101
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Information Technology Support for Clinical Genetic Testing within an Academic Medical Center. J Pers Med 2016; 6:jpm6010004. [PMID: 26805890 PMCID: PMC4810383 DOI: 10.3390/jpm6010004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/08/2015] [Accepted: 12/28/2015] [Indexed: 12/30/2022] Open
Abstract
Academic medical centers require many interconnected systems to fully support genetic testing processes. We provide an overview of the end-to-end support that has been established surrounding a genetic testing laboratory within our environment, including both laboratory and clinician facing infrastructure. We explain key functions that we have found useful in the supporting systems. We also consider ways that this infrastructure could be enhanced to enable deeper assessment of genetic test results in both the laboratory and clinic.
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102
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Exploring the landscape of pathogenic genetic variation in the ExAC population database: insights of relevance to variant classification. Genet Med 2015; 18:850-4. [PMID: 26681313 DOI: 10.1038/gim.2015.180] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/30/2015] [Indexed: 11/08/2022] Open
Abstract
PURPOSE We evaluated the Exome Aggregation Consortium (ExAC) database as a control cohort to classify variants across a diverse set of genes spanning dominant and recessively inherited disorders. METHODS The frequency of pathogenic variants in ExAC was compared with the estimated maximal pathogenic allele frequency (MPAF), based on the disease prevalence, penetrance, inheritance, allelic and locus heterogeneity of each gene. Additionally, the observed carrier frequency and the ethnicity-specific variant distribution were compared between ExAC and the published literature. RESULTS The carrier frequency and ethnic distribution of pathogenic variants in ExAC were concordant with reported estimates. Of 871 pathogenic/likely pathogenic variants across 19 genes, only 3 exceeded the estimated MPAF. Eighty-four percent of variants with ExAC frequencies above the estimated MPAF were classified as "benign." Additionally, 20% of the cardiac and 19% of the Lynch syndrome gene variants originally classified as "VUS" occurred with ExAC frequencies above the estimated MPAF, making these suitable for reassessment. CONCLUSIONS The ExAC database is a useful source for variant classification and is not overrepresented for pathogenic variants in the genes evaluated. However, the mutational spectrum, pseudogenes, genetic heterogeneity, and paucity of literature should be considered in deriving meaningful classifications using ExAC.Genet Med 18 8, 850-854.
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103
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Ceyhan-Birsoy O, Pugh TJ, Bowser MJ, Hynes E, Frisella AL, Mahanta LM, Lebo MS, Amr SS, Funke BH. Next generation sequencing-based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies. Mol Genet Genomic Med 2015; 4:143-51. [PMID: 27066507 PMCID: PMC4799872 DOI: 10.1002/mgg3.187] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/04/2022] Open
Abstract
Background Diagnostic testing for genetic cardiomyopathies has undergone dramatic changes in the last decade with next generation sequencing (NGS) expanding the number of genes that can be interrogated simultaneously. Exon resolution copy number analysis is increasingly incorporated into routine diagnostic testing via cytogenomic arrays and more recently via NGS. While NGS is an attractive option for laboratories that have no access to array platforms, its higher false positive rate requires weighing the added cost incurred by orthogonal confirmation against the magnitude of the increase in diagnostic yield. Although copy number variants (CNVs) have been reported in various cardiomyopathy genes, their contribution has not been systematically studied. Methods We performed single exon resolution NGS‐based deletion/duplication analysis for up to 46 cardiomyopathy genes in >1400 individuals with cardiomyopathies including HCM, DCM, ARVC, RCM, and LVNC. Results and Conclusion Clinically significant deletions and duplications were identified in only 9 of 1425 (0.63%) individuals. The majority of those (6/9) represented intragenic events. We conclude that the added benefit of exon level deletion/duplication analysis is low for currently known cardiomyopathy genes and may not outweigh the increased cost and complexity of incorporating it into routine diagnostic testing for these disorders.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Laboratory for Molecular MedicinePartners HealthCare Personalized MedicineCambridgeMassachusetts; Department of PathologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Trevor J Pugh
- Department of Medical Biophysics Princess Margaret Cancer Centre University Health Network University of Toronto Toronto Ontario Canada
| | - Mark J Bowser
- Laboratory for Molecular Medicine Partners HealthCare Personalized Medicine Cambridge Massachusetts
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine Partners HealthCare Personalized Medicine Cambridge Massachusetts
| | - Ashley L Frisella
- Laboratory for Molecular Medicine Partners HealthCare Personalized Medicine Cambridge Massachusetts
| | - Lisa M Mahanta
- Laboratory for Molecular Medicine Partners HealthCare Personalized Medicine Cambridge Massachusetts
| | - Matt S Lebo
- Laboratory for Molecular MedicinePartners HealthCare Personalized MedicineCambridgeMassachusetts; Department of PathologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Sami S Amr
- Laboratory for Molecular MedicinePartners HealthCare Personalized MedicineCambridgeMassachusetts; Department of PathologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusetts
| | - Birgit H Funke
- Laboratory for Molecular MedicinePartners HealthCare Personalized MedicineCambridgeMassachusetts; Department of PathologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusetts
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104
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Abou Tayoun AN, Al Turki SH, Oza AM, Bowser MJ, Hernandez AL, Funke BH, Rehm HL, Amr SS. Improving hearing loss gene testing: a systematic review of gene evidence toward more efficient next-generation sequencing-based diagnostic testing and interpretation. Genet Med 2015; 18:545-53. [PMID: 26562227 DOI: 10.1038/gim.2015.141] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/27/2015] [Indexed: 12/11/2022] Open
Abstract
PURPOSE With next generation sequencing technology improvement and cost reductions, it has become technically feasible to sequence a large number of genes in one diagnostic test. This is especially relevant for diseases with large genetic and/or phenotypic heterogeneity, such as hearing loss. However, variant interpretation remains the major bottleneck. This is further exacerbated by the lack in the clinical genetics community of consensus criteria for defining the evidence necessary to include genes on targeted disease panels or in genomic reports, and the consequent risk of reporting variants in genes with no relevance to disease. METHODS We describe a systematic evidence-based approach for assessing gene-disease associations and for curating relevant genes for different disease aspects, including mode of inheritance, phenotypic severity, and mutation spectrum. RESULTS By applying this approach to clinically available hearing loss gene panels with a total of 163 genes, we show that a significant number (45%) of genes lack sufficient evidence of association with disease and thus are expected to increase uncertainty and patient anxiety, in addition to intensifying the interpretation burden. Information about all curated genes is summarized. Our retrospective analysis of 539 hearing loss cases tested by our previous OtoGenomeV2 panel demonstrates the impact of including genes with weak disease association in laboratory wet-bench and interpretation processes. CONCLUSION Our study is, to our knowledge, the first to highlight the urgent need for defining the clinical validity of gene-disease relationships for more efficient and accurate clinical testing and reporting.Genet Med 18 6, 545-553.
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Affiliation(s)
- Ahmad N Abou Tayoun
- Genetics Training Program, Harvard Medical School, Cambridge, Massachusetts, USA.,Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Saeed H Al Turki
- Genetics Training Program, Harvard Medical School, Cambridge, Massachusetts, USA
| | - Andrea M Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Mark J Bowser
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Amy L Hernandez
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA
| | - Birgit H Funke
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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105
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Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, Strom CM, Keiles SB, Higgins JJ. A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. Hum Mutat 2015; 37:127-34. [PMID: 26467025 PMCID: PMC4737317 DOI: 10.1002/humu.22918] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/07/2015] [Indexed: 11/08/2022]
Abstract
We developed a rules‐based scoring system to classify DNA variants into five categories including pathogenic, likely pathogenic, variant of uncertain significance (VUS), likely benign, and benign. Over 16,500 pathogenicity assessments on 11,894 variants from 338 genes were analyzed for pathogenicity based on prediction tools, population frequency, co‐occurrence, segregation, and functional studies collected from internal and external sources. Scores were calculated by trained scientists using a quantitative framework that assigned differential weighting to these five types of data. We performed descriptive and comparative statistics on the dataset and tested interobserver concordance among the trained scientists. Private variants defined as variants found within single families (n = 5,182), were either VUS (80.5%; n = 4,169) or likely pathogenic (19.5%; n = 1,013). The remaining variants (n = 6,712) were VUS (38.4%; n = 2,577) or likely benign/benign (34.7%; n = 2,327) or likely pathogenic/pathogenic (26.9%, n = 1,808). Exact agreement between the trained scientists on the final variant score was 98.5% [95% confidence interval (CI) (98.0, 98.9)] with an interobserver consistency of 97% [95% CI (91.5, 99.4)]. Variant scores were stable and showed increasing odds of being in agreement with new data when re‐evaluated periodically. This carefully curated, standardized variant pathogenicity scoring system provides reliable pathogenicity scores for DNA variants encountered in a clinical laboratory setting.
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Affiliation(s)
- Izabela Karbassi
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Glenn A Maston
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Angela Love
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | | | - Corey D Braastad
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | | | - Alison R Bright
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Domenic Previte
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Ke Zhang
- Quest Diagnostics, Nichols Institute, San Juan Capistrano, California
| | | | - Michele McCarthy
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | | | - Felicita Dubois
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | | | - Sat Dev Batish
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Jeffrey Jones
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Khalida Liaquat
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Carol A Hoffman
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | | | - Zhenyuan Wang
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
| | - Weimin Sun
- Quest Diagnostics, Nichols Institute, San Juan Capistrano, California
| | | | - Charles M Strom
- Quest Diagnostics, Nichols Institute, San Juan Capistrano, California
| | - Steven B Keiles
- Quest Diagnostics, Nichols Institute, San Juan Capistrano, California
| | - Joseph J Higgins
- Quest Diagnostics, Athena Diagnostics, Marlborough, Massachusetts
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Tayoun ANA, Mason-Suares H, Frisella AL, Bowser M, Duffy E, Mahanta L, Funke B, Rehm HL, Amr SS. Targeted Droplet-Digital PCR as a Tool for Novel Deletion Discovery at the DFNB1 Locus. Hum Mutat 2015; 37:119-26. [DOI: 10.1002/humu.22912] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/21/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Ahmad N. Abou Tayoun
- Harvard Medical School Genetics Training Program; Harvard; Cambridge MA
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
- Division of Genomic Diagnostics; The Children's Hospital of Philadelphia; The University of Pennsylvania Perelman School of Medicine; PA
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
- Department of Pathology; Brigham and Women's Hospital; Harvard Medical School; Boston MA
| | - Ashley L. Frisella
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
| | - Mark Bowser
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
| | - Elizabeth Duffy
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
| | - Lisa Mahanta
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
| | - Birgit Funke
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
- Department of Pathology; Brigham and Women's Hospital; Harvard Medical School; Boston MA
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
- Department of Pathology; Brigham and Women's Hospital; Harvard Medical School; Boston MA
| | - Sami S. Amr
- Laboratory for Molecular Medicine; Partners Healthcare Personalized Medicine; Cambridge MA
- Department of Pathology; Brigham and Women's Hospital; Harvard Medical School; Boston MA
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107
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Krier JB, Green RC. Management of Incidental Findings in Clinical Genomic Sequencing. ACTA ACUST UNITED AC 2015; 87:9.23.1-9.23.16. [PMID: 26439717 DOI: 10.1002/0471142905.hg0923s87] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genomic sequencing is becoming accurate, fast, and increasingly inexpensive, and is rapidly being incorporated into clinical practice. Incidental or secondary findings, which can occur in large numbers from genomic sequencing, are a potential barrier to the utility of this new technology due to their relatively high prevalence and the lack of evidence or guidelines available to guide their clinical interpretation. This unit reviews the definition, classification, and management of incidental findings from genomic sequencing. The unit focuses on the clinical aspects of handling incidental findings, with an emphasis on the key role of clinical context in defining incidental findings and determining their clinical relevance and utility.
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Affiliation(s)
- Joel B Krier
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Robert C Green
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.,Broad Institute, Boston, Massachusetts
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108
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Biancalana V, Laporte J. Diagnostic use of Massively Parallel Sequencing in Neuromuscular Diseases: Towards an Integrated Diagnosis. J Neuromuscul Dis 2015; 2:193-203. [PMID: 27858740 PMCID: PMC5240547 DOI: 10.3233/jnd-150092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is revolutionizing the genetic testing in diagnosis laboratories, replacing gene-by-gene investigations with a "gene panel" strategy. This new approach is particularly promising for the diagnosis of neuromuscular disorders affecting children as well as adults, which is constrained by strong clinical and genetic heterogeneity. While it leads to a strong improvement in molecular diagnosis, this new approach is dramatically changing the whole diagnosis process, establishing new decision trees and requiring integrated strategies between clinicians and laboratories. To have an overview of the implementation and benefit of these novel sequencing strategies for the diagnosis of neuromuscular disorders, we surveyed the current literature on the application of targeted genes panel sequencing, exome sequencing and genome sequencing. We highlight advantages and disadvantages of these different strategies in a diagnosis setting, discuss about unresolved cases, and point potential validation approaches and outcomes of massively parallel sequencing. It appears important to integrate such novel strategies with clinical, histopathological and imaging investigations, for a faster and more accurate diagnosis and patient care, and to foster research projects and clinical trials.
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Affiliation(s)
- Valérie Biancalana
- Faculté de Médecine, Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Strasbourg, France
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
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109
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Farrugia A, Keyser C, Hollard C, Raul J, Muller J, Ludes B. Targeted next generation sequencing application in cardiac channelopathies: Analysis of a cohort of autopsy-negative sudden unexplained deaths. Forensic Sci Int 2015; 254:5-11. [DOI: 10.1016/j.forsciint.2015.06.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/22/2015] [Accepted: 06/24/2015] [Indexed: 12/19/2022]
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110
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Delio M, Patel K, Maslov A, Marion RW, McDonald TV, Cadoff EM, Golden A, Greally JM, Vijg J, Morrow B, Montagna C. Development of a Targeted Multi-Disorder High-Throughput Sequencing Assay for the Effective Identification of Disease-Causing Variants. PLoS One 2015; 10:e0133742. [PMID: 26214305 PMCID: PMC4516357 DOI: 10.1371/journal.pone.0133742] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/30/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND While next generation sequencing (NGS) is a useful tool for the identification of genetic variants to aid diagnosis and support therapy decision, high sequencing costs have limited its application within routine clinical care, especially in economically depressed areas. To investigate the utility of a multi-disease NGS based genetic test, we designed a custom sequencing assay targeting over thirty disease-associated areas including cardiac disorders, intellectual disabilities, hearing loss, collagenopathies, muscular dystrophy, Ashkenazi Jewish genetic disorders, and complex Mendelian disorders. We focused on these specific areas based on the interest of our collaborative clinical team, suggesting these diseases being the ones in need for the development of a sequencing-screening assay. RESULTS We targeted all coding, untranslated regions (UTR) and flanking intronic regions of 650 known disease-associated genes using the Roche-NimbleGen EZ SeqCapV3 capture system and sequenced on the Illumina HiSeq 2500 Rapid Run platform. Eight controls with known variants and one HapMap sample were first sequenced to assess the performance of the panel. Subsequently, as a proof of principle and to explore the possible utility of our test, we analyzed test disease subjects (n = 16). Eight had known Mendelian disorders and eight had complex pediatric diseases. In addition to assess whether copy number variation may be of utility as a companion assay relative to these specific disease areas, we used the Affymetrix Genome-Wide SNP Array 6.0 to analyze the same samples. CONCLUSION We identified potentially disease-associated variants: 22 missense, 4 nonsense, 1 frameshift, and 1 splice variants (16 previously identified, 12 novel among dbSNP and 15 novel among NHLBI Exome Variant Server). We found multi-disease targeted high-throughput sequencing to be a cost efficient approach in detecting disease-associated variants to aid diagnosis.
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Affiliation(s)
- Maria Delio
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Kunjan Patel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Alex Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Robert W. Marion
- Divisions of Developmental Medicine & Genetics, Children's Hospital at Montefiore, Bronx, New York, United States of America
| | - Thomas V. McDonald
- Department of Medicine/Cardiology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Evan M. Cadoff
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Aaron Golden
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Bernice Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, United States of America
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111
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Gorokhova S, Biancalana V, Lévy N, Laporte J, Bartoli M, Krahn M. Clinical massively parallel sequencing for the diagnosis of myopathies. Rev Neurol (Paris) 2015; 171:558-71. [PMID: 26022190 DOI: 10.1016/j.neurol.2015.02.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 01/28/2015] [Accepted: 02/04/2015] [Indexed: 02/07/2023]
Abstract
Massively parallel sequencing, otherwise known as high-throughput or next-generation sequencing, is rapidly gaining wide use in clinical practice due to possibility of simultaneous exploration of multiple genomic regions. More than 300 genes have been implicated in neuromuscular disorders, meaning that many genes need to be considered in a differential diagnosis for a patient affected with myopathy. By providing sequencing information for numerous genes at the same time, massively parallel sequencing greatly accelerates the diagnostic processes of myopathies compared to the classical "gene-after-gene" approach by Sanger sequencing. In this review, we describe multiple advantages of this powerful sequencing method for applications in myopathy diagnosis. We also outline recent studies that used this approach to discover new myopathy-causing genes and to diagnose cohorts of patients with muscular disorders. Finally, we highlight the key aspects and limitations of massively parallel sequencing that a neurologist considering this test needs to know in order to interpret the results of the test and to deal with other issues concerning the test.
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Affiliation(s)
- S Gorokhova
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France
| | - V Biancalana
- Laboratoire Diagnostic Génétique, Nouvel Hôpital Civil, 1, place de l'Hôpital, BP 426, 67091 Strasbourg cedex, France; Department of Translational Medicine and Neurogenetics, I.G.B.M.C., INSERM U964, CNRS UMR7104, Strasbourg University, 1, rue Laurent-Fries, 67404 Illkirch, France
| | - N Lévy
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France; AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, 264, rue Saint-Pierre, 13385 Marseille cedex 05, France
| | - J Laporte
- Department of Translational Medicine and Neurogenetics, I.G.B.M.C., INSERM U964, CNRS UMR7104, Strasbourg University, 1, rue Laurent-Fries, 67404 Illkirch, France
| | - M Bartoli
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France; AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, 264, rue Saint-Pierre, 13385 Marseille cedex 05, France
| | - M Krahn
- Aix Marseille Université, INSERM, GMGF, UMR_S 910, Faculté de Médecine, secteur Timone, 27, boulevard Jean-Moulin, 13385 Marseille cedex, France; AP-HM, Département de Génétique Médicale, Hôpital Timone Enfants, 264, rue Saint-Pierre, 13385 Marseille cedex 05, France.
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Perreault-Micale C, Davie J, Breton B, Hallam S, Greger V. A rigorous approach for selection of optimal variant sets for carrier screening with demonstration of clinical utility. Mol Genet Genomic Med 2015; 3:363-73. [PMID: 26247052 PMCID: PMC4521971 DOI: 10.1002/mgg3.148] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 03/24/2015] [Accepted: 03/24/2015] [Indexed: 11/29/2022] Open
Abstract
Carrier screening for certain diseases is recommended by major medical and Ashkenazi Jewish (AJ) societies. Most carrier screening panels test only for common, ethnic-specific variants. However, with formerly isolated ethnic groups becoming increasingly intermixed, this approach is becoming inadequate. Our objective was to develop a rigorous process to curate all variants, for relevant genes, into a database and then apply stringent clinical validity classification criteria to each in order to retain only those with clear evidence for pathogenicity. The resulting variant set, in conjunction with next-generation DNA sequencing (NGS), then affords the capability for an ethnically diverse, comprehensive, highly specific carrier-screening assay. The clinical utility of our approach was demonstrated by screening a pan-ethnic population of 22,864 individuals for Bloom syndrome carrier status using a BLM variant panel comprised of 50 pathogenic variants. In addition to carriers of the common AJ founder variant, we identified 57 carriers of other pathogenic BLM variants. All variants reported had previously been curated and their clinical validity documented, or were of a type that met our stringent, preassigned validity criteria. Thus, it was possible to confidently report an increased number of Bloom’s syndrome carriers compared to traditional, ethnicity-based screening, while not reducing the specificity of the screening due to reporting variants of unknown clinical significance.
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Affiliation(s)
| | - Jocelyn Davie
- Good Start Genetics, Inc. 237 Putnam Avenue, Cambridge, Massachusetts, 02139
| | - Benjamin Breton
- Good Start Genetics, Inc. 237 Putnam Avenue, Cambridge, Massachusetts, 02139
| | - Stephanie Hallam
- Good Start Genetics, Inc. 237 Putnam Avenue, Cambridge, Massachusetts, 02139
| | - Valerie Greger
- Good Start Genetics, Inc. 237 Putnam Avenue, Cambridge, Massachusetts, 02139
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113
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Lerner-Ellis J, Wang M, White S, Lebo MS. Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations. J Med Genet 2015; 52:438-45. [PMID: 25904639 PMCID: PMC4501169 DOI: 10.1136/jmedgenet-2014-102933] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/15/2015] [Indexed: 11/14/2022]
Abstract
Background The Canadian Open Genetics Repository is a collaborative effort for the collection, storage, sharing and robust analysis of variants reported by medical diagnostics laboratories across Canada. As clinical laboratories adopt modern genomics technologies, the need for this type of collaborative framework is increasingly important. Methods A survey to assess existing protocols for variant classification and reporting was delivered to clinical genetics laboratories across Canada. Based on feedback from this survey, a variant assessment tool was made available to all laboratories. Each participating laboratory was provided with an instance of GeneInsight, a software featuring versioning and approval processes for variant assessments and interpretations and allowing for variant data to be shared between instances. Guidelines were established for sharing data among clinical laboratories and in the final outreach phase, data will be made readily available to patient advocacy groups for general use. Results The survey demonstrated the need for improved standardisation and data sharing across the country. A variant assessment template was made available to the community to aid with standardisation. Instances of the GeneInsight tool were provided to clinical diagnostic laboratories across Canada for the purpose of uploading, transferring, accessing and sharing variant data. Conclusions As an ongoing endeavour and a permanent resource, the Canadian Open Genetics Repository aims to serve as a focal point for the collaboration of Canadian laboratories with other countries in the development of tools that take full advantage of laboratory data in diagnosing, managing and treating genetic diseases.
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Affiliation(s)
- Jordan Lerner-Ellis
- Laboratory Medicine and Pathobiology, University of Toronto & Mount Sinai Hospital, Toronto, Ontario, Canada Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marina Wang
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Shana White
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts, USA Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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114
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Aziz N, Zhao Q, Bry L, Driscoll DK, Funke B, Gibson JS, Grody WW, Hegde MR, Hoeltge GA, Leonard DGB, Merker JD, Nagarajan R, Palicki LA, Robetorye RS, Schrijver I, Weck KE, Voelkerding KV. College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests. Arch Pathol Lab Med 2015; 139:481-93. [DOI: 10.5858/arpa.2014-0250-cp] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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115
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Arboleda VA, Lee H, Dorrani N, Zadeh N, Willis M, Macmurdo CF, Manning MA, Kwan A, Hudgins L, Barthelemy F, Miceli MC, Quintero-Rivera F, Kantarci S, Strom SP, Deignan JL, Grody WW, Vilain E, Nelson SF. De novo nonsense mutations in KAT6A, a lysine acetyl-transferase gene, cause a syndrome including microcephaly and global developmental delay. Am J Hum Genet 2015; 96:498-506. [PMID: 25728775 DOI: 10.1016/j.ajhg.2015.01.017] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/20/2015] [Indexed: 12/19/2022] Open
Abstract
Chromatin remodeling through histone acetyltransferase (HAT) and histone deactylase (HDAC) enzymes affects fundamental cellular processes including the cell-cycle, cell differentiation, metabolism, and apoptosis. Nonsense mutations in genes that are involved in histone acetylation and deacetylation result in multiple congenital anomalies with most individuals displaying significant developmental delay, microcephaly and dysmorphism. Here, we report a syndrome caused by de novo heterozygous nonsense mutations in KAT6A (a.k.a., MOZ, MYST3) identified by clinical exome sequencing (CES) in four independent families. The same de novo nonsense mutation (c.3385C>T [p.Arg1129∗]) was observed in three individuals, and the fourth individual had a nearby de novo nonsense mutation (c.3070C>T [p.Arg1024∗]). Neither of these variants was present in 1,815 in-house exomes or in public databases. Common features among all four probands include primary microcephaly, global developmental delay including profound speech delay, and craniofacial dysmorphism, as well as more varied features such as feeding difficulties, cardiac defects, and ocular anomalies. We further demonstrate that KAT6A mutations result in dysregulation of H3K9 and H3K18 acetylation and altered P53 signaling. Through histone and non-histone acetylation, KAT6A affects multiple cellular processes and illustrates the complex role of acetylation in regulating development and disease.
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Affiliation(s)
- Valerie A Arboleda
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Naghmeh Dorrani
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA, USA
| | - Neda Zadeh
- Division of Medical Genetics, CHOC Children's Hospital of Orange County, CA 92868, USA; Genetics Center, Orange, CA 92868, USA
| | - Mary Willis
- Department of Pediatrics, Naval Medical Center, San Diego, 92134, USA
| | - Colleen Forsyth Macmurdo
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Melanie A Manning
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrea Kwan
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Louanne Hudgins
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Florian Barthelemy
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - M Carrie Miceli
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sibel Kantarci
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric Vilain
- Department of Pediatrics, Division of Medical Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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116
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Thormaehlen AS, Schuberth C, Won HH, Blattmann P, Joggerst-Thomalla B, Theiss S, Asselta R, Duga S, Merlini PA, Ardissino D, Lander ES, Gabriel S, Rader DJ, Peloso GM, Pepperkok R, Kathiresan S, Runz H. Systematic cell-based phenotyping of missense alleles empowers rare variant association studies: a case for LDLR and myocardial infarction. PLoS Genet 2015; 11:e1004855. [PMID: 25647241 PMCID: PMC4409815 DOI: 10.1371/journal.pgen.1004855] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/27/2014] [Indexed: 01/08/2023] Open
Abstract
A fundamental challenge to contemporary genetics is to distinguish rare missense alleles that disrupt protein functions from the majority of alleles neutral on protein activities. High-throughput experimental tools to securely discriminate between disruptive and non-disruptive missense alleles are currently missing. Here we establish a scalable cell-based strategy to profile the biological effects and likely disease relevance of rare missense variants in vitro. We apply this strategy to systematically characterize missense alleles in the low-density lipoprotein receptor (LDLR) gene identified through exome sequencing of 3,235 individuals and exome-chip profiling of 39,186 individuals. Our strategy reliably identifies disruptive missense alleles, and disruptive-allele carriers have higher plasma LDL-cholesterol (LDL-C). Importantly, considering experimental data refined the risk of rare LDLR allele carriers from 4.5- to 25.3-fold for high LDL-C, and from 2.1- to 20-fold for early-onset myocardial infarction. Our study generates proof-of-concept that systematic functional variant profiling may empower rare variant-association studies by orders of magnitude. Exome sequencing has proven powerful to identify protein-coding variation across the human genome, unravel the basis of monogenic diseases and discover rare alleles that confer risk for complex disease. Nevertheless, two key challenges limit its application to complex phenotypes: first, most alleles identified in a population are extremely rare; and second, most alleles are neutral on protein activities. Consequently, association tests that rely on enumerating rare alleles in cases and controls (termed rare variant association studies, RVAS) are typically underpowered, as the many neutral alleles dampen signals that arise from the few alleles that disrupt protein functions. Strategies to securely discriminate disruptive from neutral variants are immature, in particular for missense variants. Here we show that the statistical power of RVAS improves dramatically if variants are stratified according to their in vitro ascertained functions. We establish scalable technology to objectively profile the biological effects of exome-identified missense variants in the low-density lipoprotein receptor (LDLR) through systematic overexpression and complementation experiments in cells. We demonstrate that carriers of LDLR alleles, which our experiments identify as “disruptive-missense”, have higher plasma LDL-C, and that considering in vitro data may make it possible to reduce RVAS sample sizes by more than 2-fold.
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Affiliation(s)
- Aenne S. Thormaehlen
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg/ EMBL, Heidelberg, Germany
| | - Christian Schuberth
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg/ EMBL, Heidelberg, Germany
| | - Hong-Hee Won
- Center of Human Genetic Research (CHGR), Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Blattmann
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg/ EMBL, Heidelberg, Germany
- Cell Biology/Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Brigitte Joggerst-Thomalla
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg/ EMBL, Heidelberg, Germany
| | - Susanne Theiss
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Daniel J. Rader
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Gina M. Peloso
- Center of Human Genetic Research (CHGR), Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Rainer Pepperkok
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg/ EMBL, Heidelberg, Germany
- Cell Biology/Biophysics Unit, European Molecular Biological Laboratory, Heidelberg, Germany
| | - Sekar Kathiresan
- Center of Human Genetic Research (CHGR), Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Division of Cardiology, Ospedale Niguarda, Milan, Italy
| | - Heiko Runz
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), University of Heidelberg/ EMBL, Heidelberg, Germany
- Center of Human Genetic Research (CHGR), Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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117
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Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, Murray ML, Tokita MJ, Gallego CJ, Kim DS, Bennett JT, Crosslin DR, Ranchalis J, Jones KL, Rosenthal EA, Jarvik ER, Itsara A, Turner EH, Herman DS, Schleit J, Burt A, Jamal SM, Abrudan JL, Johnson AD, Conlin LK, Dulik MC, Santani A, Metterville DR, Kelly M, Foreman AKM, Lee K, Taylor KD, Guo X, Crooks K, Kiedrowski LA, Raffel LJ, Gordon O, Machini K, Desnick RJ, Biesecker LG, Lubitz SA, Mulchandani S, Cooper GM, Joffe S, Richards CS, Yang Y, Rotter JI, Rich SS, O'Donnell CJ, Berg JS, Spinner NB, Evans JP, Fullerton SM, Leppig KA, Bennett RL, Bird T, Sybert VP, Grady WM, Tabor HK, Kim JH, Bamshad MJ, Wilfond B, Motulsky AG, Scott CR, Pritchard CC, Walsh TD, Burke W, Raskind WH, Byers P, Hisama FM, Rehm H, Nickerson DA, Jarvik GP. Actionable exomic incidental findings in 6503 participants: challenges of variant classification. Genome Res 2015; 25:305-15. [PMID: 25637381 PMCID: PMC4352885 DOI: 10.1101/gr.183483.114] [Citation(s) in RCA: 262] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Recommendations for laboratories to report incidental findings from genomic tests have stimulated interest in such results. In order to investigate the criteria and processes for assigning the pathogenicity of specific variants and to estimate the frequency of such incidental findings in patients of European and African ancestry, we classified potentially actionable pathogenic single-nucleotide variants (SNVs) in all 4300 European- and 2203 African-ancestry participants sequenced by the NHLBI Exome Sequencing Project (ESP). We considered 112 gene-disease pairs selected by an expert panel as associated with medically actionable genetic disorders that may be undiagnosed in adults. The resulting classifications were compared to classifications from other clinical and research genetic testing laboratories, as well as with in silico pathogenicity scores. Among European-ancestry participants, 30 of 4300 (0.7%) had a pathogenic SNV and six (0.1%) had a disruptive variant that was expected to be pathogenic, whereas 52 (1.2%) had likely pathogenic SNVs. For African-ancestry participants, six of 2203 (0.3%) had a pathogenic SNV and six (0.3%) had an expected pathogenic disruptive variant, whereas 13 (0.6%) had likely pathogenic SNVs. Genomic Evolutionary Rate Profiling mammalian conservation score and the Combined Annotation Dependent Depletion summary score of conservation, substitution, regulation, and other evidence were compared across pathogenicity assignments and appear to have utility in variant classification. This work provides a refined estimate of the burden of adult onset, medically actionable incidental findings expected from exome sequencing, highlights challenges in variant classification, and demonstrates the need for a better curated variant interpretation knowledge base.
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Affiliation(s)
- Laura M Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Michael O Dorschner
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peggy D Robertson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Joseph S Salama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Ragan Hart
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Mitzi L Murray
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Mari J Tokita
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Carlos J Gallego
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Daniel Seung Kim
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - James T Bennett
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - David R Crosslin
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jane Ranchalis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Kelly L Jones
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Elisabeth A Rosenthal
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Ella R Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Andy Itsara
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Emily H Turner
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Daniel S Herman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Amber Burt
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Seema M Jamal
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Jenica L Abrudan
- Department of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Andrew D Johnson
- The Framingham Heart Study, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts 01702, USA
| | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Matthew C Dulik
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Avni Santani
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | - Melissa Kelly
- Partners Healthcare Personalized Medicine, Partners Healthcare, Boston, Massachusetts 02115, USA
| | - Ann Katherine M Foreman
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kristy Lee
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kent D Taylor
- Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Xiuqing Guo
- Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Kristy Crooks
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - Lesli A Kiedrowski
- Department of Cancer Genetics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Leslie J Raffel
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Ora Gordon
- Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Kalotina Machini
- Laboratory of Molecular Medicine, Partners Healthcare, Boston, Massachusetts 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Robert J Desnick
- Department of Genetic and Genomic Medicine, Division of Medical Genetics, Mount Sinai Hospital, New York, New York 10029, USA
| | - Leslie G Biesecker
- Genetic Diseases Research Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Steven A Lubitz
- Cardiac Arrhythmia Service and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Surabhi Mulchandani
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Greg M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Steven Joffe
- Department of Medical Ethics and Health Policy, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Yaoping Yang
- Department of Pediatrics, Division of Infectious Disease, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Jerome I Rotter
- Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA, Torrence, California 90502, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Christopher J O'Donnell
- The Framingham Heart Study, Division of Intramural Research, National Heart, Lung and Blood Institute, Framingham, Massachusetts 01702, USA; Division of Cardiology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jonathan S Berg
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nancy B Spinner
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - James P Evans
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA
| | - Kathleen A Leppig
- Genetic Services, Group Health Cooperative, Seattle, Washington 98112, USA
| | - Robin L Bennett
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Thomas Bird
- Department of Neurology, University of Washington, Seattle, Washington 98195, USA; Veterans Affairs Puget Sound Health Care System Geriatric Research, Education, and Clinical Center, Seattle, Washington 98108, USA
| | - Virginia P Sybert
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Dermatology, Group Health Cooperative, Seattle, Washington 98112, USA
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Department of Medicine, Division of Gastroenterology, University of Washington, Seattle, Washington 98195, USA
| | - Holly K Tabor
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA; Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, Seattle, Washington 98105, USA
| | - Jerry H Kim
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, Seattle, Washington 98105, USA; Department of Pediatrics, Division of Bioethics, University of Washington, Seattle, Washington 98195, USA
| | - Arno G Motulsky
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - C Ronald Scott
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Tom D Walsh
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Wylie Burke
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA
| | - Wendy H Raskind
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Peter Byers
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Fuki M Hisama
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Heidi Rehm
- Laboratory of Molecular Medicine, Partners Healthcare, Boston, Massachusetts 02115, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Debbie A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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118
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Alfares AA, Kelly MA, McDermott G, Funke BH, Lebo MS, Baxter SB, Shen J, McLaughlin HM, Clark EH, Babb LJ, Cox SW, DePalma SR, Ho CY, Seidman JG, Seidman CE, Rehm HL. Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. Genet Med 2015; 17:880-8. [PMID: 25611685 DOI: 10.1038/gim.2014.205] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/12/2014] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Hypertrophic cardiomyopathy (HCM) is caused primarily by pathogenic variants in genes encoding sarcomere proteins. We report genetic testing results for HCM in 2,912 unrelated individuals with nonsyndromic presentations from a broad referral population over 10 years. METHODS Genetic testing was performed by Sanger sequencing for 10 genes from 2004 to 2007, by HCM CardioChip for 11 genes from 2007 to 2011 and by next-generation sequencing for 18, 46, or 51 genes from 2011 onward. RESULTS The detection rate is ~32% among unselected probands, with inconclusive results in an additional 15%. Detection rates were not significantly different between adult and pediatric probands but were higher in females compared with males. An expanded gene panel encompassing more than 50 genes identified only a very small number of additional pathogenic variants beyond those identifiable in our original panels, which examined 11 genes. Familial genetic testing in at-risk family members eliminated the need for longitudinal cardiac evaluations in 691 individuals. Based on the projected costs derived from Medicare fee schedules for the recommended clinical evaluations of HCM family members by the American College of Cardiology Foundation/American Heart Association, our data indicate that genetic testing resulted in a minimum cost savings of about $0.7 million. CONCLUSION Clinical HCM genetic testing provides a definitive molecular diagnosis for many patients and provides cost savings to families. Expanded gene panels have not substantively increased the clinical sensitivity of HCM testing, suggesting major additional causes of HCM still remain to be identified.
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Affiliation(s)
- Ahmed A Alfares
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pediatrics, Qassim University, Buraydah, Saudi Arabia
| | - Melissa A Kelly
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Gregory McDermott
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Birgit H Funke
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew S Lebo
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Samantha B Baxter
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Jun Shen
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Heather M McLaughlin
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugene H Clark
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Larry J Babb
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Stephanie W Cox
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA
| | - Steven R DePalma
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Carolyn Y Ho
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E Seidman
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
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Campuzano O, Allegue C, Fernandez A, Iglesias A, Brugada R. Determining the pathogenicity of genetic variants associated with cardiac channelopathies. Sci Rep 2015; 5:7953. [PMID: 25608792 PMCID: PMC4302303 DOI: 10.1038/srep07953] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/22/2014] [Indexed: 01/08/2023] Open
Abstract
Advancements in genetic screening have generated massive amounts of data on genetic variation; however, a lack of clear pathogenic stratification has left most variants classified as being of unknown significance. This is a critical limitation for translating genetic data into clinical practice. Genetic screening is currently recommended in the guidelines for diagnosis and treatment of cardiac channelopathies, which are major contributors to sudden cardiac death in young people. We propose to characterize the pathogenicity of genetic variants associated with cardiac channelopathies using a stratified scoring system. The development of this system was considered by using all of the tools currently available to define pathogenicity. The use of this scoring system could help clinicians to understand the limitations of genetic associations with a disease, and help them better define the role that genetics can have in their clinical routine.
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Affiliation(s)
- Oscar Campuzano
- 1] Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona (IDIBGI) and Universitat de Girona (UdG), Girona, Spain [2] Medical Science Department, School of Medicine, University of Girona, Girona, Spain
| | - Catarina Allegue
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona (IDIBGI) and Universitat de Girona (UdG), Girona, Spain
| | - Anna Fernandez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona (IDIBGI) and Universitat de Girona (UdG), Girona, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona (IDIBGI) and Universitat de Girona (UdG), Girona, Spain
| | - Ramon Brugada
- 1] Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona (IDIBGI) and Universitat de Girona (UdG), Girona, Spain [2] Medical Science Department, School of Medicine, University of Girona, Girona, Spain [3] Cardiology Service, Hospital Josep Trueta, Girona, Spain
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120
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Vassy JL, McLaughlin HM, McLaughlin HL, MacRae CA, Seidman CE, Lautenbach D, Krier JB, Lane WJ, Kohane IS, Murray MF, McGuire AL, Rehm HL, Green RC. A one-page summary report of genome sequencing for the healthy adult. Public Health Genomics 2015; 18:123-9. [PMID: 25612602 DOI: 10.1159/000370102] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/25/2014] [Indexed: 11/19/2022] Open
Abstract
As genome sequencing technologies increasingly enter medical practice, genetics laboratories must communicate sequencing results effectively to nongeneticist physicians. We describe the design and delivery of a clinical genome sequencing report, including a one-page summary suitable for interpretation by primary care physicians. To illustrate our preliminary experience with this report, we summarize the genomic findings from 10 healthy participants in a study of genome sequencing in primary care.
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Affiliation(s)
- Jason L Vassy
- Division of General Internal Medicine and Primary Care, Boston, Mass., USA
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121
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McLaughlin HM, Ceyhan-Birsoy O, Christensen KD, Kohane IS, Krier J, Lane WJ, Lautenbach D, Lebo MS, Machini K, MacRae CA, Azzariti DR, Murray MF, Seidman CE, Vassy JL, Green RC, Rehm HL. A systematic approach to the reporting of medically relevant findings from whole genome sequencing. BMC MEDICAL GENETICS 2014; 15:134. [PMID: 25714468 PMCID: PMC4342199 DOI: 10.1186/s12881-014-0134-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/03/2014] [Indexed: 01/22/2023]
Abstract
Background The MedSeq Project is a randomized clinical trial developing approaches to assess the impact of integrating genome sequencing into clinical medicine. To facilitate the return of results of potential medical relevance to physicians and patients participating in the MedSeq Project, we sought to develop a reporting approach for the effective communication of such findings. Methods Genome sequencing was performed on the Illumina HiSeq platform. Variants were filtered, interpreted, and validated according to methods developed by the Laboratory for Molecular Medicine and consistent with current professional guidelines. The GeneInsight software suite, which is integrated with the Partners HealthCare electronic health record, was used for variant curation, report drafting, and delivery. Results We developed a concise 5–6 page Genome Report (GR) featuring a single-page summary of results of potential medical relevance with additional pages containing structured variant, gene, and disease information along with supporting evidence for reported variants and brief descriptions of associated diseases and clinical implications. The GR is formatted to provide a succinct summary of genomic findings, enabling physicians to take appropriate steps for disease diagnosis, prevention, and management in their patients. Conclusions Our experience highlights important considerations for the reporting of results of potential medical relevance and provides a framework for interpretation and reporting practices in clinical genome sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s12881-014-0134-1) contains supplementary material, which is available to authorized users.
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122
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Identification of Genetic Alterations, as Causative Genetic Defects in Long QT Syndrome, Using Next Generation Sequencing Technology. PLoS One 2014; 9:e114894. [PMID: 25494010 PMCID: PMC4262446 DOI: 10.1371/journal.pone.0114894] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 11/15/2014] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Long QT Syndrome is an inherited channelopathy leading to sudden cardiac death due to ventricular arrhythmias. Despite that several genes have been associated with the disease, nearly 20% of cases remain without an identified genetic cause. Other genetic alterations such as copy number variations have been recently related to Long QT Syndrome. Our aim was to take advantage of current genetic technologies in a family affected by Long QT Syndrome in order to identify the cause of the disease. METHODS Complete clinical evaluation was performed in all family members. In the index case, a Next Generation Sequencing custom-built panel, including 55 sudden cardiac death-related genes, was used both for detection of sequence and copy number variants. Next Generation Sequencing variants were confirmed by Sanger method. Copy number variations variants were confirmed by Multiplex Ligation dependent Probe Amplification method and at the mRNA level. Confirmed variants and copy number variations identified in the index case were also analyzed in relatives. RESULTS In the index case, Next Generation Sequencing revealed a novel variant in TTN and a large deletion in KCNQ1, involving exons 7 and 8. Both variants were confirmed by alternative techniques. The mother and the brother of the index case were also affected by Long QT Syndrome, and family cosegregation was observed for the KCNQ1 deletion, but not for the TTN variant. CONCLUSIONS Next Generation Sequencing technology allows a comprehensive genetic analysis of arrhythmogenic diseases. We report a copy number variation identified using Next Generation Sequencing analysis in Long QT Syndrome. Clinical and familiar correlation is crucial to elucidate the role of genetic variants identified to distinguish the pathogenic ones from genetic noise.
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Abstract
PURPOSE OF REVIEW The review is designed to outline the major developments in genetic testing in the cardiovascular arena in the past year or so. This is an exciting time in genetic testing as whole exome and whole genome approaches finally reach the clinic. These new approaches offer insight into disease causation in families in which this might previously have been inaccessible, and also bring a wide range of interpretative challenges. RECENT FINDINGS Among the most significant recent findings has been the extent of physiologic rare coding variation in the human genome. New disease genes have been identified through whole exome studies in neonatal arrhythmia, congenital heart disease and coronary artery disease that were simply inaccessible with other techniques. This has not only shed light on the challenges of genetic testing at this scale, but has also sharply defined the limits of prior gene-panel focused testing. As novel therapies targeting specific genetic subsets of disease become available, genetic testing will become a part of routine clinical care. SUMMARY The pace of change in sequencing technologies has begun to transform clinical medicine, and cardiovascular disease is no exception. The complexity of such studies emphasizes the importance of real-time communication between the genetics laboratory and genetically informed clinicians. New efforts in data and knowledge management will be central to the continued advancement of genetic testing.
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Angrist M, Cook-Deegan R. Distributing the future: The weak justifications for keeping human genomic databases secret and the challenges and opportunities in reverse engineering them. Appl Transl Genom 2014; 3:124-127. [PMID: 25642409 PMCID: PMC4307597 DOI: 10.1016/j.atg.2014.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Misha Angrist
- Science and Society, Social Science Research Institute, Duke University, Durham, NC, United States
| | - Robert Cook-Deegan
- Sanford School of Public Policy, Duke University, Durham, NC, United States
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Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CGS, Dipple KM, Grody WW, Vilain E, Nelson SF. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA 2014; 312:1880-7. [PMID: 25326637 PMCID: PMC4278636 DOI: 10.1001/jama.2014.14604] [Citation(s) in RCA: 717] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
IMPORTANCE Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders. OBJECTIVE To report on initial clinical indications for CES referrals and molecular diagnostic rates for different indications and for different test types. DESIGN, SETTING, AND PARTICIPANTS Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available. MAIN OUTCOMES AND MEASURES Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES. RESULTS Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 [95% CI, 1.6-33.1]) of trio-CES was due to the identification of de novo and compound heterozygous variants. CONCLUSIONS AND RELEVANCE In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.
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Affiliation(s)
- Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Naghmeh Dorrani
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Sibel Kantarci
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Kingshuk Das
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Traci Toy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles
| | - Bret Harry
- Institute for Digital Research and Education, University of California, Los Angeles
| | - Michael Yourshaw
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Michelle Fox
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Brent L Fogel
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles
| | - Julian A Martinez-Agosto
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
| | - Derek A Wong
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Vivian Y Chang
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles
| | - Perry B Shieh
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles
| | - Christina G S Palmer
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles7Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles
| | - Katrina M Dipple
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen
| | - Eric Vilain
- Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles3Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Geffen School of Medicine
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles2Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles6Department of Human Genetics, David Ge
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Post-mortem genetic analysis in juvenile cases of sudden cardiac death. Forensic Sci Int 2014; 245:30-7. [PMID: 25447171 DOI: 10.1016/j.forsciint.2014.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/18/2014] [Accepted: 10/04/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND The reason behind a sudden death of a young individual remains unknown in up to 50% of postmortem cases. Pathogenic mutations in genes encoding heart proteins are known to cause sudden cardiac death. OBJECTIVE The aim of our study was to ascertain whether genetic alterations could provide an explanation for sudden cardiac death in a juvenile cohort with no-conclusive cause of death after comprehensive autopsy. METHODS Twenty-nine cases <15 years showing no-conclusive cause of death after a complete autopsy were studied. Genetic analysis of 7 main genes associated with sudden cardiac death was performed using Sanger technology in low quality DNA cases, while in good quality cases the analysis of 55 genes associated with sudden cardiac death was performed using Next Generation Sequencing technology. RESULTS Thirty-five genetic variants were identified in 12 cases (41.37%). Ten genetic/variants in genes encoding cardiac ion channels were identified in 8 cases (27.58%). We also identified 9 cases (31.03%) carrying 25 genetic variants in genes encoding structural cardiac proteins. Nine cases carried more than one genetic variation, 5 of them combining structural and non-structural genes. CONCLUSIONS Our study supports the inclusion of molecular autopsy in forensic routine protocols when no conclusive cause of death is identified. Around 40% of sudden cardiac death young cases carry a genetic variant that could provide an explanation for the cause of death. Because relatives could be at risk of sudden cardiac death, our data reinforce their need of clinical assessment and, if indicated, of genetic analysis.
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127
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Angrist M, Jamal L. Living laboratory: whole-genome sequencing as a learning healthcare enterprise. Clin Genet 2014; 87:311-8. [PMID: 25045831 DOI: 10.1111/cge.12461] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/30/2014] [Accepted: 07/15/2014] [Indexed: 01/16/2023]
Abstract
With the proliferation of affordable large-scale human genomic data come profound and vexing questions about management of such data and their clinical uncertainty. These issues challenge the view that genomic research on human beings can (or should) be fully segregated from clinical genomics, either conceptually or practically. Here, we argue that the sharp distinction between clinical care and research is especially problematic in the context of large-scale genomic sequencing of people with suspected genetic conditions. Core goals of both enterprises (e.g. understanding genotype-phenotype relationships; generating an evidence base for genomic medicine) are more likely to be realized at a population scale if both those ordering and those undergoing sequencing for diagnostic reasons are routinely and longitudinally studied. Rather than relying on expensive and lengthy randomized clinical trials and meta-analyses, we propose leveraging nascent clinical-research hybrid frameworks into a broader, more permanent instantiation of exploratory medical sequencing. Such an investment could enlighten stakeholders about the real-life challenges posed by whole-genome sequencing, such as establishing the clinical actionability of genetic variants, returning 'off-target' results to families, developing effective service delivery models and monitoring long-term outcomes.
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Affiliation(s)
- M Angrist
- Science and Society, Social Science Research Institute and Sanford School of Public Policy, Duke University, Durham, NC, USA
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128
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Functional analysis of novel splicing and missense mutations identified in the ASS1 gene in classical citrullinemia patients. Clin Chim Acta 2014; 438:323-9. [PMID: 25179242 DOI: 10.1016/j.cca.2014.08.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 08/16/2014] [Accepted: 08/23/2014] [Indexed: 01/23/2023]
Abstract
BACKGROUND Classical citrullinemia (CTLN1) is an inborn error of the urea cycle caused by reduced/abolished activity of argininosuccinate synthetase due to mutations in the ASS1 gene. To determine the pathogenicity of novel variants detected in patients is often a huge challenge in molecular diagnosis. The purpose of our study was to characterize novel ASS1 gene mutations identified in CTLN1 patients. METHODS Exon trapping assay with pSPL3 was used to confirm splice aberrations while bioinformatics structural analysis predicted the possible effects of missense mutations. RESULTS Novel donor site (c.174+1G>A) and missense (p.V141G) mutations were detected in a patient exhibiting a biochemical phenotype only. The splice mutation provoked exon skipping hence the truncated product. The mutation p.V141G, is predicted to disturb a hydrophobic pocket in the ATP binding domain in the ASS. Both mutations are predicted to lower binding of ATP. The second patient presented with early onset neonatal citrullinemia marked by an elevated biochemical profile and a clinical phenotype. Analysis revealed a donor site (c.773+1G>A) mutation leading to both exon skipping and intron retention. Subsequent introduction of premature stop codons would result in severely truncated products likely to be degraded. A previously reported R265C is predicted to distort the citrulline binding site. CONCLUSIONS Three novel mutations are reported in this study. They expand the spectrum of genetic pathology underlying CTLN1. Overall this study provides new insight of CTLN1 and illustrates a comprehensive protocol investigating inborn errors of metabolism at the molecular level.
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The Rapidly Emerging Role for Whole Exome Sequencing in Clinical Genetics. CURRENT GENETIC MEDICINE REPORTS 2014. [DOI: 10.1007/s40142-014-0044-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Affiliation(s)
- Leslie G Biesecker
- From the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD (L.G.B.); and the Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, and Partners Healthcare Personalized Medicine - all in Boston (R.C.G.)
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Freudenberg-Hua Y, Freudenberg J, Vacic V, Abhyankar A, Emde AK, Ben-Avraham D, Barzilai N, Oschwald D, Christen E, Koppel J, Greenwald B, Darnell RB, Germer S, Atzmon G, Davies P. Disease variants in genomes of 44 centenarians. Mol Genet Genomic Med 2014; 2:438-50. [PMID: 25333069 PMCID: PMC4190879 DOI: 10.1002/mgg3.86] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 12/14/2022] Open
Abstract
To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide variants were called with the genome analysis toolkit (GATK). We identified 130 coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database and that are infrequent in the general population. These variants were previously reported to cause a wide range of degenerative, neoplastic, and cardiac diseases with autosomal dominant, autosomal recessive, and X-linked inheritance. Several of these variants are located in genes that harbor actionable incidental findings, according to the recommendations of the American College of Medical Genetics. In addition, we found risk variants for late-onset neurodegenerative diseases, such as the APOE ε4 allele that was even present in a homozygous state in one centenarian who did not develop Alzheimer's disease. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions. In genome sequences of 44 Ashkenazi centenarians, we identified many coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions.
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Affiliation(s)
- Yun Freudenberg-Hua
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030 ; Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Jan Freudenberg
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
| | - Vladimir Vacic
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Avinash Abhyankar
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Anne-Katrin Emde
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Danny Ben-Avraham
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Nir Barzilai
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Dayna Oschwald
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Erika Christen
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
| | - Jeremy Koppel
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030 ; Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Blaine Greenwald
- Division of Geriatric Psychiatry, Zucker Hillside Hospital, North Shore-LIJ Glen Oaks, New York, 11040
| | - Robert B Darnell
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013 ; Department of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University 1230 York Avenue, New York, New York, 10065
| | - Soren Germer
- New York Genome Center 101 Avenue of the Americas, New York, New York, 10013
| | - Gil Atzmon
- Institute for Aging Research Departments of Medicine and Genetics, Albert Einstein College of Medicine 1300 Morris Park Avenue, Bronx, New York, 10461
| | - Peter Davies
- The Litwin-Zucker Research Center for the Study of Alzheimer's Disease and Memory Disorders, The Feinstein Institute for Medical Research, North Shore-LIJ Manhasset, New York, 11030
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Gowrisankar S, Lebo MS. Designing algorithms for determining significance of DNA missense changes. Methods Mol Biol 2014; 1168:251-62. [PMID: 24870140 DOI: 10.1007/978-1-4939-0847-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Humans differ from each other in their genomes by <1 %. This determines the difference in susceptibility to disease, phenotypes, and traits. Predominantly, when looking for causal disease mutations, protein-coding sequences are screened first since those have the highest probability of affecting the function of a protein. Recent technological advances have seen a rise in the number of experiments being conducted to study a variety of diseases from monogenic to complex traits. Several computational approaches have been developed to extract putative functional missense variants. In this chapter we review some of these approaches and describe a standard step-by-step procedure that can be used to classify variants for the purpose of clinical care. We also provide two examples demonstrating this approach, one for a patient with a dilated cardiomyopathy diagnosis, and the other for a patient with an unknown etiology undergoing whole-genome sequencing (WGS).
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Affiliation(s)
- Sivakumar Gowrisankar
- Novartis Institutes for Biomedical Research, 500 Technology Square, 840-14, Cambridge, MA, 02139, USA,
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Pant S, Weiner R, Marton MJ. Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics. Front Oncol 2014; 4:78. [PMID: 24860780 PMCID: PMC4029014 DOI: 10.3389/fonc.2014.00078] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/28/2014] [Indexed: 12/11/2022] Open
Abstract
Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.
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Affiliation(s)
- Saumya Pant
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Russell Weiner
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
| | - Matthew J Marton
- Merck Research Laboratories, Molecular Biomarkers and Diagnostics , Rahway, NJ , USA
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Vassy JL, Lautenbach DM, McLaughlin HM, Kong SW, Christensen KD, Krier J, Kohane IS, Feuerman LZ, Blumenthal-Barby J, Roberts JS, Lehmann LS, Ho CY, Ubel PA, MacRae CA, Seidman CE, Murray MF, McGuire AL, Rehm HL, Green RC. The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine. Trials 2014; 15:85. [PMID: 24645908 PMCID: PMC4113228 DOI: 10.1186/1745-6215-15-85] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/28/2014] [Indexed: 11/28/2022] Open
Abstract
Background Whole genome sequencing (WGS) is already being used in certain clinical and research settings, but its impact on patient well-being, health-care utilization, and clinical decision-making remains largely unstudied. It is also unknown how best to communicate sequencing results to physicians and patients to improve health. We describe the design of the MedSeq Project: the first randomized trials of WGS in clinical care. Methods/Design This pair of randomized controlled trials compares WGS to standard of care in two clinical contexts: (a) disease-specific genomic medicine in a cardiomyopathy clinic and (b) general genomic medicine in primary care. We are recruiting 8 to 12 cardiologists, 8 to 12 primary care physicians, and approximately 200 of their patients. Patient participants in both the cardiology and primary care trials are randomly assigned to receive a family history assessment with or without WGS. Our laboratory delivers a genome report to physician participants that balances the needs to enhance understandability of genomic information and to convey its complexity. We provide an educational curriculum for physician participants and offer them a hotline to genetics professionals for guidance in interpreting and managing their patients’ genome reports. Using varied data sources, including surveys, semi-structured interviews, and review of clinical data, we measure the attitudes, behaviors and outcomes of physician and patient participants at multiple time points before and after the disclosure of these results. Discussion The impact of emerging sequencing technologies on patient care is unclear. We have designed a process of interpreting WGS results and delivering them to physicians in a way that anticipates how we envision genomic medicine will evolve in the near future. That is, our WGS report provides clinically relevant information while communicating the complexity and uncertainty of WGS results to physicians and, through physicians, to their patients. This project will not only illuminate the impact of integrating genomic medicine into the clinical care of patients but also inform the design of future studies. Trial registration ClinicalTrials.gov identifier
NCT01736566
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Robert C Green
- Genomes2People and Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Broad Institute and Harvard Medical School, 41 Avenue Louis Pasteur, Suite 301, 02115 Boston, MA, USA.
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