle AB, Macrae F, Genuardi M, Sijmons RH, Swertz MA. Evaluation of CADD Scores in Curated Mismatch Repair Gene Variants Yields a Model for Clinical Validation and Prioritization. Hum Mutat 2015; 36:712-9. [PMID: 25871441 PMCID: PMC4973827 DOI: 10.1002/humu.22798] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/30/2015] [Indexed: 12/02/2022]
Abstract
Next-generation sequencing in clinical diagnostics is providing valuable genomic variant data, which can be used to support healthcare decisions. In silico tools to predict pathogenicity are crucial to assess such variants and we have evaluated a new tool, Combined Annotation Dependent Depletion (CADD), and its classification of gene variants in Lynch syndrome by using a set of 2,210 DNA mismatch repair gene variants. These had already been classified by experts from InSiGHT's Variant Interpretation Committee. Overall, we found CADD scores do predict pathogenicity (Spearman's ρ = 0.595, P < 0.001). However, we discovered 31 major discrepancies between the InSiGHT classification and the CADD scores; these were explained in favor of the expert classification using population allele frequencies, cosegregation analyses, disease association studies, or a second-tier test. Of 751 variants that could not be clinically classified by InSiGHT, CADD indicated that 47 variants were worth further study to confirm their putative pathogenicity. We demonstrate CADD is valuable in prioritizing variants in clinically relevant genes for further assessment by expert classification teams.
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Affiliation(s)
- K. Joeri van der Velde
- Genomics Coordination CenterUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Joël Kuiper
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of EpidemiologyUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Bryony A. Thompson
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - John‐Paul Plazzer
- Department of Colorectal Medicine and GeneticsRoyal Melbourne HospitalMelbourneAustralia
| | - Gert van Valkenhoef
- Department of EpidemiologyUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Mark de Haan
- Genomics Coordination CenterUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Jan D.H. Jongbloed
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Cisca Wijmenga
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Tom J. de Koning
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Kristin M. Abbott
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Richard Sinke
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Finlay Macrae
- Department of Colorectal Medicine and GeneticsRoyal Melbourne HospitalMelbourneAustralia
- Department of MedicineThe Royal Melbourne HospitalUniversity of MelbourneMelbourneAustralia
| | - Maurizio Genuardi
- Institute of Medical Genetics“A. Gemelli” School of MedicineCatholic University of the Sacred HeartRomeItaly
| | - Rolf H. Sijmons
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - Morris A. Swertz
- Genomics Coordination CenterUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
| | - InSiGHT Group
- Department of GeneticsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
- Department of Colorectal Medicine and GeneticsRoyal Melbourne HospitalMelbourneAustralia
- Department of MedicineThe Royal Melbourne HospitalUniversity of MelbourneMelbourneAustralia
- Institute of Medical Genetics“A. Gemelli” School of MedicineCatholic University of the Sacred HeartRomeItaly
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331
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Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat Genet 2015; 47:717-726. [PMID: 25985138 PMCID: PMC4601524 DOI: 10.1038/ng.3304] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 04/22/2015] [Indexed: 12/12/2022]
Abstract
To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.
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Affiliation(s)
- Jenny C Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hilary C Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stefano Lise
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - John Broxholme
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Andy Rimmer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexander Kanapin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon Fiddy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Allan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Radu Aricescu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David Beeson
- Neurosciences Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Celeste Bento
- Hematology Department, Centro Hospitalar e Universitário de Coimbra, Portugal
| | - Patricia Bignell
- Molecular Haematology Department, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Edward Blair
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Katherine Bull
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Ondrej Cais
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - Helen Chapel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Richard R Copley
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Richard Cornall
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Jude Craft
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Karin Dahan
- Centre de Génétique Humaine, Institut de Génétique et de Pathologie, Gosselies, Belgium
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Calliope Dendrou
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olivier Devuyst
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Aimée L Fenwick
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lars Fugger
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rodney D Gilbert
- University Hospital Southampton NHS Foundation Trust, University of Southampton, Southampton, UK
| | - Anne Goriely
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Anja V Gruszczyk
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert Hastings
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Edouard Hatton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Doug Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adrian Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chris Holmes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Malcolm Howard
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Linda Hughes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Johnson
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Fredrik Karpe
- Oxford Laboratory for Integrative Physiology, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan Krohn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Craig Langman
- Kidney Diseases, Feinberg School of Medicine, Northwestern University and the Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Lorne Lonie
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Joshua Luck
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Davis McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon J McGowan
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Kerry A Miller
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lisa Murray
- Illumina Cambridge Limited, Saffron Walden, UK
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - M Andrew Nesbit
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - David Nutt
- Centre for Neuropsychopharmacology, Division of Brain Sciences, Imperial College, London, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Annette Bang Oturai
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alistair Pagnamenta
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Smita Y Patel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Melanie Percy
- Department of Haematology, Belfast City Hospital, Belfast, UK
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sian E Piret
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Niko Popitsch
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lynn Quek
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter A Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Kathryn Robson
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alexandra Russo
- Department of Pediatrics, University Hospital, Mainz, Germany
| | - Natasha Sahgal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Anna Schuh
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Earl Silverman
- Division of Rheumatology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Per Soelberg Sørensen
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford NHS Regional Molecular Genetics Laboratory, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Ian Tomlinson
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen Rf Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tim Vyse
- Division of Genetics, King's College London, Guy's Hospital, London, UK
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michael P Whyte
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospital for Children, St Louis, Missouri, USA
| | - Lorna Witty
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ben Wright
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - Andrew Om Wilkie
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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332
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Marshall JD, Muller J, Collin GB, Milan G, Kingsmore SF, Dinwiddie D, Farrow EG, Miller NA, Favaretto F, Maffei P, Dollfus H, Vettor R, Naggert JK. Alström Syndrome: Mutation Spectrum of ALMS1. Hum Mutat 2015; 36:660-8. [PMID: 25846608 PMCID: PMC4475486 DOI: 10.1002/humu.22796] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 03/25/2015] [Accepted: 03/29/2015] [Indexed: 12/24/2022]
Abstract
Alström Syndrome (ALMS), a recessive, monogenic ciliopathy caused by mutations in ALMS1, is typically characterized by multisystem involvement including early cone-rod retinal dystrophy and blindness, hearing loss, childhood obesity, type 2 diabetes mellitus, cardiomyopathy, fibrosis, and multiple organ failure. The precise function of ALMS1 remains elusive, but roles in endosomal and ciliary transport and cell cycle regulation have been shown. The aim of our study was to further define the spectrum of ALMS1 mutations in patients with clinical features of ALMS. Mutational analysis in a world-wide cohort of 204 families identified 109 novel mutations, extending the number of known ALMS1 mutations to 239 and highlighting the allelic heterogeneity of this disorder. This study represents the most comprehensive mutation analysis in patients with ALMS, identifying the largest number of novel mutations in a single study worldwide. Here, we also provide an overview of all ALMS1 mutations identified to date.
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Affiliation(s)
- Jan D. Marshall
- The Jackson Laboratory, Bar Harbor, Maine USA
- Alström Syndrome International, Mount Desert, ME USA
| | - Jean Muller
- IGBMC, CNRS UMR 7104/INSERM U964/University of Strasbourg, Illkirch Cedex, France
- Laboratoire ICUBE, UMR CNRS 7357, LBGI, Université de Strasbourg, Strasbourg, France
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, 67091 Strasbourg Cedex, France
| | | | | | - Stephen F. Kingsmore
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, MO
| | - Darrell Dinwiddie
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, MO
- Department of Pediatrics, University of New Mexico, Albuquerque, NM
| | - Emily G. Farrow
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, MO
| | - Neil A. Miller
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, MO
| | | | - Pietro Maffei
- Department of Medicine, University of Padua, Padua, Italy
| | - Hélène Dollfus
- Laboratoire de Génétique médicale, UMR_S INSERM U1112, IGMA, Faculté de Médecine FMTS, Université de Strasbourg, Strasbourg, France
- Service de Génétique Médicale, Centre de Référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Roberto Vettor
- Department of Medicine, University of Padua, Padua, Italy
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333
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Jiang Y, Turinsky AL, Brudno M. The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection. Nucleic Acids Res 2015; 43:7217-28. [PMID: 26130710 PMCID: PMC4551921 DOI: 10.1093/nar/gkv677] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/19/2015] [Indexed: 12/22/2022] Open
Abstract
With the development of High-Throughput Sequencing (HTS) thousands of human genomes have now been sequenced. Whenever different studies analyze the same genome they usually agree on the amount of single-nucleotide polymorphisms, but differ dramatically on the number of insertion and deletion variants (indels). Furthermore, there is evidence that indels are often severely under-reported. In this manuscript we derive the total number of indel variants in a human genome by combining data from different sequencing technologies, while assessing the indel detection accuracy. Our estimate of approximately 1 million indels in a Yoruban genome is much higher than the results reported in several recent HTS studies. We identify two key sources of difficulties in indel detection: the insufficient coverage, read length or alignment quality; and the presence of repeats, including short interspersed elements and homopolymers/dimers. We quantify the effect of these factors on indel detection. The quality of sequencing data plays a major role in improving indel detection by HTS methods. However, many indels exist in long homopolymers and repeats, where their detection is severely impeded. The true number of indel events is likely even higher than our current estimates, and new techniques and technologies will be required to detect them.
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Affiliation(s)
- Yue Jiang
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, 150001, China
| | - Andrei L Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Michael Brudno
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada Department of Computer Science, University of Toronto, Toronto, ON, M5S 3G4, Canada
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334
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Lee S, Park SM, Kim HJ, Kim JW, Yu DS, Lee YB. Genomic diagnosis by whole genome sequencing in a Korean family with atypical progeroid syndrome. J Dermatol 2015; 42:1149-52. [PMID: 26122271 DOI: 10.1111/1346-8138.13005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/20/2015] [Indexed: 11/30/2022]
Abstract
Clinical genomic diagnosis is unfamiliar to many dermatologists. Limited knowledge of bioinformatics has limited the use of the next generation sequencing method in dermatological clinics. We evaluated the usefulness of whole genome sequencing as a diagnostic approach to inherited dermatological disease. Here, we present our experience with two female siblings with atypical familial generalized lipodystrophy with diabetes mellitus and dyslipidemia. Whole genome sequencing was performed to diagnose the inherited disease. We compared control genomic databases using the Exome Aggregation Consortium, and filtered false-positive calls with the segmental duplication, non-flagged single nucleotide variants and COSMIC mutation databases, and applied the prediction tools of SIFT and PolyPhen2. The two siblings who presented with generalized lipodystrophy were diagnosed with an atypical progeroid syndrome with a p.D136H mutation in the LMNA gene (NM_005572). We diagnosed a familial atypical progeroid syndrome using whole genome sequencing. In this paper, we present our experience with whole genome sequencing and demonstrate that it can provide useful information for clinical genomic diagnosis of inherited diseases with atypical clinical features, such as atypical progeroid syndrome.
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Affiliation(s)
- Seungbok Lee
- Seoul National University Hospital, Seoul, Korea
| | - Sae Mi Park
- Department of Dermatology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hyun Ji Kim
- Department of Dermatology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin-Wou Kim
- Department of Dermatology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dong Soo Yu
- Department of Dermatology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Young Bok Lee
- Department of Dermatology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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335
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Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases. Genome Biol 2015; 16:134. [PMID: 26112015 PMCID: PMC4499193 DOI: 10.1186/s13059-015-0693-2] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 06/12/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND To understand the contribution of Mendelian mutations to the burden of undiagnosed diseases that are suspected to be genetic in origin, we developed a next-generation sequencing-based multiplexing assay that encompasses the ~3000 known Mendelian genes. This assay, which we term the Mendeliome, comprises 13 gene panels based on clinical themes, covering the spectrum of pediatric and adult clinical genetic medicine. We explore how these panels compare with clinical whole exome sequencing (WES). RESULTS We tested 2357 patients referred with suspected genetic diagnoses from virtually every medical specialty. A likely causal mutation was identified in 1018 patients, with an overall clinical sensitivity of 43 %, comparing favorably with WES. Furthermore, the cost of clinical-grade WES is high (typically more than 4500 US dollars), whereas the cost of running a sample on one of our panels is around 75-150 US dollars, depending on the panel. Of the "negative" cases, 11 % were subsequently found by WES to harbor a likely causal mutation in a known disease gene (largely in genes identified after the design of our assay), as inferred from a representative sample of 178. Although our study population is enriched for consanguinity, 245 (24 %) of solved cases were autosomal dominant and 35 (4 %) were X-linked, suggesting that our assay is also applicable to outbred populations. CONCLUSIONS Despite missing a significant number of cases, the current version of the Mendeliome assay can account for a large proportion of suspected genetic disorders, and provides significant practical advantages over clinical WES.
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336
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Jamuar SS, Tan EC. Clinical application of next-generation sequencing for Mendelian diseases. Hum Genomics 2015; 9:10. [PMID: 26076878 PMCID: PMC4482154 DOI: 10.1186/s40246-015-0031-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/01/2015] [Indexed: 01/25/2023] Open
Abstract
Over the past decade, next-generation sequencing (NGS) has led to an exponential increase in our understanding of the genetic basis of Mendelian diseases. NGS allows for the analysis of multiple regions of the genome in one single reaction and has been shown to be a cost-effective and efficient tool in investigating patients with Mendelian diseases. More recently, NGS has been successfully deployed in the clinics, with a reported diagnostic yield of ~25 %. However, recommendations on clinical implementation of NGS are still evolving with numerous key challenges that impede the widespread use of genetics in everyday medicine. These challenges include when to order, on whom to order, what type of test to order, and how to interpret and communicate the results, including incidental findings, to the patient and family. In this review, we discuss these challenges and suggest guidelines on implementing NGS in the routine clinical workflow.
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Affiliation(s)
- Saumya Shekhar Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore.,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Ene-Choo Tan
- Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, Singapore. .,KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, 229899, Singapore, Singapore.
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337
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Abstract
The field of clinical genetics has advanced at an unprecedented pace. Today, with the aid of several high-resolution and high-precision technologies, physicians are able to make molecular genetic diagnoses for many infants affected with genetic disease. It is imperative, however, that perinatologists and neonatologists understand the strengths and limitations of genetic testing. This article discusses the different genetic testing options available for perinatal and neonatal diagnostics, along with their clinical utilities and indications. From variant-specific testing to whole-exome and genome sequencing, the article covers the whole gamut of genetic testing, with some thoughts on the changing paradigm of medical genetics.
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Affiliation(s)
- Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA
| | - Madhuri R Hegde
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Atlanta, GA 30322, USA.
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338
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Abstract
Making the diagnosis of genetic syndromes in the neonatal period can be challenging, as limited information concerning growth and development is available. The pattern of dysmorphic features and malformations is, therefore, correspondingly more important in syndrome recognition. The authors provide specific examples of the differences in the presentation for selected syndromes between the newborn period and later childhood. The purpose is to describe the variation in presentation that can occur with chronologic age and to aid in the early diagnosis of these conditions.
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339
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Mousallem T, Urban TJ, McSweeney KM, Kleinstein SE, Zhu M, Adeli M, Parrott RE, Roberts JL, Krueger B, Buckley RH, Goldstein DB. Clinical application of whole-genome sequencing in patients with primary immunodeficiency. J Allergy Clin Immunol 2015; 136:476-9.e6. [PMID: 25981738 DOI: 10.1016/j.jaci.2015.02.040] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 12/19/2014] [Accepted: 02/03/2015] [Indexed: 11/17/2022]
Affiliation(s)
- Talal Mousallem
- Departments of Internal Medicine and Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC; Department of Pediatrics, Duke University Medical Center, Durham, NC.
| | - Thomas J Urban
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC
| | - K Melodi McSweeney
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Sarah E Kleinstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Mingfu Zhu
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC
| | | | - Roberta E Parrott
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Joseph L Roberts
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Brian Krueger
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
| | - Rebecca H Buckley
- Department of Pediatrics, Duke University Medical Center, Durham, NC; Department of Immunology, Duke University School of Medicine, Durham, NC.
| | - David B Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC; Institute for Genomic Medicine, Columbia University Medical Center, New York, NY
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340
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Thiffault I, Saunders C, Jenkins J, Raje N, Canty K, Sharma M, Grote L, Welsh HI, Farrow E, Twist G, Miller N, Zwick D, Zellmer L, Kingsmore SF, Safina NP. A patient with polymerase E1 deficiency (POLE1): clinical features and overlap with DNA breakage/instability syndromes. BMC MEDICAL GENETICS 2015; 16:31. [PMID: 25948378 PMCID: PMC4630961 DOI: 10.1186/s12881-015-0177-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/24/2015] [Indexed: 12/21/2022]
Abstract
Background Chromosome instability syndromes are a group of inherited conditions associated with chromosomal instability and breakage, often leading to immunodeficiency, growth retardation and increased risk of malignancy. Case presentation We performed exome sequencing on a girl with a suspected chromosome instability syndrome that manifested as growth retardation, microcephaly, developmental delay, dysmorphic features, poikiloderma, immune deficiency with pancytopenia, and myelodysplasia. She was homozygous for a previously reported splice variant, c.4444 + 3A > G in the POLE1 gene, which encodes the catalytic subunit of DNA polymerase E. Conclusion This is the second family with POLE1-deficency, with the affected individual demonstrating a more severe phenotype than previously described. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0177-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA. .,Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA. .,Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Janda Jenkins
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Nikita Raje
- Pediatric Allergy, Asthma and Immunology Clinic, Children's Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Kristi Canty
- Dermatology Clinic, Children's Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Mukta Sharma
- Department of Hematology and Oncology, Children's Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Lauren Grote
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Holly I Welsh
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Emily Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - David Zwick
- Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA. .,Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Nicole P Safina
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
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341
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Char DS. Whole-genome sequencing in critically ill infants and emerging ethical challenges. THE LANCET RESPIRATORY MEDICINE 2015; 3:333-5. [PMID: 25937000 DOI: 10.1016/s2213-2600(15)00151-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 04/14/2015] [Indexed: 11/26/2022]
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342
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Goyal M, Bijarnia-Mahay S, Kingsmore S, Farrow E, Saunders C, Saxena R, Verma IC. Molecular diagnosis of infantile Neuro axonal Dystrophy by Next Generation Sequencing. Indian J Pediatr 2015; 82:474-7. [PMID: 25348461 PMCID: PMC4390426 DOI: 10.1007/s12098-014-1608-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/01/2014] [Indexed: 11/29/2022]
Abstract
Infantile Neuro axonal Dystrophy (INAD), is a rare inherited neurological disorder which affects nerve axons causing progressive loss of mental skills, muscular control and vision. The authors present a case of 5.8-y-old girl with INAD who was diagnosed after Next Generation Sequencing (NGS). She was born to a non-consanguineous couple and presented with hypotonia, developmental delay followed by neuroregression and nystagmus after 2 years of age. On examination, bilateral horizontal nystagmus and normal head circumference were noted. Brain MRI showed cerebellar atrophy and altered signal intensities in bilateral globus pallidi and thalami. Magnetic resonance spectroscopy (MRS) showed elevation of lactate. Metabolic testing with Tandem Mass Spectrometry (TMS) and Gas Chromatography Mass Spectrometry (GC-MS) were normal. Mitochondrial disorder was suspected in view of clinical presentation, increased lactate and neuro-imaging suggestive of Leigh syndrome. Mitochondrial Leigh mutations and SURF1 gene sequencing yielded normal results. Lack of a clear diagnosis led to performance of NGS using panel of about 514 genes. A homozygous novel mutation at position c.2277-1G>C in PLA2G6 gene presumed to give rise to altered splicing, was detected, thus confirming the diagnosis of INAD. This report provides evidence of the usefulness of NGS technology as a quick and accurate diagnostic tool for an otherwise complicated genetic disease. To the authors knowledge, this is the first case report with mutations in PLA2G6 gene from India.
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Affiliation(s)
- Manisha Goyal
- Division of Genetics & Metabolism, Department of Pediatrics, Maulana Azad Medical College, New Delhi, India
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343
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Bhattacharjee A, Sokolsky T, Wyman SK, Reese MG, Puffenberger E, Strauss K, Morton H, Parad RB, Naylor EW. Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing. Genet Med 2015; 17:337-47. [PMID: 25255367 DOI: 10.1038/gim.2014.117] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/31/2014] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Genetic testing is routinely used for second-tier confirmation of newborn sequencing results to rule out false positives and to confirm diagnoses in newborns undergoing inpatient and outpatient care. We developed a targeted next-generation sequencing panel coupled with a variant processing pipeline and demonstrated utility and performance benchmarks across multiple newborn disease presentations in a retrospective clinical study. METHODS The test utilizes an in silico gene filter that focuses directly on 126 genes related to newborn screening diseases and is applied to the exome or a next-generation sequencing panel called NBDx. NBDx targets the 126 genes and additional newborn-specific disorders. It integrates DNA isolation from minimally invasive biological specimens, targeted next-generation screening, and rapid characterization of genetic variation. RESULTS We report a rapid parallel processing of 8 to 20 cases within 105 hours with high coverage on our NBDx panel. Analytical sensitivity of 99.8% was observed across known mutation hotspots. Concordance calls with or without clinical summaries were 94% and 75%, respectively. CONCLUSION Rapid, automated targeted next-generation sequencing and analysis are practical in newborns for second-tier confirmation and neonatal intensive care unit diagnoses, laying a foundation for future primary DNA-based molecular screening of additional disorders and improving existing molecular testing options for newborns.
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Affiliation(s)
| | | | | | | | | | - Kevin Strauss
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Holmes Morton
- Clinic for Special Children, Strasburg, Pennsylvania, USA
| | - Richard B Parad
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin W Naylor
- 1] Parabase Genomics, Boston, Massachusetts, USA [2] Division of Genetics, Department of Pediatrics, Medical University of South Carolina, Charleston, South Carolina, USA
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344
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Willig LK, Petrikin JE, Smith LD, Saunders CJ, Thiffault I, Miller NA, Soden SE, Cakici JA, Herd SM, Twist G, Noll A, Creed M, Alba PM, Carpenter SL, Clements MA, Fischer RT, Hays JA, Kilbride H, McDonough RJ, Rosterman JL, Tsai SL, Zellmer L, Farrow EG, Kingsmore SF. Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings. THE LANCET RESPIRATORY MEDICINE 2015; 3:377-87. [PMID: 25937001 DOI: 10.1016/s2213-2600(15)00139-3] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/28/2022]
Abstract
BACKGROUND Genetic disorders and congenital anomalies are the leading causes of infant mortality. Diagnosis of most genetic diseases in neonatal and paediatric intensive care units (NICU and PICU) is not sufficiently timely to guide acute clinical management. We used rapid whole-genome sequencing (STATseq) in a level 4 NICU and PICU to assess the rate and types of molecular diagnoses, and the prevalence, types, and effect of diagnoses that are likely to change medical management in critically ill infants. METHODS We did a retrospective comparison of STATseq and standard genetic testing in a case series from the NICU and PICU of a large children's hospital between Nov 11, 2011, and Oct 1, 2014. The participants were families with an infant younger than 4 months with an acute illness of suspected genetic cause. The intervention was STATseq of trios (both parents and their affected infant). The main measures were the diagnostic rate, time to diagnosis, and rate of change in management after standard genetic testing and STATseq. FINDINGS 20 (57%) of 35 infants were diagnosed with a genetic disease by use of STATseq and three (9%) of 32 by use of standard genetic testing (p=0·0002). Median time to genome analysis was 5 days (range 3-153) and median time to STATseq report was 23 days (5-912). 13 (65%) of 20 STATseq diagnoses were associated with de-novo mutations. Acute clinical usefulness was noted in 13 (65%) of 20 infants with a STATseq diagnosis, four (20%) had diagnoses with strongly favourable effects on management, and six (30%) were started on palliative care. 120-day mortality was 57% (12 of 21) in infants with a genetic diagnosis. INTERPRETATION In selected acutely ill infants, STATseq had a high rate of diagnosis of genetic disorders. Most diagnoses altered the management of infants in the NICU or PICU. The very high infant mortality rate indicates a substantial need for rapid genomic diagnoses to be allied with a novel framework for precision medicine for infants in NICU and PICU who are diagnosed with genetic diseases to improve outcomes. FUNDING Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Human Genome Research Institute, and National Center for Advancing Translational Sciences.
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Affiliation(s)
- Laurel K Willig
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Josh E Petrikin
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Laurie D Smith
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Neil A Miller
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Sarah E Soden
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Julie A Cakici
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Suzanne M Herd
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Aaron Noll
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Mitchell Creed
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Patria M Alba
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Shannon L Carpenter
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Mark A Clements
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Ryan T Fischer
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - J Allyson Hays
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Howard Kilbride
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Ryan J McDonough
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Jamie L Rosterman
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Sarah L Tsai
- Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pediatrics, Children's Mercy-Kansas City, Kansas City, MO, USA; Department of Pathology, Children's Mercy-Kansas City, Kansas City, MO, USA; School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri 64108, USA.
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345
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Richer J, Daoud H, Geier P, Jarinova O, Carson N, Feberova J, Ben Fadel N, Unrau J, Bareke E, Khatchadourian K, Bulman DE, Majewski J, Boycott KM, Dyment DA. Resolution of refractory hypotension and anuria in a premature newborn with loss-of-function of ACE. Am J Med Genet A 2015; 167:1654-8. [PMID: 25899979 DOI: 10.1002/ajmg.a.37067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/05/2015] [Indexed: 11/07/2022]
Abstract
We present the investigation and management of a premature, hypotensive neonate born after a pregnancy complicated by anhydramnios to highlight the impact of early and informed management for rare kidney disease. Vasopressin was used to successfully treat refractory hypotension and anuria in the neonate born at 27 weeks of gestation. Next generation sequencing of a targeted panel of genes was then performed in the neonate and parents. Subsequently, two compound heterozygous deletions leading to frameshift mutations were identified in the angiotensin 1-converting enzyme gene ACE; exon 5:c.820_821delAG (p.Arg274Glyfs*117) and exon24: c.3521delG (p.Gly1174Alafs*12), consistent with a diagnosis of renal tubular dysgenesis. In light of the molecular diagnosis, identification, and treatment of associated low aldosterone level resulted in further improvement in renal function and only mild residual chronic renal failure is present at 14 months of age. Truncating alterations in ACE most often result in fetal demise during gestation or in the first days of life and typically as a result of the Potter sequence. The premature delivery, and serendipitous early treatment with vasopressin, and then later fludrocortisone, resulted in an optimal outcome in an otherwise lethal condition.
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Affiliation(s)
- Julie Richer
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Hussein Daoud
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Pavel Geier
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Olga Jarinova
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Nancy Carson
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Jana Feberova
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Jennifer Unrau
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Eric Bareke
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | - Karine Khatchadourian
- Division of Endocrinology, Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Dennis E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montréal, Québec, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - David A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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346
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Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants. Proc Natl Acad Sci U S A 2015; 112:5473-8. [PMID: 25827230 DOI: 10.1073/pnas.1418631112] [Citation(s) in RCA: 396] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We compared whole-exome sequencing (WES) and whole-genome sequencing (WGS) in six unrelated individuals. In the regions targeted by WES capture (81.5% of the consensus coding genome), the mean numbers of single-nucleotide variants (SNVs) and small insertions/deletions (indels) detected per sample were 84,192 and 13,325, respectively, for WES, and 84,968 and 12,702, respectively, for WGS. For both SNVs and indels, the distributions of coverage depth, genotype quality, and minor read ratio were more uniform for WGS than for WES. After filtering, a mean of 74,398 (95.3%) high-quality (HQ) SNVs and 9,033 (70.6%) HQ indels were called by both platforms. A mean of 105 coding HQ SNVs and 32 indels was identified exclusively by WES whereas 692 HQ SNVs and 105 indels were identified exclusively by WGS. We Sanger-sequenced a random selection of these exclusive variants. For SNVs, the proportion of false-positive variants was higher for WES (78%) than for WGS (17%). The estimated mean number of real coding SNVs (656 variants, ∼3% of all coding HQ SNVs) identified by WGS and missed by WES was greater than the number of SNVs identified by WES and missed by WGS (26 variants). For indels, the proportions of false-positive variants were similar for WES (44%) and WGS (46%). Finally, WES was not reliable for the detection of copy-number variations, almost all of which extended beyond the targeted regions. Although currently more expensive, WGS is more powerful than WES for detecting potential disease-causing mutations within WES regions, particularly those due to SNVs.
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347
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Identification of a large set of rare complete human knockouts. Nat Genet 2015; 47:448-52. [PMID: 25807282 DOI: 10.1038/ng.3243] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 02/13/2015] [Indexed: 12/17/2022]
Abstract
Loss-of-function mutations cause many mendelian diseases. Here we aimed to create a catalog of autosomal genes that are completely knocked out in humans by rare loss-of-function mutations. We sequenced the whole genomes of 2,636 Icelanders and imputed the sequence variants identified in this set into 101,584 additional chip-genotyped and phased Icelanders. We found a total of 6,795 autosomal loss-of-function SNPs and indels in 4,924 genes. Of the genotyped Icelanders, 7.7% are homozygotes or compound heterozygotes for loss-of-function mutations with a minor allele frequency (MAF) below 2% in 1,171 genes (complete knockouts). Genes that are highly expressed in the brain are less often completely knocked out than other genes. Homozygous loss-of-function offspring of two heterozygous parents occurred less frequently than expected (deficit of 136 per 10,000 transmissions for variants with MAF <2%, 95% confidence interval (CI) = 10-261).
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348
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Bowdin SC, Hayeems RZ, Monfared N, Cohn RD, Meyn MS. The SickKids Genome Clinic: developing and evaluating a pediatric model for individualized genomic medicine. Clin Genet 2015; 89:10-9. [PMID: 25813238 DOI: 10.1111/cge.12579] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 02/01/2015] [Accepted: 02/23/2015] [Indexed: 01/16/2023]
Abstract
Our increasing knowledge of how genomic variants affect human health and the falling costs of whole-genome sequencing are driving the development of individualized genomic medicine. This new clinical paradigm uses knowledge of an individual's genomic variants to anticipate, diagnose and manage disease. While individualized genetic medicine offers the promise of transformative change in health care, it forces us to reconsider existing ethical, scientific and clinical paradigms. The potential benefits of pre-symptomatic identification of at-risk individuals, improved diagnostics, individualized therapy, accurate prognosis and avoidance of adverse drug reactions coexist with the potential risks of uninterpretable results, psychological harm, outmoded counseling models and increased health care costs. Here we review the challenges, opportunities and limits of integrating genomic analysis into pediatric clinical practice and describe a model for implementing individualized genomic medicine. Our multidisciplinary team of bioinformaticians, health economists, health services and policy researchers, ethicists, geneticists, genetic counselors and clinicians has designed a 'Genome Clinic' research project that addresses multiple challenges in pediatric genomic medicine--ranging from development of bioinformatics tools for the clinical assessment of genomic variants and the discovery of disease genes to health policy inquiries, assessment of clinical care models, patient preference and the ethics of consent.
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Affiliation(s)
- S C Bowdin
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada.,Department of Paediatrics, University of Toronto, Toronto, Canada
| | - R Z Hayeems
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada.,Program in Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada.,Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada
| | - N Monfared
- Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada
| | - R D Cohn
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Paediatrics, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - M S Meyn
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada.,Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Paediatrics, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
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349
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Shashi V, McConkie-Rosell A, Schoch K, Kasturi V, Rehder C, Jiang YH, Goldstein DB, McDonald MT. Practical considerations in the clinical application of whole-exome sequencing. Clin Genet 2015; 89:173-81. [PMID: 25678066 DOI: 10.1111/cge.12569] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/04/2015] [Accepted: 02/08/2015] [Indexed: 01/17/2023]
Abstract
Despite the exciting advent of whole-exome sequencing (WES) in medical genetics practices, the optimal interpretation of results requires further actions such as reconsidering clinical information and obtaining further laboratory testing. There are no published data to guide clinicians in this process. In a retrospective study on 93 patients who underwent clinical WES, we set out to assess and resolve these practical challenges. With the laboratories reporting a molecular diagnostic rate of 25.8%, the medical geneticists and the laboratories were 90% concordant in their interpretation of the WES results. Divergence occurred when the medical geneticist reconsidered clinical information and/or additional information regarding pathogenicity of a variant. Variants of uncertain significance were reported in 86% of patients, with 53.7% needing follow-up, such as additional laboratory tests and genotyping of family members. By layering clinical data (e.g. mode of inheritance and phenotypic fit) on to the laboratory results, we developed clinical categories for the WES results. These categories of definite diagnosis (14/93), likely diagnosis (8/93), possible diagnosis (13/93) and no diagnosis (58/93) could be used to convey results to patients uniformly. Our framework for a clinically informed interpretation of the results enhances the utility of WES within medical genetics practices.
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Affiliation(s)
- V Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - A McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - K Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - V Kasturi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - C Rehder
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Y H Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - D B Goldstein
- Center for Human Genome Variation, Duke University Medical Center, Durham, NC, USA
| | - M T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
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350
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Dodson DS, Goldenberg AJ, Davis MM, Singer DC, Tarini BA. Parent and public interest in whole-genome sequencing. Public Health Genomics 2015; 18:151-9. [PMID: 25765282 DOI: 10.1159/000375115] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/12/2015] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE The aim of this study was to assess the baseline interest of the public in whole-genome sequencing (WGS) for oneself, parents' interest in WGS for their youngest children, and factors associated with such interest. METHODS A random sample of adults from a probability-based nationally representative online panel was surveyed. All participants were provided basic information about WGS and then asked about their interest in WGS for themselves. Those participants who were parents were additionally asked about their interest in WGS for their children. The order in which parents were asked about their interest in WGS for themselves and for their child was randomized. The relationship between parent/child characteristics and interest in WGS was examined. RESULTS The overall response rate was 62% (55% among parents). 58.6% of the total population (parents and nonparents) was interested in WGS for themselves. Similarly, 61.8% of the parents were interested in WGS for themselves and 57.8% were interested in WGS for their youngest children. Of note, 84.7% of the parents showed an identical interest level in WGS for themselves and their youngest children. Mothers as a group and parents whose youngest children had ≥2 health conditions had significantly more interest in WGS for themselves and their youngest children, while those with conservative political ideologies had considerably less. CONCLUSIONS While US adults have varying interest levels in WGS, parents appear to have similar interests in genome testing for themselves and their youngest children. As WGS technology becomes available in the clinic and private market, clinicians should be prepared to discuss WGS risks and benefits with their patients.
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Affiliation(s)
- Daniel S Dodson
- Child Health Evaluation and Research (CHEAR) Unit, University of Michigan, Ann Arbor, Mich., USA
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