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Zarate YA, Bell C, Schaefer GB. Radioulnar Synostosis and Brain Abnormalities in a Patient With 17q21.31 Microdeletion Involving EFTUD2. Cleft Palate Craniofac J 2014; 52:237-9. [PMID: 24805776 DOI: 10.1597/13-221] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mandibulofacial dysostosis with microcephaly is a rare syndromic craniofacial condition caused by heterozygous loss-of-function mutations of the EFTUD2 gene on 17q21.31. Thus far, the described musculoskeletal findings in patients with this condition include proximally placed or duplicated thumbs, overlapping toes, and toe syndactyly. We describe a severe case of a patient with a 17q21.31 microdeletion and many of the phenotypic features described in mandibulofacial dysostosis with microcephaly who had bilateral proximal radioulnar synostosis and brain abnormalities. This provides further evidence of the clinical overlap among mandibulofacial and acrofacial dysostoses syndromes and expands the phenotype of EFTUD2 haploinsufficiency due to larger deletions.
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252
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Strom SP, Lozano R, Lee H, Dorrani N, Mann J, O'Lague PF, Mans N, Deignan JL, Vilain E, Nelson SF, Grody WW, Quintero-Rivera F. De Novo variants in the KMT2A (MLL) gene causing atypical Wiedemann-Steiner syndrome in two unrelated individuals identified by clinical exome sequencing. BMC MEDICAL GENETICS 2014; 15:49. [PMID: 24886118 PMCID: PMC4072606 DOI: 10.1186/1471-2350-15-49] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/10/2014] [Indexed: 01/23/2023]
Abstract
Background Wiedemann-Steiner Syndrome (WSS) is characterized by short stature, a variety of dysmorphic facial and skeletal features, characteristic hypertrichosis cubiti (excessive hair on the elbows), mild-to-moderate developmental delay and intellectual disability. [MIM#: 605130]. Here we report two unrelated children for whom clinical exome sequencing of parent-proband trios was performed at UCLA, resulting in a molecular diagnosis of WSS and atypical clinical presentation. Case presentation For patient 1, clinical features at 9 years of age included developmental delay, craniofacial abnormalities, and multiple minor anomalies. Patient 2 presented at 1 year of age with developmental delay, microphthalmia, partial 3–4 left hand syndactyly, and craniofacial abnormalities. A de novo missense c.4342T>C variant and a de novo splice site c.4086+G>A variant were identified in the KMT2A gene in patients 1 and 2, respectively. Conclusions Based on the clinical and molecular findings, both patients appear to have novel presentations of WSS. As the hallmark hypertrichosis cubiti was not initially appreciated in either case, this syndrome was not suspected during the clinical evaluation. This report expands the phenotypic spectrum of the clinical phenotypes and KMT2A variants associated with WSS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Fabiola Quintero-Rivera
- Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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253
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Corominas R, Yang X, Lin GN, Kang S, Shen Y, Ghamsari L, Broly M, Rodriguez M, Tam S, Trigg SA, Fan C, Yi S, Tasan M, Lemmens I, Kuang X, Zhao N, Malhotra D, Michaelson JJ, Vacic V, Calderwood MA, Roth FP, Tavernier J, Horvath S, Salehi-Ashtiani K, Korkin D, Sebat J, Hill DE, Hao T, Vidal M, Iakoucheva LM. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nat Commun 2014; 5:3650. [PMID: 24722188 PMCID: PMC3996537 DOI: 10.1038/ncomms4650] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Accepted: 03/14/2014] [Indexed: 02/04/2023] Open
Abstract
Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases.
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Affiliation(s)
- Roser Corominas
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, USA,These authors contributed equally to this work
| | - Xinping Yang
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,These authors contributed equally to this work
| | - Guan Ning Lin
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, USA,These authors contributed equally to this work
| | - Shuli Kang
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, USA,These authors contributed equally to this work
| | - Yun Shen
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Lila Ghamsari
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,Present address: Columbia University, New York, New York 10032, USA
| | - Martin Broly
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Maria Rodriguez
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stanley Tam
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shelly A. Trigg
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,Present address: Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Changyu Fan
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Song Yi
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Murat Tasan
- Donnelly Centre and Departments of Molecular Genetics & Computer Science, University of Toronto, and Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada M5S 3E1
| | - Irma Lemmens
- Department of Medical Protein Research, VIB, and Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Xingyan Kuang
- Department of Computer Science and Informatics Institute, University of Missouri, Columbia, Missouri 65203, USA
| | - Nan Zhao
- Department of Computer Science and Informatics Institute, University of Missouri, Columbia, Missouri 65203, USA
| | - Dheeraj Malhotra
- Beyster Center for Genomics of Psychiatric Diseases and Department of Psychiatry, University of California San Diego, La Jolla, California 92093, USA
| | - Jacob J. Michaelson
- Beyster Center for Genomics of Psychiatric Diseases and Department of Psychiatry, University of California San Diego, La Jolla, California 92093, USA,Present address: Department of Psychiatry, University of Iowa, Iowa City, Iowa 52242, USA
| | | | - Michael A. Calderwood
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Frederick P. Roth
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,Donnelly Centre and Departments of Molecular Genetics & Computer Science, University of Toronto, and Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, Ontario, Canada M5S 3E1
| | - Jan Tavernier
- Department of Medical Protein Research, VIB, and Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Steve Horvath
- Department of Human Genetics and Biostatistics, University of California, Los Angeles, California 90095, USA
| | - Kourosh Salehi-Ashtiani
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,Present address: Division of Science and Math, and Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Dmitry Korkin
- Department of Computer Science and Informatics Institute, University of Missouri, Columbia, Missouri 65203, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases and Department of Psychiatry, University of California San Diego, La Jolla, California 92093, USA
| | - David E. Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA,
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, USA,
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Danielsson K, Mun LJ, Lordemann A, Mao J, Lin CHJ. Next-generation sequencing applied to rare diseases genomics. Expert Rev Mol Diagn 2014; 14:469-87. [PMID: 24702023 DOI: 10.1586/14737159.2014.904749] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genomics has revolutionized the study of rare diseases. In this review, we overview the latest technological development, rare disease discoveries, implementation obstacles and bioethical challenges. First, we discuss the technology of genome and exome sequencing, including the different next-generation platforms and exome enrichment technologies. Second, we survey the pioneering centers and discoveries for rare diseases, including few of the research institutions that have contributed to the field, as well as an overview survey of different types of rare diseases that have had new discoveries due to next-generation sequencing. Third, we discuss the obstacles and challenges that allow for clinical implementation, including returning of results, informed consent and privacy. Last, we discuss possible outlook as clinical genomics receives wider adoption, as third-generation sequencing is coming onto the horizon, and some needs in informatics and software to further advance the field.
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Affiliation(s)
- Krissi Danielsson
- Rare Genomics Institute, 4100 Forest Park Ave, Suite 204, St. Louis, MO 63108, USA
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255
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Machini K, Douglas J, Braxton A, Tsipis J, Kramer K. Genetic counselors' views and experiences with the clinical integration of genome sequencing. J Genet Couns 2014; 23:496-505. [PMID: 24671342 DOI: 10.1007/s10897-014-9709-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 03/05/2014] [Indexed: 01/28/2023]
Abstract
In recent years, new sequencing technologies known as next generation sequencing (NGS) have provided scientists the ability to rapidly sequence all known coding as well as non-coding sequences in the human genome. As the two emerging approaches, whole exome (WES) and whole genome (WGS) sequencing, have started to be integrated in the clinical arena, we sought to survey health care professionals who are likely to be involved in the implementation process now and/or in the future (e.g., genetic counselors, geneticists and nurse practitioners). Two hundred twenty-one genetic counselors- one third of whom currently offer WES/WGS-participated in an anonymous online survey. The aims of the survey were first, to identify barriers to the implementation of WES/WGS, as perceived by survey participants; second, to provide the first systematic report of current practices regarding the integration of WES/WGS in clinic and/or research across the US and Canada and to illuminate the roles and challenges of genetic counselors participating in this process; and third to evaluate the impact of WES/WGS on patient care. Our results showed that genetic counseling practices with respect to WES/WGS are consistent with the criteria set forth in the ACMG 2012 policy statement, which highlights indications for testing, reporting, and pre/post test considerations. Our respondents described challenges related to offering WES/WGS, which included billing issues, the duration and content of the consent process, result interpretation and disclosure of incidental findings and variants of unknown significance. In addition, respondents indicated that specialty area (i.e., prenatal and cancer), lack of clinical utility of WES/WGS and concerns about interpretation of test results were factors that prevented them from offering this technology to patients. Finally, study participants identified the aspects of their professional training which have been most beneficial in aiding with the integration of WES/WGS into the clinical setting (molecular/clinical genetics, counseling and bioethics) and suggested that counseling aids (to assist them when explaining aspects of these tests to patients) and webinars focused on WES/WGS (for genetic counselors and other health care professionals) would be useful educational tools. Future research should permit us to further enhance our knowledge of pitfalls and benefits associated with the introduction of these powerful technologies in patient care and to further explore the roles and opportunities for genetic counselors in this rapidly evolving field.
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Affiliation(s)
- Kalotina Machini
- Genetic Counseling Program, Brandeis University, MS008 415 South St., Waltham, MA, 02454-9110, USA,
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Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PIW, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJH, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PMK, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol 2014; 15:R53. [PMID: 24667040 PMCID: PMC4073084 DOI: 10.1186/gb-2014-15-3-r53] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 03/25/2014] [Indexed: 12/30/2022] Open
Abstract
Background There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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Diagnostic Exome Sequencing and Tailored Bioinformatics of the Parents of a Deceased Child with Cobalamin Deficiency Suggests Digenic Inheritance of the MTR and LMBRD1 Genes. JIMD Rep 2014; 15:29-37. [PMID: 24664876 DOI: 10.1007/8904_2014_294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 01/06/2014] [Accepted: 01/16/2014] [Indexed: 01/08/2023] Open
Abstract
Disorders of cobalamin deficiency are a heterogeneous group of disorders with at least 19 autosomal recessive-associated genes. Familial samples of an infant who died due to presumed cobalamin deficiency were referred for clinical exome sequencing. The patient died before obtaining a blood sample or skin biopsy, autopsy was declined, and DNA yielded from the newborn screening blood spot was insufficient for diagnostic testing. Whole-exome sequencing of the mother, father, and unaffected sister and tailored bioinformatics analysis was applied to search for mutations in underlying disorders with recessive inheritance. This approach identified alterations within two genes, each of which was carried by one parent. The mother carried a missense alteration in the MTR gene (c.3518C>T; p.P1173L) which was absent in the father and the sister. The father carried a translational frameshift alteration in the LMBRD1 gene (c.1056delG; p.L352Lfs*18) which was absent in the mother and present in the heterozygous state in the sister. These mutations in the MTR (MIM# 156570) and LMBRD1 (MIM# 612625) genes have been described in patients with disorders of cobalamin metabolism complementation groups cblG and cblF, respectively. The child's clinical presentation and biochemical results demonstrated overlap with both cblG and cblF. Sanger sequencing using DNA from the infant's blood spot confirmed the inheritance of the two alterations in compound heterozygous form. We present the first example of exome sequencing leading to a diagnosis in the absence of the affected patient. Furthermore, the data support the possibility for potential digenic inheritance associated with cobalamin deficiency.
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258
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The shifting model in clinical diagnostics: how next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated. Genet Med 2014; 16:736-7. [PMID: 24651604 DOI: 10.1038/gim.2014.23] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 02/10/2014] [Indexed: 11/08/2022] Open
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259
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Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf CP, Boyle S, Butte AJ, Chen R, Chen R, Clark MJ, Haraksingh R, Cowan TM, He P, Langlois S, Zoghbi HY, Snyder M, Gibbs RA, Freeze HH, Goldstein DB. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genet Med 2014; 16:751-8. [PMID: 24651605 DOI: 10.1038/gim.2014.22] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/09/2014] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The endoplasmic reticulum-associated degradation pathway is responsible for the translocation of misfolded proteins across the endoplasmic reticulum membrane into the cytosol for subsequent degradation by the proteasome. To define the phenotype associated with a novel inherited disorder of cytosolic endoplasmic reticulum-associated degradation pathway dysfunction, we studied a series of eight patients with deficiency of N-glycanase 1. METHODS Whole-genome, whole-exome, or standard Sanger sequencing techniques were employed. Retrospective chart reviews were performed in order to obtain clinical data. RESULTS All patients had global developmental delay, a movement disorder, and hypotonia. Other common findings included hypolacrima or alacrima (7/8), elevated liver transaminases (6/7), microcephaly (6/8), diminished reflexes (6/8), hepatocyte cytoplasmic storage material or vacuolization (5/6), and seizures (4/8). The nonsense mutation c.1201A>T (p.R401X) was the most common deleterious allele. CONCLUSION NGLY1 deficiency is a novel autosomal recessive disorder of the endoplasmic reticulum-associated degradation pathway associated with neurological dysfunction, abnormal tear production, and liver disease. The majority of patients detected to date carry a specific nonsense mutation that appears to be associated with severe disease. The phenotypic spectrum is likely to enlarge as cases with a broader range of mutations are detected.
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Affiliation(s)
- Gregory M Enns
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Matthew Bainbridge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michael J Gambello
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Farah R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Rebecca Crimian
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Julia Platt
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Rachel Cox
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Division of Medical Genetics, Lucile Packard Children's Hospital, Stanford University, Stanford, California, USA
| | - Mena Scavina
- Division of Pediatric Neurology, Department of Pediatrics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Rhonda S Walter
- Division of Developmental Medicine, Department of Pediatrics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Audrey Bibb
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Melanie Jones
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Madhuri Hegde
- Department of Human Genetics, Division of Medical Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Anna C Need
- Department of Medicine, Imperial College, London, UK
| | - Angelica Oviedo
- Department of Pathology and Laboratory Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Christian P Schaaf
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA [2] Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Sean Boyle
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Atul J Butte
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Rui Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rong Chen
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Michael J Clark
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Rajini Haraksingh
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Tina M Cowan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Ping He
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Huda Y Zoghbi
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA [2] Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA [3] Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Richard A Gibbs
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA [2] Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Hudson H Freeze
- Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - David B Goldstein
- 1] Center for Human Genome Variation and Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA [2] Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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Lehalle D, Gordon CT, Oufadem M, Goudefroye G, Boutaud L, Alessandri JL, Baena N, Baujat G, Baumann C, Boute-Benejean O, Caumes R, Decaestecker C, Gaillard D, Goldenberg A, Gonzales M, Holder-Espinasse M, Jacquemont ML, Lacombe D, Manouvrier-Hanu S, Marlin S, Mathieu-Dramard M, Morin G, Pasquier L, Petit F, Rio M, Smigiel R, Thauvin-Robinet C, Vasiljevic A, Verloes A, Malan V, Munnich A, de Pontual L, Vekemans M, Lyonnet S, Attié-Bitach T, Amiel J. Delineation of EFTUD2 haploinsufficiency-related phenotypes through a series of 36 patients. Hum Mutat 2014; 35:478-85. [PMID: 24470203 DOI: 10.1002/humu.22517] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/10/2014] [Indexed: 12/29/2022]
Abstract
Mandibulofacial dysostosis, Guion-Almeida type (MFDGA) is a recently delineated multiple congenital anomalies/mental retardation syndrome characterized by the association of mandibulofacial dysostosis (MFD) with external ear malformations, hearing loss, cleft palate, choanal atresia, microcephaly, intellectual disability, oesophageal atresia (OA), congenital heart defects (CHDs), and radial ray defects. MFDGA emerges as a clinically recognizable entity, long underdiagnosed due to highly variable presentations. The main differential diagnoses are CHARGE and Feingold syndromes, oculoauriculovertebral spectrum, and other MFDs. EFTUD2, located on 17q21.31, encodes a component of the major spliceosome and is disease causing in MFDGA, due to heterozygous loss-of-function (LoF) mutations. Here, we describe a series of 36 cases of MFDGA, including 24 previously unreported cases, and we review the literature in order to delineate the clinical spectrum ascribed to EFTUD2 LoF. MFD, external ear anomalies, and intellectual deficiency occur at a higher frequency than microcephaly. We characterize the evolution of the facial gestalt at different ages and describe novel renal and cerebral malformations. The most frequent extracranial malformation in this series is OA, followed by CHDs and skeletal abnormalities. MFDGA is probably more frequent than other syndromic MFDs such as Nager or Miller syndromes. Although the wide spectrum of malformations complicates diagnosis, characteristic facial features provide a useful handle.
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Affiliation(s)
- Daphné Lehalle
- Département de Génétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
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261
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Abstract
Genetics has been revolutionised by recent technologies. The latest addition to these advances is next-generation sequencing, which is set to transform clinical diagnostics in every branch of medicine. In the research arena this has already been instrumental in identifying hundreds of novel genetic syndromes, making a molecular diagnosis possible for the first time in numerous refractory cases. However, the pace of change has left many clinicians bewildered by new terminology and the implications of next-generation sequencing for their clinical practice. The rapid developments have also left many diagnostic laboratories struggling to implement these new technologies with limited resources. This review explains the basic concepts of next-generation sequencing, gives examples of its role in clinically applied research and examines the challenges of its introduction into clinical practice.
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262
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Baasch AL, Hüning I, Gilissen C, Klepper J, Veltman JA, Gillessen-Kaesbach G, Hoischen A, Lohmann K. Exome sequencing identifies a de novoSCN2Amutation in a patient with intractable seizures, severe intellectual disability, optic atrophy, muscular hypotonia, and brain abnormalities. Epilepsia 2014; 55:e25-9. [DOI: 10.1111/epi.12554] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Anna-Lena Baasch
- Institute of Neurogenetics; University of Lübeck; Lübeck Germany
| | - Irina Hüning
- Institut für Humangenetik; Universität zu Lübeck; Lübeck Germany
| | - Christian Gilissen
- Department of Human Genetics; Nijmegen Center for Molecular Life Sciences; Institute for Genetic and Metabolic Disease; Radboud University Medical Center; Nijmegen The Netherlands
| | - Joerg Klepper
- Children's Hospital Aschaffenburg; Aschaffenburg Germany
| | - Joris A. Veltman
- Department of Human Genetics; Nijmegen Center for Molecular Life Sciences; Institute for Genetic and Metabolic Disease; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Alexander Hoischen
- Department of Human Genetics; Nijmegen Center for Molecular Life Sciences; Institute for Genetic and Metabolic Disease; Radboud University Medical Center; Nijmegen The Netherlands
| | - Katja Lohmann
- Institute of Neurogenetics; University of Lübeck; Lübeck Germany
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263
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Williams JL, Faucett WA, Smith-Packard B, Wagner M, Williams MS. An assessment of time involved in pre-test case review and counseling for a whole genome sequencing clinical research program. J Genet Couns 2014; 23:516-21. [PMID: 24573557 PMCID: PMC4090811 DOI: 10.1007/s10897-014-9697-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 01/05/2014] [Indexed: 12/25/2022]
Abstract
Whole genome sequencing (WGS) is being used for evaluation of individuals with undiagnosed disease of suspected genetic origin. Implementing WGS into clinical practice will place an increased burden upon care teams with regard to pre-test patient education and counseling about results. To quantitate the time needed for appropriate pre-test evaluation of participants in WGS testing, we documented the time spent by our clinical research group on various activities related to program preparation, participant screening, and consent prior to WGS. Participants were children or young adults with autism, intellectual or developmental disability, and/or congenital anomalies, who have remained undiagnosed despite previous evaluation, and their biologic parents. Results showed that significant time was spent in securing allocation of clinical research space to counsel participants and families, and in acquisition and review of participant’s medical records. Pre-enrollment chart review identified two individuals with existing diagnoses resulting in savings of $30,000 for the genome sequencing alone, as well as saving hours of personnel time for genome interpretation and communication of WGS results. New WGS programs should plan for costs associated with additional pre-test administrative planning and patient evaluation time that will be required to provide high quality care.
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Affiliation(s)
- Janet L Williams
- Genomic Medicine Institute, Geisinger Health System, 100 N Academy Ave., Danville, PA, 17822, USA,
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264
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Atwal PS, Brennan ML, Cox R, Niaki M, Platt J, Homeyer M, Kwan A, Parkin S, Schelley S, Slattery L, Wilnai Y, Bernstein JA, Enns GM, Hudgins L. Clinical whole-exome sequencing: are we there yet? Genet Med 2014; 16:717-9. [PMID: 24525916 DOI: 10.1038/gim.2014.10] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/13/2014] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Clinical laboratories began offering whole-exome sequencing in 2011 at a cost between $4,500 and $9,000. Reported detection rates for deleterious mutations range from 25 to 50%. Based on the experience of our clinical genetics service, actual success rates may be lower than estimated rates. We report results from our own experience along with a survey of clinical geneticists to ascertain (i) current success rates for causal gene detection in a clinical setting; (ii) if there are insurance authorization issues; and (iii) if turnaround times quoted by the clinical laboratories are accurate; we also gauge provider opinions toward clinical whole-exome sequencing. METHODS We reviewed our results and the results of a survey that was electronically distributed to 47 clinical genetics centers. RESULTS A total of 35 exome reports were available. If all positive results are collated, we observe a success rate of 22.8%. One result incorrectly identified a known benign variant as pathogenic. Some insurers covered all testing, whereas others denied any insurance coverage. Only three (23.1%) of our reports were available within the laboratory's quoted turnaround times. More than 50% of clinicians queried in our survey had not ordered whole-exome sequencing at the current time, many stating concerns regarding interpretation, insurance coverage, and cost. CONCLUSION Clinical whole-exome sequencing has proven diagnostic utility; however, currently many clinicians have concerns regarding interpretation of results, insurance coverage, and cost.
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Affiliation(s)
- Paldeep Singh Atwal
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Marie-Louise Brennan
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Rachel Cox
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Michael Niaki
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Julia Platt
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Margaret Homeyer
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Andrea Kwan
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Sylvie Parkin
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Susan Schelley
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Leah Slattery
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Yael Wilnai
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | | | - Gregory M Enns
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University Medical Center, Stanford, California, USA
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265
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Patel ZH, Kottyan LC, Lazaro S, Williams MS, Ledbetter DH, Tromp H, Rupert A, Kohram M, Wagner M, Husami A, Qian Y, Valencia CA, Zhang K, Hostetter MK, Harley JB, Kaufman KM. The struggle to find reliable results in exome sequencing data: filtering out Mendelian errors. Front Genet 2014; 5:16. [PMID: 24575121 PMCID: PMC3921572 DOI: 10.3389/fgene.2014.00016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/16/2014] [Indexed: 12/30/2022] Open
Abstract
Next Generation Sequencing studies generate a large quantity of genetic data in a relatively cost and time efficient manner and provide an unprecedented opportunity to identify candidate causative variants that lead to disease phenotypes. A challenge to these studies is the generation of sequencing artifacts by current technologies. To identify and characterize the properties that distinguish false positive variants from true variants, we sequenced a child and both parents (one trio) using DNA isolated from three sources (blood, buccal cells, and saliva). The trio strategy allowed us to identify variants in the proband that could not have been inherited from the parents (Mendelian errors) and would most likely indicate sequencing artifacts. Quality control measurements were examined and three measurements were found to identify the greatest number of Mendelian errors. These included read depth, genotype quality score, and alternate allele ratio. Filtering the variants on these measurements removed ~95% of the Mendelian errors while retaining 80% of the called variants. These filters were applied independently. After filtering, the concordance between identical samples isolated from different sources was 99.99% as compared to 87% before filtering. This high concordance suggests that different sources of DNA can be used in trio studies without affecting the ability to identify causative polymorphisms. To facilitate analysis of next generation sequencing data, we developed the Cincinnati Analytical Suite for Sequencing Informatics (CASSI) to store sequencing files, metadata (eg. relatedness information), file versioning, data filtering, variant annotation, and identify candidate causative polymorphisms that follow either de novo, rare recessive homozygous or compound heterozygous inheritance models. We conclude the data cleaning process improves the signal to noise ratio in terms of variants and facilitates the identification of candidate disease causative polymorphisms.
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Affiliation(s)
- Zubin H Patel
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA ; Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati OH, USA
| | - Leah C Kottyan
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA ; Department of Veterans Affairs, Veterans Affairs Medical Center - Cincinnati, Cincinnati OH, USA
| | - Sara Lazaro
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA ; Department of Veterans Affairs, Veterans Affairs Medical Center - Cincinnati, Cincinnati OH, USA
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger Health System, Danville PA, USA
| | - David H Ledbetter
- Genomic Medicine Institute, Geisinger Health System, Danville PA, USA
| | - Hbgerard Tromp
- Genomic Medicine Institute, Geisinger Health System, Danville PA, USA
| | - Andrew Rupert
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - Mojtaba Kohram
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - Michael Wagner
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - Ammar Husami
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - Yaping Qian
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - C Alexander Valencia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - Kejian Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - Margaret K Hostetter
- Division of Infectious Disease, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA
| | - John B Harley
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA ; Department of Veterans Affairs, Veterans Affairs Medical Center - Cincinnati, Cincinnati OH, USA
| | - Kenneth M Kaufman
- Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati OH, USA ; Department of Veterans Affairs, Veterans Affairs Medical Center - Cincinnati, Cincinnati OH, USA
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266
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Severino G, Squassina A, Costa M, Pisanu C, Calza S, Alda M, Del Zompo M, Manchia M. Pharmacogenomics of bipolar disorder. Pharmacogenomics 2014; 14:655-74. [PMID: 23570469 DOI: 10.2217/pgs.13.51] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bipolar disorder (BD) is a lifelong severe psychiatric condition with high morbidity, disability and excess mortality. The longitudinal clinical trajectory of BD is significantly modified by pharmacological treatment(s), both in acute and in long-term stages. However, a large proportion of BD patients have inadequate response to pharmacological treatments. Pharmacogenomic research may lead to the identification of molecular predictors of treatment response. When integrated with clinical information, pharmacogenomic findings may be used in the future to determine the probability of response/nonresponse to treatment on an individual basis. Here we present a selective review of pharmacogenomic findings in BD. In light of the evidence suggesting a genetic effect of lithium reponse in BD, we focused particularly on the pharmacogenomic literature relevant to this trait. The article contributes a detailed overview of the current status of pharmacogenomics in BD and offers a perspective on the challenges that can hinder its transition to personalized healthcare.
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Affiliation(s)
- Giovanni Severino
- Laboratory of Molecular Genetics, Section of Neuroscience & Clinical Pharmacology, Department of Biomedical Sciences, Sp 8, Sestu-Monserrato, Km 0.700 CA, University of Cagliari, Cagliari, Italy
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267
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Schmidlen TJ, Wawak L, Kasper R, García-España JF, Christman MF, Gordon ES. Personalized genomic results: analysis of informational needs. J Genet Couns 2014; 23:578-87. [PMID: 24488620 DOI: 10.1007/s10897-014-9693-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 01/21/2014] [Indexed: 08/30/2023]
Abstract
Use of genomic information in healthcare is increasing; however data on the needs of consumers of genomic information is limited. The Coriell Personalized Medicine Collaborative (CPMC) is a longitudinal study investigating the utility of personalized medicine. Participants receive results reflecting risk of common complex conditions and drug-gene pairs deemed actionable by an external review board. To explore the needs of individuals receiving genomic information we reviewed all genetic counseling sessions with CPMC participants. A retrospective qualitative review of notes from 157 genetic counseling inquiries was conducted. Notes were coded for salient themes. Five primary themes; "understanding risk", "basic genetics", "complex disease genetics", "what do I do now?" and "other" were identified. Further review revealed that participants had difficulty with basic genetic concepts, confused relative and absolute risks, and attributed too high a risk burden to individual single nucleotide polymorphisms (SNPs). Despite these hurdles, counseled participants recognized that behavior changes could potentially mitigate risk and there were few comments alluding to an overly deterministic or fatalistic interpretation of results. Participants appeared to recognize the multifactorial nature of the diseases for which results were provided; however education to understand the complexities of genomic risk information was often needed.
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Affiliation(s)
- Tara J Schmidlen
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ, 08103, USA,
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268
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Pangrazio A, Puddu A, Oppo M, Valentini M, Zammataro L, Vellodi A, Gener B, Llano-Rivas I, Raza J, Atta I, Vezzoni P, Superti-Furga A, Villa A, Sobacchi C. Exome sequencing identifies CTSK mutations in patients originally diagnosed as intermediate osteopetrosis. Bone 2014; 59:122-6. [PMID: 24269275 PMCID: PMC3885796 DOI: 10.1016/j.bone.2013.11.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/04/2013] [Accepted: 11/14/2013] [Indexed: 12/15/2022]
Abstract
Autosomal Recessive Osteopetrosis is a genetic disorder characterized by increased bone density due to lack of resorption by the osteoclasts. Genetic studies have widely unraveled the molecular basis of the most severe forms, while cases of intermediate severity are more difficult to characterize, probably because of a large heterogeneity. Here, we describe the use of exome sequencing in the molecular diagnosis of 2 siblings initially thought to be affected by "intermediate osteopetrosis", which identified a homozygous mutation in the CTSK gene. Prompted by this finding, we tested by Sanger sequencing 25 additional patients addressed to us for recessive osteopetrosis and found CTSK mutations in 4 of them. In retrospect, their clinical and radiographic features were found to be compatible with, but not typical for, Pycnodysostosis. We sought to identify modifier genes that might have played a role in the clinical manifestation of the disease in these patients, but our results were not informative. In conclusion, we underline the difficulties of differential diagnosis in some patients whose clinical appearance does not fit the classical malignant or benign picture and recommend that CTSK gene be included in the molecular diagnosis of high bone density conditions.
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Affiliation(s)
- Alessandra Pangrazio
- UOS/IRGB, Milan Unit, CNR, Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Italy
| | - Alessandro Puddu
- CRS4 Bioinformatics Laboratory, Parco Scientifico e Tecnologico POLARIS, Pula, Italy; IRGB-CNR, Cittadella Universitaria di Monserrato, Cagliari, Italy
| | - Manuela Oppo
- CRS4 Bioinformatics Laboratory, Parco Scientifico e Tecnologico POLARIS, Pula, Italy
| | - Maria Valentini
- CRS4 Bioinformatics Laboratory, Parco Scientifico e Tecnologico POLARIS, Pula, Italy
| | | | - Ashok Vellodi
- Great Ormond Street Children's Hospital, London, United Kingdom
| | - Blanca Gener
- Servicio de Genética, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo, Spain
| | - Isabel Llano-Rivas
- Servicio de Genética, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo, Spain
| | - Jamal Raza
- National Institute of Child Health, Karachi, Pakistan
| | - Irum Atta
- National Institute of Child Health, Karachi, Pakistan
| | - Paolo Vezzoni
- UOS/IRGB, Milan Unit, CNR, Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Italy
| | - Andrea Superti-Furga
- Department of Pediatrics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Anna Villa
- UOS/IRGB, Milan Unit, CNR, Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Italy
| | - Cristina Sobacchi
- UOS/IRGB, Milan Unit, CNR, Milan, Italy; Humanitas Clinical and Research Center, Rozzano, Italy.
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269
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McDonell LM, Warman Chardon J, Schwartzentruber J, Foster D, Beaulieu CL, Majewski J, Bulman DE, Boycott KM. The utility of exome sequencing for genetic diagnosis in a familial microcephaly epilepsy syndrome. BMC Neurol 2014; 14:22. [PMID: 24479948 PMCID: PMC3916514 DOI: 10.1186/1471-2377-14-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/22/2014] [Indexed: 11/30/2022] Open
Abstract
Background Despite remarkable advances in genetic testing, many adults with syndromic epilepsy remain without a molecular diagnosis. The challenge in providing genetic testing for this patient population lies in the extensive genetic heterogeneity associated with epilepsy. Even for the subset of epilepsy patients that present with a defining feature, such as microcephaly, the number of possible genes that would require interrogation by Sanger sequencing is extensive and often prohibitively expensive. Case presentation We report a family of French Canadian descent with four adult children affected with severe intellectual disability, epilepsy and microcephaly born to consanguineous parents and evaluated by the Genetics Service to provide informed genetic counseling to unaffected family members regarding possible recurrence risks. We used whole-exome sequencing (WES) of DNA from one affected sibling as a first-line diagnostic tool and compared the prioritization of variants using two strategies: 1) focusing on genes with homozygous variants; and, 2) focusing on genes associated with microcephaly. Both approaches prioritized the same homozygous novel frameshift mutation (p.Arg608Serfs*26) in WDR62, a gene known to cause autosomal recessive primary microcephaly. Sanger sequencing confirmed the presence of the homozygous mutation in the other three affected siblings. Conclusions WES and subsequent filtering of the rare variants in a single affected family member led to the rapid and cost-effective identification of a novel homozygous frameshift mutation in WDR62, thereby explaining the severe neurodevelopmental disorder in this family and facilitating genetic counseling. Our findings support WES as an effective first-line diagnostic tool in families presenting with rare genetically heterogeneous neurological disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
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270
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Urban TJ, Goldstein DB. Pharmacogenetics at 50: Genomic Personalization Comes of Age. Sci Transl Med 2014; 6:220ps1. [DOI: 10.1126/scitranslmed.3005237] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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271
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Abstract
Genomic tools have evolved with remarkable rapidity, but their clinical relevance and application have lagged behind. Now, consistent clinical applications have finally arrived and bring with them the promise of identifying the underlying causes of complex neurological disorders in a patient-specific manner.
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Affiliation(s)
- Norman Delanty
- Department of Neurology, Beaumont Hospital, Royal College of Surgeons, Dublin 9, Ireland.
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272
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McCarthy JJ, McLeod HL, Ginsburg GS. Genomic medicine: a decade of successes, challenges, and opportunities. Sci Transl Med 2014; 5:189sr4. [PMID: 23761042 DOI: 10.1126/scitranslmed.3005785] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genomic medicine--an aspirational term 10 years ago--is gaining momentum across the entire clinical continuum from risk assessment in healthy individuals to genome-guided treatment in patients with complex diseases. We review the latest achievements in genome research and their impact on medicine, primarily in the past decade. In most cases, genomic medicine tools remain in the realm of research, but some tools are crossing over into clinical application, where they have the potential to markedly alter the clinical care of patients. In this State of the Art Review, we highlight notable examples including the use of next-generation sequencing in cancer pharmacogenomics, in the diagnosis of rare disorders, and in the tracking of infectious disease outbreaks. We also discuss progress in dissecting the molecular basis of common diseases, the role of the host microbiome, the identification of drug response biomarkers, and the repurposing of drugs. The significant challenges of implementing genomic medicine are examined, along with the innovative solutions being sought. These challenges include the difficulty in establishing clinical validity and utility of tests, how to increase awareness and promote their uptake by clinicians, a changing regulatory and coverage landscape, the need for education, and addressing the ethical aspects of genomics for patients and society. Finally, we consider the future of genomics in medicine and offer a glimpse of the forces shaping genomic medicine, such as fundamental shifts in how we define disease, how medicine is delivered to patients, and how consumers are managing their own health and affecting change.
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Affiliation(s)
- Jeanette J McCarthy
- Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA
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273
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Wellness and health omics linked to the environment: the WHOLE approach to personalized medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 799:1-14. [PMID: 24292959 DOI: 10.1007/978-1-4614-8778-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The WHOLE approach to personalized medicine represents an effort to integrate clinical and genomic profiling jointly into preventative health care and the promotion of wellness. Our premise is that genotypes alone are insufficient to predict health outcomes, since they fail to account for individualized responses to the environment and life history. Instead, integrative genomic approaches incorporating whole genome sequences and transcriptome and epigenome profiles, all combined with extensive clinical data obtained at annual health evaluations, have the potential to provide more informative wellness classification. As with traditional medicine where the physician interprets subclinical signs in light of the person's health history, truly personalized medicine will be founded on algorithms that extract relevant information from genomes but will also require interpretation in light of the triggers, behaviors, and environment that are unique to each person. This chapter discusses some of the major obstacles to implementation, from development of risk scores through integration of diverse omic data types to presentation of results in a format that fosters development of personal health action plans.
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274
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Chantret I, Couvineau A, Moore S. [Novel deglycosylation-independent roles for peptide N-glycanase]. Med Sci (Paris) 2014; 30:47-54. [PMID: 24472459 DOI: 10.1051/medsci/20143001013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The primary function of peptide N-glycanase (PNGase) is thought to be the deglycosylation of endoplasmic reticulum associated degradation (ERAD) substrates. However, inhibition of PNGase appears to have little effect upon the destruction rate of many ERAD substrates, and recent data demonstrate deglycosylation-independent functions for PNGase. Whatever the roles of PNGase turn out to be, the identification of a patient presenting with PNGase deficiency will advance our understanding of the importance of this multifunctional protein in human physiology.
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Affiliation(s)
- Isabelle Chantret
- Inserm U773, centre de recherche Bichat Beaujon CRB3, Faculté de médecine Xavier Bichat, 75018 Paris, France - Université Paris 7 Denis Diderot, site Bichat, 16, rue Henri Huchard, 75018, Paris, France
| | - Alain Couvineau
- Inserm U773, centre de recherche Bichat Beaujon CRB3, Faculté de médecine Xavier Bichat, 75018 Paris, France - Université Paris 7 Denis Diderot, site Bichat, 16, rue Henri Huchard, 75018, Paris, France
| | - Stuart Moore
- Inserm U773, centre de recherche Bichat Beaujon CRB3, Faculté de médecine Xavier Bichat, 75018 Paris, France - Université Paris 7 Denis Diderot, site Bichat, 16, rue Henri Huchard, 75018, Paris, France
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275
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Abstract
Understanding human genetic variation and how it impacts on gene function is a major focus in genomic-based research. Translation of this knowledge into clinical care is exemplified by pharmacogenetics/pharmacogenomics. The identification of particular gene variants that might influence drug uptake, metabolism, distribution or excretion promises a more effective personalised medicine approach in choosing the right drug or its dose for any particular individual. Adverse drug responses can then be avoided or mitigated. An understanding of germline or acquired (somatic) DNA mutations can also be used to identify drugs that are more likely to be therapeutically beneficial. This represents an area of growing interest in the treatment of cancer.
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276
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Levenson D. Next-generation sequencing may reduce cost and wait time for some genetic diagnoses: Experts argue that clinical evaluation remains crucial. Am J Med Genet A 2013; 161A:vii-viii. [DOI: 10.1002/ajmg.a.36349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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277
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Zheng Z, Geng J, Yao RE, Li C, Ying D, Shen Y, Ying L, Yu Y, Fu Q. Molecular defects identified by whole exome sequencing in a child with Fanconi anemia. Gene 2013; 530:295-300. [DOI: 10.1016/j.gene.2013.08.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 08/01/2013] [Accepted: 08/09/2013] [Indexed: 01/25/2023]
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278
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O'Brien JE, Meisler MH. Sodium channel SCN8A (Nav1.6): properties and de novo mutations in epileptic encephalopathy and intellectual disability. Front Genet 2013; 4:213. [PMID: 24194747 PMCID: PMC3809569 DOI: 10.3389/fgene.2013.00213] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/04/2013] [Indexed: 11/13/2022] Open
Abstract
The sodium channel Nav1.6, encoded by the gene SCN8A, is one of the major voltage-gated channels in human brain. The sequences of sodium channels have been highly conserved during evolution, and minor changes in biophysical properties can have a major impact in vivo. Insight into the role of Nav1.6 has come from analysis of spontaneous and induced mutations of mouse Scn8a during the past 18 years. Only within the past year has the role of SCN8A in human disease become apparent from whole exome and genome sequences of patients with sporadic disease. Unique features of Nav1.6 include its contribution to persistent current, resurgent current, repetitive neuronal firing, and subcellular localization at the axon initial segment (AIS) and nodes of Ranvier. Loss of Nav1.6 activity results in reduced neuronal excitability, while gain-of-function mutations can increase neuronal excitability. Mouse Scn8a (med) mutants exhibit movement disorders including ataxia, tremor and dystonia. Thus far, more than ten human de novo mutations have been identified in patients with two types of disorders, epileptic encephalopathy and intellectual disability. We review these human mutations as well as the unique features of Nav1.6 that contribute to its role in determining neuronal excitability in vivo. A supplemental figure illustrating the positions of amino acid residues within the four domains and 24 transmembrane segments of Nav1.6 is provided to facilitate the location of novel mutations within the channel protein.
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Affiliation(s)
- Janelle E O'Brien
- Department of Human Genetics, University of Michigan Ann Arbor, MI, USA
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279
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Neveling K, Feenstra I, Gilissen C, Hoefsloot LH, Kamsteeg EJ, Mensenkamp AR, Rodenburg RJT, Yntema HG, Spruijt L, Vermeer S, Rinne T, van Gassen KL, Bodmer D, Lugtenberg D, de Reuver R, Buijsman W, Derks RC, Wieskamp N, van den Heuvel B, Ligtenberg MJL, Kremer H, Koolen DA, van de Warrenburg BPC, Cremers FPM, Marcelis CLM, Smeitink JAM, Wortmann SB, van Zelst-Stams WAG, Veltman JA, Brunner HG, Scheffer H, Nelen MR. A post-hoc comparison of the utility of sanger sequencing and exome sequencing for the diagnosis of heterogeneous diseases. Hum Mutat 2013; 34:1721-6. [PMID: 24123792 DOI: 10.1002/humu.22450] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 09/04/2013] [Indexed: 01/20/2023]
Abstract
The advent of massive parallel sequencing is rapidly changing the strategies employed for the genetic diagnosis and research of rare diseases that involve a large number of genes. So far it is not clear whether these approaches perform significantly better than conventional single gene testing as requested by clinicians. The current yield of this traditional diagnostic approach depends on a complex of factors that include gene-specific phenotype traits, and the relative frequency of the involvement of specific genes. To gauge the impact of the paradigm shift that is occurring in molecular diagnostics, we assessed traditional Sanger-based sequencing (in 2011) and exome sequencing followed by targeted bioinformatics analysis (in 2012) for five different conditions that are highly heterogeneous, and for which our center provides molecular diagnosis. We find that exome sequencing has a much higher diagnostic yield than Sanger sequencing for deafness, blindness, mitochondrial disease, and movement disorders. For microsatellite-stable colorectal cancer, this was low under both strategies. Even if all genes that could have been ordered by physicians had been tested, the larger number of genes captured by the exome would still have led to a clearly superior diagnostic yield at a fraction of the cost.
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Affiliation(s)
- Kornelia Neveling
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands; Institute for Genetic and Metabolic Disease, Radboud university medical centre, Nijmegen, The Netherlands
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280
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Lescai F, Marasco E, Bacchelli C, Stanier P, Mantovani V, Beales P. Identification and validation of loss of function variants in clinical contexts. Mol Genet Genomic Med 2013; 2:58-63. [PMID: 24498629 PMCID: PMC3907911 DOI: 10.1002/mgg3.42] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 09/05/2013] [Indexed: 12/20/2022] Open
Abstract
The choice of an appropriate variant calling pipeline for exome sequencing data is becoming increasingly more important in translational medicine projects and clinical contexts. Within GOSgene, which facilitates genetic analysis as part of a joint effort of the University College London and the Great Ormond Street Hospital, we aimed to optimize a variant calling pipeline suitable for our clinical context. We implemented the GATK/Queue framework and evaluated the performance of its two callers: the classical UnifiedGenotyper and the new variant discovery tool HaplotypeCaller. We performed an experimental validation of the loss-of-function (LoF) variants called by the two methods using Sequenom technology. UnifiedGenotyper showed a total validation rate of 97.6% for LoF single-nucleotide polymorphisms (SNPs) and 92.0% for insertions or deletions (INDELs), whereas HaplotypeCaller was 91.7% for SNPs and 55.9% for INDELs. We confirm that GATK/Queue is a reliable pipeline in translational medicine and clinical context. We conclude that in our working environment, UnifiedGenotyper is the caller of choice, being an accurate method, with a high validation rate of error-prone calls like LoF variants. We finally highlight the importance of experimental validation, especially for INDELs, as part of a standard pipeline in clinical environments.
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Affiliation(s)
- Francesco Lescai
- University College London, Institute of Child Health, GOSgene team London, U.K ; Department of Biomedicine, Human Genetics, Aarhus University Aarhus, Denmark
| | - Elena Marasco
- CRBA Centro Ricerca Biomedica Applicata, Azienda Ospedaliero-Universitaria Policlinico S. Orsola - Malpighi Bologna, Italy
| | - Chiara Bacchelli
- University College London, Institute of Child Health, GOSgene team London, U.K
| | - Philip Stanier
- University College London, Institute of Child Health, GOSgene team London, U.K
| | - Vilma Mantovani
- Department of Biomedicine, Human Genetics, Aarhus University Aarhus, Denmark
| | - Philip Beales
- University College London, Institute of Child Health, GOSgene team London, U.K
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281
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Clouthier DE, Passos-Bueno MR, Tavares ALP, Lyonnet S, Amiel J, Gordon CT. Understanding the basis of auriculocondylar syndrome: Insights from human, mouse and zebrafish genetic studies. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:306-17. [PMID: 24123988 DOI: 10.1002/ajmg.c.31376] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Among human birth defect syndromes, malformations affecting the face are perhaps the most striking due to cultural and psychological expectations of facial shape. One such syndrome is auriculocondylar syndrome (ACS), in which patients present with defects in ear and mandible development. Affected structures arise from cranial neural crest cells, a population of cells in the embryo that reside in the pharyngeal arches and give rise to most of the bone, cartilage and connective tissue of the face. Recent studies have found that most cases of ACS arise from defects in signaling molecules associated with the endothelin signaling pathway. Disruption of this signaling pathway in both mouse and zebrafish results in loss of identity of neural crest cells of the mandibular portion of the first pharyngeal arch and the subsequent repatterning of these cells, leading to homeosis of lower jaw structures into more maxillary-like structures. These findings illustrate the importance of endothelin signaling in normal human craniofacial development and illustrate how clinical and basic science approaches can coalesce to improve our understanding of the genetic basis of human birth defect syndromes. Further, understanding the genetic basis for ACS that lies outside of known endothelin signaling components may help elucidate unknown aspects critical to the establishment of neural crest cell patterning during facial morphogenesis.
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282
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Pengelly RJ, Gibson J, Andreoletti G, Collins A, Mattocks CJ, Ennis S. A SNP profiling panel for sample tracking in whole-exome sequencing studies. Genome Med 2013; 5:89. [PMID: 24070238 PMCID: PMC3978886 DOI: 10.1186/gm492] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/16/2013] [Indexed: 12/17/2022] Open
Abstract
Whole-exome sequencing provides a cost-effective means to sequence protein coding regions within the genome, which are significantly enriched for etiological variants. We describe a panel of single nucleotide polymorphisms (SNPs) to facilitate the validation of data provenance in whole-exome sequencing studies. This is particularly significant where multiple processing steps necessitate transfer of sample custody between clinical, laboratory and bioinformatics facilities. SNPs captured by all commonly used exome enrichment kits were identified, and filtered for possible confounding properties. The optimised panel provides a simple, yet powerful, method for the assignment of intrinsic, highly discriminatory identifiers to genetic samples.
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Affiliation(s)
- Reuben J Pengelly
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
| | - Jane Gibson
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
| | - Gaia Andreoletti
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
| | - Andrew Collins
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
| | - Christopher J Mattocks
- National Genetics Reference Laboratory (Wessex), Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Duthie Building (MP 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
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283
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Lehrach H. DNA sequencing methods in human genetics and disease research. F1000PRIME REPORTS 2013; 5:34. [PMID: 24049638 PMCID: PMC3768324 DOI: 10.12703/p5-34] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA sequencing has revolutionized biological and medical research, and is poised to have a similar impact in medicine. This tool is just one of a number of developments in our capability to identify, quantitate and functionally characterize the components of the biological networks keeping us healthy or making us sick, but in many respects it has played the leading role in this process. The new technologies do, however, also provide a bridge between genotype and phenotype, both in man and model (as well as all other) organisms, revolutionize the identification of elements involved in a multitude of human diseases or other phenotypes, and generate a wealth of medically relevant information on every single person, as the basis of a truly personalized medicine of the future.
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Affiliation(s)
- Hans Lehrach
- Max Planck Institute for Molecular GeneticsIhnestrasse 73, 14195, BerlinGermany
- Dahlem Centre for Genome Research and Medical Systems BiologyFabeckstrasse 60-62, 14195 BerlinGermany
- Alacris Theranostics GmbHFabeckstrasse. 60-62, 14195 BerlinGermany
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284
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Carmichael H, Shen Y, T T, Hirschhorn JN, Dauber A. Whole exome sequencing in a patient with uniparental disomy of chromosome 2 and a complex phenotype. Clin Genet 2013; 84:213-22. [PMID: 23167750 PMCID: PMC3996682 DOI: 10.1111/cge.12064] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 11/15/2012] [Accepted: 11/15/2012] [Indexed: 12/11/2022]
Abstract
Whole exome sequencing and chromosomal microarrays are two powerful technologies that have transformed the ability of researchers to search for potentially causal variants in human disease. This study combines these tools to search for causal variants in a patient found to have maternal uniparental isodisomy of chromosome 2. This subject has a complex phenotype including skeletal and renal dysplasia, immune deficiencies, growth failure, retinal degeneration and ovarian insufficiency. Eighteen non-synonymous, rare homozygous variants were identified on chromosome 2. Additionally, five genes with compound heterozygous mutations were detected on other chromosomes that could lead to a disease phenotype independent of the uniparental disomy found in this case. Several candidate genes with potential connection to the phenotype are described but none are definitively proven to be causal. This study highlights the potential for detection of a large number of candidate genes using whole exome sequencing complicating interpretation in both the research and clinical settings. Forums must be created for publication and sharing of detailed phenotypic and genotypic reports to facilitate further biological discoveries and clinical counseling.
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Affiliation(s)
| | - Yiping Shen
- Department of Laboratory Medicine, Boston Children's Hospital
- Department of Pathology, Harvard Medical School
| | - Thutrang T
- Division of Endocrinology, Boston Children’s Hospital
- Center for Basic and Translational Obesity Research, Boston Children’s Hospital
| | - Joel N Hirschhorn
- Division of Endocrinology, Boston Children’s Hospital
- Program in Medical and Population Genetics, Broad Institute
- Center for Basic and Translational Obesity Research, Boston Children’s Hospital
- Department of Genetics, Harvard Medical School
| | - Andrew Dauber
- Division of Endocrinology, Boston Children’s Hospital
- Program in Medical and Population Genetics, Broad Institute
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285
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Shashi V, McConkie-Rosell A, Rosell B, Schoch K, Vellore K, McDonald M, Jiang YH, Xie P, Need A, Goldstein DB, Goldstein DG. The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders. Genet Med 2013; 16:176-82. [PMID: 23928913 DOI: 10.1038/gim.2013.99] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/11/2013] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The purpose of this study was to assess the diagnostic yield of the traditional, comprehensive clinical evaluation and targeted genetic testing, within a general genetics clinic. These data are critically needed to develop clinically and economically grounded diagnostic algorithms that consider presenting phenotype, traditional genetics testing, and the emerging role of next-generation sequencing (whole-exome/genome sequencing). METHODS We retrospectively analyzed a cohort of 500 unselected consecutive patients who received traditional genetic diagnostic evaluations at a tertiary medical center. We calculated the diagnosis rate, number of visits to diagnosis, genetic tests, and the cost of testing. RESULTS Thirty-nine patients were determined to not have a genetic disorder; 212 of the remaining 461 (46%) received a genetic diagnosis, and 72% of these were diagnosed on the first visit. The cost per subsequent successful genetic diagnosis was estimated at $25,000. CONCLUSION Almost half of the patients were diagnosed using the traditional approach, most at the initial visit. For those remaining undiagnosed, next-generation sequencing may be clinically and economically beneficial. Estimating a 50% success rate for next-generation sequencing in undiagnosed genetic disorders, its application after the first clinical visit could result in a higher rate of genetic diagnosis at a considerable cost savings per successful diagnosis.
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Affiliation(s)
- Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Bruce Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Kasturi Vellore
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Marie McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Pingxing Xie
- Center for Human Genome Variation, Duke University Medical Center, Durham, North Carolina, USA
| | - Anna Need
- Center for Human Genome Variation, Duke University Medical Center, Durham, North Carolina, USA
| | | | - David G Goldstein
- Center for Human Genome Variation, Duke University Medical Center, Durham, North Carolina, USA
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286
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Handel AE, Disanto G, Ramagopalan SV. Next-generation sequencing in understanding complex neurological disease. Expert Rev Neurother 2013; 13:215-27. [PMID: 23368808 DOI: 10.1586/ern.12.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing techniques have made vast quantities of data on human genomes and transcriptomes available to researchers. Huge progress has been made towards understanding the basis of many Mendelian neurological conditions, but progress has been considerably slower in complex neurological diseases (multiple sclerosis, migraine, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and so on). The authors review current next-generation sequencing methodologies and present selected studies illustrating how these have been used to cast light on the genetic etiology of complex neurological diseases with specific focus on multiple sclerosis. The authors highlight particular pitfalls in next-generation sequencing experiments and speculate on both clinical and research applications of these sequencing platforms for complex neurological disorders in the future.
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Affiliation(s)
- Adam E Handel
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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287
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Carney PR. Special issue on epilepsy. Exp Neurol 2013; 244:1-3. [PMID: 23651566 DOI: 10.1016/j.expneurol.2013.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Paul R Carney
- Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
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288
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Abstract
Whole genome/exome sequencing (WGS/WES) integration into medicine will yield a new disease paradigm moving from clinical to molecular diagnosis. This paradigm will present significant challenges in the interpretation of sequence data and clinicians will face dilemmas about if, when and how to offer information to patients. Sequencing will ultimately reshape psychiatry in predicting disease risk and lead to greater understanding of aetiology, prognosis and/or treatment response. This commentary on the ethics of returning WGS/WES results describes the nature of the data as a dynamic health resource, the importance of understanding participant motivations, determinations of personal utility and potential effects of WGS/WES on self-concept and well-being. As this technology unfurls, ethical challenges will not be novel but they will be compounded by the volume and scope of the data. Research into participant/patient perceptions, preferences and outcomes will identify areas of caution and prepare psychiatrists for eventual integration into clinical care.
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289
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Voigt C, Mégarbané A, Neveling K, Czeschik JC, Albrecht B, Callewaert B, von Deimling F, Hehr A, Falkenberg Smeland M, König R, Kuechler A, Marcelis C, Puiu M, Reardon W, Riise Stensland HMF, Schweiger B, Steehouwer M, Teller C, Martin M, Rahmann S, Hehr U, Brunner HG, Lüdecke HJ, Wieczorek D. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies - expanding the phenotypes associated with EFTUD2 mutations. Orphanet J Rare Dis 2013; 8:110. [PMID: 23879989 PMCID: PMC3727992 DOI: 10.1186/1750-1172-8-110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/05/2013] [Indexed: 12/25/2022] Open
Abstract
Background Mutations in EFTUD2 were proven to cause a very distinct mandibulofacial dysostosis type Guion-Almeida (MFDGA, OMIM #610536). Recently, gross deletions and mutations in EFTUD2 were determined to cause syndromic esophageal atresia (EA), as well. We set forth to find further conditions caused by mutations in the EFTUD2 gene (OMIM *603892). Methods and results We performed exome sequencing in two familial cases with clinical features overlapping with MFDGA and EA, but which were previously assumed to represent distinct entities, a syndrome with esophageal atresia, hypoplasia of zygomatic complex, microcephaly, cup-shaped ears, congenital heart defect, and intellectual disability in a mother and her two children [AJMG 143A(11):1135-1142, 2007] and a supposedly autosomal recessive oto-facial syndrome with midline malformations in two sisters [AJMG 132(4):398-401, 2005]. While the analysis of our exome data was in progress, a recent publication made EFTUD2 mutations highly likely in these families. This hypothesis could be confirmed with exome as well as with Sanger sequencing. Also, in three further sporadic patients, clinically overlapping to these two families, de novo mutations within EFTUD2 were identified by Sanger sequencing. Our clinical and molecular workup of the patients discloses a broad phenotypic spectrum, and describes for the first time an instance of germline mosaicism for an EFTUD2 mutation. Conclusions The clinical features of the eight patients described here further broaden the phenotypic spectrum caused by EFTUD2 mutations or deletions. We here show, that it not only includes mandibulofacial dysostosis type Guion-Almeida, which should be reclassified as an acrofacial dysostosis because of thumb anomalies (present in 12/35 or 34% of patients) and syndromic esophageal atresia [JMG 49(12). 737-746, 2012], but also the two new syndromes, namely oto-facial syndrome with midline malformations published by Mégarbané et al. [AJMG 132(4): 398-401, 2005] and the syndrome published by Wieczorek et al. [AJMG 143A(11): 1135-1142, 2007] The finding of mild phenotypic features in the mother of one family that could have been overlooked and the possibility of germline mosaicism in apparently healthy parents in the other family should be taken into account when counseling such families.
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Affiliation(s)
- Claudia Voigt
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
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290
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Abstract
Genomic technologies are reaching the point of being able to detect genetic variation in patients at high accuracy and reduced cost, offering the promise of fundamentally altering medicine. Still, although scientists and policy advisers grapple with how to interpret and how to handle the onslaught and ambiguity of genome-wide data, established and well-validated molecular technologies continue to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities. Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics. In parallel, we outline implementation challenges that will be necessary to address to ensure the future of genetic medicine.
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291
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Key Informants’ Perspectives of Implementing Chromosomal Microarrays Into Clinical Practice in Australia. Twin Res Hum Genet 2013; 16:833-9. [DOI: 10.1017/thg.2013.43] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
High-resolution genomic tests have the potential to revolutionize healthcare by vastly improving mutation detection. The use of chromosomal microarray (CMA) represents one of the earliest examples of these new genomic tests being introduced and disseminated in the clinic. While CMA has clear advantages over traditional karyotyping in terms of mutation detection, little research has investigated the process by which CMA was implemented in clinical settings. Fifteen key informants, six clinicians, and nine laboratory scientists from four Australian states were interviewed about their experiences during and in the time since CMA was adopted for clinical use. Participants discussed challenges such as result interpretation and communication. Strengths were also highlighted, including the collaborative approaches of some centers. Clinical experiences and opinions can inform larger studies with a range of stakeholders, including patients. The historical perspectives from this retrospective study can be helpful in guiding the implementation of future genomic technologies such as whole exome/genome sequencing.
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292
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Wade CH, Tarini BA, Wilfond BS. Growing up in the genomic era: implications of whole-genome sequencing for children, families, and pediatric practice. Annu Rev Genomics Hum Genet 2013; 14:535-55. [PMID: 23875800 DOI: 10.1146/annurev-genom-091212-153425] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Whole-genome sequencing (WGS) has advanced to a point where it is beginning to be integrated into pediatric practice. With little consensus on how to maximize the benefits of WGS for children, there is a growing need for focused efforts that connect researchers, clinicians, and families to chart a path forward. To illustrate relevant concerns, two contrasting applications of pediatric WGS are explored: clinical use with children who have undiagnosed conditions, and population-based screening. Specific challenges for health care services, policy development, and the well-being of children are discussed in light of current research. In the interest of ensuring evidence-based pediatric WGS, strategies are identified for advancing our understanding of what it means for children to grow up with WGS results guiding their health care.
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Affiliation(s)
- Christopher H Wade
- Nursing and Health Studies Program, University of Washington Bothell, Bothell, Washington 98011;
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293
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Carvill GL, Heavin SB, Yendle SC, McMahon JM, O’Roak BJ, Cook J, Khan A, Dorschner MO, Weaver M, Calvert S, Malone S, Wallace G, Stanley T, Bye AME, Bleasel A, Howell KB, Kivity S, Mackay MT, Rodriguez-Casero V, Webster R, Korczyn A, Afawi Z, Zelnick N, Lerman-Sagie T, Lev D, Møller RS, Gill D, Andrade DM, Freeman JL, Sadleir LG, Shendure J, Berkovic SF, Scheffer IE, Mefford HC. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. Nat Genet 2013; 45:825-30. [PMID: 23708187 PMCID: PMC3704157 DOI: 10.1038/ng.2646] [Citation(s) in RCA: 460] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 05/01/2013] [Indexed: 12/16/2022]
Abstract
Epileptic encephalopathies are a devastating group of epilepsies with poor prognosis, of which the majority are of unknown etiology. We perform targeted massively parallel resequencing of 19 known and 46 candidate genes for epileptic encephalopathy in 500 affected individuals (cases) to identify new genes involved and to investigate the phenotypic spectrum associated with mutations in known genes. Overall, we identified pathogenic mutations in 10% of our cohort. Six of the 46 candidate genes had 1 or more pathogenic variants, collectively accounting for 3% of our cohort. We show that de novo CHD2 and SYNGAP1 mutations are new causes of epileptic encephalopathies, accounting for 1.2% and 1% of cases, respectively. We also expand the phenotypic spectra explained by SCN1A, SCN2A and SCN8A mutations. To our knowledge, this is the largest cohort of cases with epileptic encephalopathies to undergo targeted resequencing. Implementation of this rapid and efficient method will change diagnosis and understanding of the molecular etiologies of these disorders.
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Affiliation(s)
- Gemma L. Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, 98195, USA
| | - Sinéad B. Heavin
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Simone C. Yendle
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Jacinta M. McMahon
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Brian J. O’Roak
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Joseph Cook
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, 98195, USA
| | - Adiba Khan
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, 98195, USA
| | - Michael O Dorschner
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, Washington, 98195, USA
- Veteran Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Molly Weaver
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, Washington, 98195, USA
- Veteran Affairs Puget Sound Health Care System, Seattle, WA 98108, USA
| | - Sophie Calvert
- Neurosciences Children’s Health Queensland, Royal and Mater Children’s Hospitals, Brisbane, Queensland, Australia
| | - Stephen Malone
- Neurosciences Children’s Health Queensland, Royal and Mater Children’s Hospitals, Brisbane, Queensland, Australia
| | - Geoffrey Wallace
- Neurosciences Children’s Health Queensland, Royal and Mater Children’s Hospitals, Brisbane, Queensland, Australia
| | - Thorsten Stanley
- Department of Paediatrics, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Ann M. E. Bye
- Department of Paediatric Neurology, University of New South Wales, Sydney Children’s Hospital, Sydney, New South Wales, Australia
| | - Andrew Bleasel
- Westmead Hospital, University of Sydney, Sydney, New South Wales, Australia
| | - Katherine B. Howell
- Department of Neurology, The Royal Children’s Hospital, Parkville, Melbourne, Victoria, Australia
| | - Sara Kivity
- Epilepsy Unit, Schneider Children’s Medical Center of Israel, Petach Tikvah, Israel
| | - Mark T. Mackay
- Department of Neurology, The Royal Children’s Hospital, Parkville, Melbourne, Victoria, Australia
- Critical Care & Neurosciences Theme, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, The Royal Children’s Hospital, Melbourne, Victoria, Australia
| | | | - Richard Webster
- TY Nelson Department of Neurology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Amos Korczyn
- Department of Neurology, Tel-Aviv University, Tel-Aviv, Israel
| | - Zaid Afawi
- Tel-Aviv University Medical School, Tel-Aviv, Israel
| | - Nathanel Zelnick
- Department of Pediatrics, Carmel Medical Center, Technion Faculty of Medicine, Haifa, Israel
| | - Tally Lerman-Sagie
- Metabolic-Neurogenetic Service, Wolfson Medical Center, Holon, and Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Dorit Lev
- Metabolic-Neurogenetic Service, Wolfson Medical Center, Holon, and Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Deepak Gill
- TY Nelson Department of Neurology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Danielle M. Andrade
- Division of Neurology, Department of Medicine, University of Toronto, Toronto Western Hospital, Krembil Neurosciences Program. Toronto, Canada
| | - Jeremy L. Freeman
- Department of Neurology, The Royal Children’s Hospital, Parkville, Melbourne, Victoria, Australia
- Critical Care & Neurosciences Theme, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Lynette G. Sadleir
- Department of Paediatrics, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Samuel F. Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Ingrid E. Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Department of Neurology, The Royal Children’s Hospital, Parkville, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, The Royal Children’s Hospital, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
| | - Heather C. Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, 98195, USA
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294
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Robinson MK, Caminis J, Brunkow ME. Sclerostin: how human mutations have helped reveal a new target for the treatment of osteoporosis. Drug Discov Today 2013; 18:637-43. [DOI: 10.1016/j.drudis.2013.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 03/29/2013] [Accepted: 04/03/2013] [Indexed: 12/14/2022]
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295
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Patel CJ, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, Chen R, Morgan AA, Martin GS, Brigham KL, Butte AJ, Gibson G. Whole genome sequencing in support of wellness and health maintenance. Genome Med 2013; 5:58. [PMID: 23806097 PMCID: PMC3967117 DOI: 10.1186/gm462] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/23/2013] [Accepted: 06/27/2013] [Indexed: 12/19/2022] Open
Abstract
Background Whole genome sequencing is poised to revolutionize personalized medicine, providing the capacity to classify individuals into risk categories for a wide range of diseases. Here we begin to explore how whole genome sequencing (WGS) might be incorporated alongside traditional clinical evaluation as a part of preventive medicine. The present study illustrates novel approaches for integrating genotypic and clinical information for assessment of generalized health risks and to assist individuals in the promotion of wellness and maintenance of good health. Methods Whole genome sequences and longitudinal clinical profiles are described for eight middle-aged Caucasian participants (four men and four women) from the Center for Health Discovery and Well Being (CHDWB) at Emory University in Atlanta. We report multivariate genotypic risk assessments derived from common variants reported by genome-wide association studies (GWAS), as well as clinical measures in the domains of immune, metabolic, cardiovascular, musculoskeletal, respiratory, and mental health. Results Polygenic risk is assessed for each participant for over 100 diseases and reported relative to baseline population prevalence. Two approaches for combining clinical and genetic profiles for the purposes of health assessment are then presented. First we propose conditioning individual disease risk assessments on observed clinical status for type 2 diabetes, coronary artery disease, hypertriglyceridemia and hypertension, and obesity. An approximate 2:1 ratio of concordance between genetic prediction and observed sub-clinical disease is observed. Subsequently, we show how more holistic combination of genetic, clinical and family history data can be achieved by visualizing risk in eight sub-classes of disease. Having identified where their profiles are broadly concordant or discordant, an individual can focus on individual clinical results or genotypes as they develop personalized health action plans in consultation with a health partner or coach. Conclusion The CHDWB will facilitate longitudinal evaluation of wellness-focused medical care based on comprehensive self-knowledge of medical risks.
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Affiliation(s)
- Chirag J Patel
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Palo Alto, CA 94304, USA ; Lucille Packard Children's Hospital, 725 Welch Rd, Palo Alto, CA 94304, USA
| | - Ambily Sivadas
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta GA 30332, USA
| | - Rubina Tabassum
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta GA 30332, USA
| | - Thanawadee Preeprem
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta GA 30332, USA
| | - Jing Zhao
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta GA 30332, USA
| | - Dalia Arafat
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta GA 30332, USA
| | - Rong Chen
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Palo Alto, CA 94304, USA ; Lucille Packard Children's Hospital, 725 Welch Rd, Palo Alto, CA 94304, USA ; Personalis, Inc., 1350 Willow Rd Suite 202, Menlo Park, CA 94025, USA
| | - Alexander A Morgan
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Palo Alto, CA 94304, USA ; Lucille Packard Children's Hospital, 725 Welch Rd, Palo Alto, CA 94304, USA
| | - Gregory S Martin
- Center for Health Discovery and Well Being, and School of Medicine, Emory University Midtown Hospital, 550 Peachtree St, Atlanta GA 30308, USA
| | - Kenneth L Brigham
- Center for Health Discovery and Well Being, and School of Medicine, Emory University Midtown Hospital, 550 Peachtree St, Atlanta GA 30308, USA
| | - Atul J Butte
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 251 Campus Drive, Palo Alto, CA 94304, USA ; Lucille Packard Children's Hospital, 725 Welch Rd, Palo Alto, CA 94304, USA
| | - Greg Gibson
- School of Biology, Georgia Institute of Technology, 310 Ferst Drive, Atlanta GA 30332, USA ; Center for Health Discovery and Well Being, and School of Medicine, Emory University Midtown Hospital, 550 Peachtree St, Atlanta GA 30308, USA
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296
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Goldstein DB, Allen A, Keebler J, Margulies EH, Petrou S, Petrovski S, Sunyaev S. Sequencing studies in human genetics: design and interpretation. Nat Rev Genet 2013; 14:460-70. [PMID: 23752795 DOI: 10.1038/nrg3455] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Next-generation sequencing is becoming the primary discovery tool in human genetics. There have been many clear successes in identifying genes that are responsible for Mendelian diseases, and sequencing approaches are now poised to identify the mutations that cause undiagnosed childhood genetic diseases and those that predispose individuals to more common complex diseases. There are, however, growing concerns that the complexity and magnitude of complete sequence data could lead to an explosion of weakly justified claims of association between genetic variants and disease. Here, we provide an overview of the basic workflow in next-generation sequencing studies and emphasize, where possible, measures and considerations that facilitate accurate inferences from human sequencing studies.
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Affiliation(s)
- David B Goldstein
- Center for Human Genome Variation, Duke University School of Medicine, 308 Research Drive, Box 91009, LSRC B Wing, Room 330, Durham, North Carolina 27708, USA.
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297
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Grove ME, Wolpert MN, Cho MK, Lee SSJ, Ormond KE. Views of genetics health professionals on the return of genomic results. J Genet Couns 2013; 23:531-8. [PMID: 23728783 DOI: 10.1007/s10897-013-9611-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 05/16/2013] [Indexed: 10/26/2022]
Abstract
As exome and whole genome sequencing become clinically available, the potential to receive a large number of clinically relevant but incidental results is a significant challenge in the provision of genomic counseling. We conducted three focus groups of a total of 35 individuals who were members of ASHG and/or NSGC, assessing views towards the return of genomic results. Participants stressed that patient autonomy was primary. There was consensus that a mechanism to return results to the healthcare provider, rather than patient, and to streamline integration into the electronic health record would ensure these results had the maximal impact on patient management. All three focus groups agreed that pharmacogenomic results were reasonable to return and that they were not felt to be stigmatizing. With regard to the return of medically relevant results, there was much debate. Participants had difficulty in consistently assigning specific diseases to 'bins' that were considered obligatory versus optional for disclosure. Consensus was reached regarding the importance of informed consent and pretest counseling visits to clarify what the return of results process would entail. Evidence based professional guidelines should continue to be developed and regularly revised to assist in consistently and appropriately providing genomic results to patients.
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Affiliation(s)
- Megan E Grove
- Department of Genetics, Stanford University, Stanford, CA, USA
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298
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Interpreting the role of de novo protein-coding mutations in neuropsychiatric disease. Nat Genet 2013; 45:234-8. [PMID: 23438595 DOI: 10.1038/ng.2555] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 01/18/2013] [Indexed: 12/15/2022]
Abstract
Pedigree, linkage and association studies are consistent with heritable variation for complex disease due to the segregation of genetic factors in families and in the population. In contrast, de novo mutations make only minor contributions to heritability estimates for complex traits. Nonetheless, some de novo variants are known to be important in disease etiology. The identification of risk-conferring de novo variants will contribute to the discovery of etiologically relevant genes and pathways and may help in genetic counseling. There is considerable interest in the role of such mutations in complex neuropsychiatric disease, largely driven by new genotyping and sequencing technologies. An important role for large de novo copy number variations has been established. Recently, whole-exome sequencing has been used to extend the investigation of de novo variation to point mutations in protein-coding regions. Here, we consider several challenges for the interpretation of such mutations in the context of their role in neuropsychiatric disease.
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299
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Johnston JJ, Wen KK, Keppler-Noreuil K, McKane M, Maiers JL, Greiner A, Sapp JC, Demali KA, Rubenstein PA, Biesecker LG. Functional analysis of a de novo ACTB mutation in a patient with atypical Baraitser-Winter syndrome. Hum Mutat 2013; 34:1242-9. [PMID: 23649928 DOI: 10.1002/humu.22350] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/30/2013] [Indexed: 11/08/2022]
Abstract
Exome sequence analysis can be instrumental in identifying the genetic etiology behind atypical disease. We report a patient presenting with microcephaly, dysmorphic features, and intellectual disability with a tentative diagnosis of Dubowitz syndrome. Exome analysis was performed on the patient and both parents. A de novo missense variant was identified in ACTB, c.349G>A, p.E117K. Recent work in Baraitser-Winter syndrome has identified ACTB and ACTG1 mutations in a cohort of individuals, and we rediagnosed the patient with atypical Baraitser-Winter syndrome. We performed functional characterization of the variant actin and show that it alters cell adhesion and polymer formation supporting its role in disease. We present the clinical findings in the patient, comparison of this patient to other patients with ACTB/ACTG1 mutations, and results from actin functional studies that demonstrate novel functional attributes of this mutant protein.
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Affiliation(s)
- Jennifer J Johnston
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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300
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Lohn Z, Adam S, Birch PH, Friedman JM. Incidental findings from clinical genome-wide sequencing: a review. J Genet Couns 2013; 23:463-73. [PMID: 23709124 DOI: 10.1007/s10897-013-9604-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 05/02/2013] [Indexed: 12/11/2022]
Abstract
There are several unresolved challenges associated with the clinical application of genome-wide sequencing technologies. One of the most discussed issues is incidental findings (IF), which are defined as discoveries made as a result of genetic testing that are unrelated to the indication for the test. The discussion surrounding IF began in the context of research, which we have used to frame consideration of IF in the clinical context. There is growing consensus that analytically valid and medically actionable IF should be offered to patients, but whether and to what extent clinicians should disclose other kinds of IF is debated. While others have systematically reviewed the literature concerning genetic IF, previous reviews focus on ethical and research-related issues and do not consider the implications for the genetic counseling profession specifically. This review discusses the practical considerations, ethical concerns and genetic counseling issues related to IF, with a particular focus on clinical genome-wide sequencing. To date, the bulk of the literature with respect to IF in the clinical context consists of commentaries, reviews and case reports. There is a need for more empirical studies to provide a foundation for institutional protocols and evidence-based clinical practice standards.
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Affiliation(s)
- Z Lohn
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada,
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