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Warman Chardon J, Beaulieu C, Hartley T, Boycott KM, Dyment DA. Axons to Exons: the Molecular Diagnosis of Rare Neurological Diseases by Next-Generation Sequencing. Curr Neurol Neurosci Rep 2016; 15:64. [PMID: 26289954 DOI: 10.1007/s11910-015-0584-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Neurological disorders secondary to single gene mutations are an extremely heterogeneous group of diseases, individually rare, and often associated with progressive and severe disability. Given the degree of both clinical and genetic heterogeneity, next-generation sequencing (NGS) has become an important diagnostic tool. Multi-gene panel testing based on NGS is now prominently used, while whole-exome sequencing and whole-genome sequencing are emerging to facilitate the molecular diagnosis for many genetic neurological diseases. Although single-gene testing remains an important first tier test for disorders with clear phenotype-genotype correlation, NGS provides an expanding unbiased approach to identify rare mutations in genes known to be associated with genetically heterogeneous diseases, and those not initially considered by the clinician due to rarity or atypical clinical presentation. Given the decreasing costs and relatively rapid time to results, NGS-based assessment is quickly becoming a standard-of-care test for patients with genetic neurological diseases.
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Affiliation(s)
- Jodi Warman Chardon
- Division of Neurology, The Ottawa Hospital, 1053 Carling Avenue, Ottawa, ON, K1Y 4E9, Canada
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152
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Hamilton A, Tétreault M, Dyment DA, Zou R, Kernohan K, Geraghty MT, Hartley T, Boycott KM. Concordance between whole-exome sequencing and clinical Sanger sequencing: implications for patient care. Mol Genet Genomic Med 2016; 4:504-12. [PMID: 27652278 PMCID: PMC5023935 DOI: 10.1002/mgg3.223] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 12/12/2022] Open
Abstract
The clinical translation of next‐generation sequencing has created a paradigm shift in the diagnostic assessment of individuals with suspected rare genetic diseases. Whole‐exome sequencing (WES) simultaneously examines the majority of the coding portion of the genome and is rapidly becoming accepted as an efficient alternative to clinical Sanger sequencing for diagnosing genetically heterogeneous disorders. Among reports of the clinical and diagnostic utility of WES, few studies to date have directly compared its concordance to Sanger sequencing, which is considered the clinical “gold standard”. We performed a direct comparison of 391 coding and noncoding polymorphisms and variants of unknown significance identified by clinical Sanger sequencing to the WES results of 26 patients. Of the 150 well‐covered coding variants identified by Sanger sequencing, 146 (97.3%) were also reported by WES. Nine genes were excluded from the comparison due to consistently low coverage in WES, which might be attributed to the use of older exome capture kits. We performed confirmatory Sanger sequencing of discordant variants; including five variants with discordant bases and four with discordant zygosity. Confirmatory Sanger sequencing supported the original Sanger report for three of the five discordant bases, one was shown to be a false positive supporting the WES data, and one result differed from both the Sanger and WES data. Two of the discordant zygosity results supported Sanger and the other two supported WES data. We report high concordance for well‐covered coding variants, supporting the use of WES as a screening tool for heterogeneous disorders, and recommend the use of supplementary Sanger sequencing for poorly‐covered genes when the clinical suspicion is high. Importantly, despite remaining difficulties with achieving complete coverage of the whole exome, 10 (38.5%) of the 26 compared patients were diagnosed through WES.
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Affiliation(s)
- Alison Hamilton
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Martine Tétreault
- Department of Human Genetics McGill UniversityMontréalQuébecCanada; McGill University and Genome Québec Innovation CenterMontréalQuébecCanada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada; Department of GeneticsChildren's Hospital of Eastern Ontario ResearchOttawaOntarioCanada
| | - Ruobing Zou
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Michael T Geraghty
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada; Division of Metabolics and Newborn ScreeningDepartment of PediatricsChildren's Hospital of Eastern OntarioOttawaOntarioCanada
| | | | | | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa Ontario Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research InstituteUniversity of OttawaOttawaOntarioCanada; Department of GeneticsChildren's Hospital of Eastern Ontario ResearchOttawaOntarioCanada
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153
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Ozantürk A, Davis EE, Sabo A, Weiss MM, Muzny D, Dugan-Perez S, Sistermans EA, Gibbs RA, Özgül KR, Yalnızoglu D, Serdaroglu E, Dursun A, Katsanis N. A t(5;16) translocation is the likely driver of a syndrome with ambiguous genitalia, facial dysmorphism, intellectual disability, and speech delay. Cold Spring Harb Mol Case Stud 2016; 2:a000703. [PMID: 27148584 PMCID: PMC4849851 DOI: 10.1101/mcs.a000703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Genetic studies grounded on monogenic paradigms have accelerated both gene discovery and molecular diagnosis. At the same time, complex genomic rearrangements are also appreciated as potent drivers of disease pathology. Here, we report two male siblings with a dysmorphic face, ambiguous genitalia, intellectual disability, and speech delay. Through quad-based whole-exome sequencing and concomitant molecular cytogenetic testing, we identified two copy-number variants (CNVs) in both affected individuals likely arising from a balanced translocation: a 13.5-Mb duplication on Chromosome 16 (16q23.1 → 16qter) and a 7.7-Mb deletion on Chromosome 5 (5p15.31 → 5pter), as well as a hemizygous missense variant in CXorf36 (also known as DIA1R). The 5p terminal deletion has been associated previously with speech delay, whereas craniofacial dysmorphia and genital/urinary anomalies have been reported in patients with a terminal duplication of 16q. However, dosage changes in either genomic region alone could not account for the overall clinical presentation in our family; functional testing of CXorf36 in zebrafish did not induce defects in neurogenesis or the craniofacial skeleton. Notably, literature and database analysis revealed a similar dosage disruption in two siblings with extensive phenotypic overlap with our patients. Taken together, our data suggest that dosage perturbation of genes within the two chromosomal regions likely drives the syndromic manifestations of our patients and highlight how multiple genetic lesions can contribute to complex clinical pathologies.
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Affiliation(s)
- Ayşegül Ozantürk
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey;; Department of Biology, Molecular Biology Section, Hacettepe University, Ankara 06800, Turkey;; Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center (Amsterdam), NL-1081 HV Amsterdam, The Netherlands
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shannon Dugan-Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center (Amsterdam), NL-1081 HV Amsterdam, The Netherlands
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Köksal R Özgül
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey
| | - Dilek Yalnızoglu
- Department of Pediatrics, Pediatric Neurology Unit, Hacettepe University, Ankara 06410, Turkey
| | - Esra Serdaroglu
- Department of Pediatrics, Pediatric Neurology Unit, Hacettepe University, Ankara 06410, Turkey
| | - Ali Dursun
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
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154
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Yang H, Douglas G, Monaghan KG, Retterer K, Cho MT, Escobar LF, Tucker ME, Stoler J, Rodan LH, Stein D, Marks W, Enns GM, Platt J, Cox R, Wheeler PG, Crain C, Calhoun A, Tryon R, Richard G, Vitazka P, Chung WK. De novo truncating variants in the AHDC1 gene encoding the AT-hook DNA-binding motif-containing protein 1 are associated with intellectual disability and developmental delay. Cold Spring Harb Mol Case Stud 2016; 1:a000562. [PMID: 27148574 PMCID: PMC4850891 DOI: 10.1101/mcs.a000562] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Whole-exome sequencing (WES) represents a significant breakthrough in clinical genetics, and identifies a genetic etiology in up to 30% of cases of intellectual disability (ID). Using WES, we identified seven unrelated patients with a similar clinical phenotype of severe intellectual disability or neurodevelopmental delay who were all heterozygous for de novo truncating variants in the AT-hook DNA-binding motif–containing protein 1 (AHDC1). The patients were all minimally verbal or nonverbal and had variable neurological problems including spastic quadriplegia, ataxia, nystagmus, seizures, autism, and self-injurious behaviors. Additional common clinical features include dysmorphic facial features and feeding difficulties associated with failure to thrive and short stature. The AHDC1 gene has only one coding exon, and the protein contains conserved regions including AT-hook motifs and a PDZ binding domain. We postulate that all seven variants detected in these patients result in a truncated protein missing critical functional domains, disrupting interactions with other proteins important for brain development. Our study demonstrates that truncating variants in AHDC1 are associated with ID and are primarily associated with a neurodevelopmental phenotype.
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Affiliation(s)
- Hui Yang
- GeneDx, Gaithersburg, Maryland 20877, USA
| | | | | | | | | | - Luis F Escobar
- Peyton Manning Children's Hospital at St. Vincent, Indianapolis, Indiana 46260, USA
| | - Megan E Tucker
- Peyton Manning Children's Hospital at St. Vincent, Indianapolis, Indiana 46260, USA
| | - Joan Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Diane Stein
- Stein Life Child Neurology, Irvine, California 92604, USA
| | - Warren Marks
- Cook Children's Medical Center, Fort Worth, Texas 76104, USA
| | - Gregory M Enns
- Division of Medical Genetics, Lucile Packard Children's Hospital Stanford, Palo Alto, California 94304, USA
| | - Julia Platt
- Division of Medical Genetics, Lucile Packard Children's Hospital Stanford, Palo Alto, California 94304, USA
| | - Rachel Cox
- Division of Medical Genetics, Lucile Packard Children's Hospital Stanford, Palo Alto, California 94304, USA
| | | | - Carrie Crain
- Nemours Children's Hospital, Orlando, Florida 32827, USA
| | - Amy Calhoun
- University of Minnesota Medical Center, Minneapolis, Minnesota 55454, USA
| | - Rebecca Tryon
- University of Minnesota Medical Center, Minneapolis, Minnesota 55454, USA
| | | | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, New York 10032, USA
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155
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Armour CM, Smith A, Hartley T, Chardon JW, Sawyer S, Schwartzentruber J, Hennekam R, Majewski J, Bulman DE, Suri M, Boycott KM. Syndrome disintegration: Exome sequencing reveals that Fitzsimmons syndrome is a co-occurrence of multiple events. Am J Med Genet A 2016; 170:1820-5. [DOI: 10.1002/ajmg.a.37684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 04/14/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Christine M. Armour
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Amanda Smith
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Jodi Warman Chardon
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Sarah Sawyer
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | | | - Raoul Hennekam
- Department of Pediatrics; Academic Medical Centre, University of Amsterdam; Amsterdam The Netherlands
| | - Jacek Majewski
- Department of Human Genetics; McGill University; Montreal Canada
| | - Dennis E. Bulman
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
| | - Mohnish Suri
- Nottingham Clinical Genetics Service; City Hospital Campus, Nottingham University Hospitals NHS Trust; Nottingham UK
| | - Kym M. Boycott
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Canada
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156
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Molnár J, Szakács G, Tusnády GE. Characterization of Disease-Associated Mutations in Human Transmembrane Proteins. PLoS One 2016; 11:e0151760. [PMID: 26986070 PMCID: PMC4795776 DOI: 10.1371/journal.pone.0151760] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/03/2016] [Indexed: 11/21/2022] Open
Abstract
Transmembrane protein coding genes are commonly associated with human diseases. We characterized disease causing mutations and natural polymorphisms in transmembrane proteins by mapping missense genetic variations from the UniProt database on the transmembrane protein topology listed in the Human Transmembrane Proteome database. We found characteristic differences in the spectrum of amino acid changes within transmembrane regions: in the case of disease associated mutations the non-polar to non-polar and non-polar to charged amino acid changes are equally frequent. In contrast, in the case of natural polymorphisms non-polar to charged amino acid changes are rare while non-polar to non-polar changes are common. The majority of disease associated mutations result in glycine to arginine and leucine to proline substitutions. Mutations to positively charged amino acids are more common in the center of the lipid bilayer, where they cause more severe structural and functional anomalies. Our analysis contributes to the better understanding of the effect of disease associated mutations in transmembrane proteins, which can help prioritize genetic variations in personal genomic investigations.
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Affiliation(s)
- János Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Gábor E. Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
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157
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Stark Z, Tan TY, Chong B, Brett GR, Yap P, Walsh M, Yeung A, Peters H, Mordaunt D, Cowie S, Amor DJ, Savarirayan R, McGillivray G, Downie L, Ekert PG, Theda C, James PA, Yaplito-Lee J, Ryan MM, Leventer RJ, Creed E, Macciocca I, Bell KM, Oshlack A, Sadedin S, Georgeson P, Anderson C, Thorne N, Gaff C, White SM. A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders. Genet Med 2016; 18:1090-1096. [DOI: 10.1038/gim.2016.1] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/23/2015] [Indexed: 12/16/2022] Open
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158
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Lal D, Neubauer BA, Toliat MR, Altmüller J, Thiele H, Nürnberg P, Kamrath C, Schänzer A, Sander T, Hahn A, Nothnagel M. Increased Probability of Co-Occurrence of Two Rare Diseases in Consanguineous Families and Resolution of a Complex Phenotype by Next Generation Sequencing. PLoS One 2016; 11:e0146040. [PMID: 26789268 PMCID: PMC4720433 DOI: 10.1371/journal.pone.0146040] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/11/2015] [Indexed: 12/11/2022] Open
Abstract
Massively parallel sequencing of whole genomes and exomes has facilitated a direct assessment of causative genetic variation, now enabling the identification of genetic factors involved in rare diseases (RD) with Mendelian inheritance patterns on an almost routine basis. Here, we describe the illustrative case of a single consanguineous family where this strategy suffered from the difficulty to distinguish between two etiologically distinct disorders, namely the co-occurrence of hereditary hypophosphatemic rickets (HRR) and congenital myopathies (CM), by their phenotypic manifestation alone. We used parametric linkage analysis, homozygosity mapping and whole exome-sequencing to identify mutations underlying HRR and CM. We also present an approximate approach for assessing the probability of co-occurrence of two unlinked recessive RD in a single family as a function of the degree of consanguinity and the frequency of the disease-causing alleles. Linkage analysis and homozygosity mapping yielded elusive results when assuming a single RD, but whole-exome sequencing helped to identify two mutations in two genes, namely SLC34A3 and SEPN1, that segregated independently in this family and that have previously been linked to two etiologically different diseases. We assess the increase in chance co-occurrence of rare diseases due to consanguinity, i.e. under circumstances that generally favor linkage mapping of recessive disease, and show that this probability can increase by several orders of magnitudes. We conclude that such potential co-occurrence represents an underestimated risk when analyzing rare or undefined diseases in consanguineous families and should be given more consideration in the clinical and genetic evaluation.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- * E-mail: (DL); (MN)
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
| | - Mohammad R. Toliat
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Clemens Kamrath
- Department of Pediatrics, University Medical Faculty Giessen, 35392, Giessen, Germany
| | - Anne Schänzer
- Institute of Neuropathology University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - Andreas Hahn
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, 35392, Giessen, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
- * E-mail: (DL); (MN)
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159
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Sobreira N, Schiettecatte F, Boehm C, Valle D, Hamosh A. New tools for Mendelian disease gene identification: PhenoDB variant analysis module; and GeneMatcher, a web-based tool for linking investigators with an interest in the same gene. Hum Mutat 2015; 36:425-31. [PMID: 25684268 DOI: 10.1002/humu.22769] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/09/2015] [Indexed: 01/10/2023]
Abstract
Identifying the causative variant from among the thousands identified by whole-exome sequencing or whole-genome sequencing is a formidable challenge. To make this process as efficient and flexible as possible, we have developed a Variant Analysis Module coupled to our previously described Web-based phenotype intake tool, PhenoDB (http://researchphenodb.net and http://phenodb.org). When a small number of candidate-causative variants have been identified in a study of a particular patient or family, a second, more difficult challenge becomes proof of causality for any given variant. One approach to this problem is to find other cases with a similar phenotype and mutations in the same candidate gene. Alternatively, it may be possible to develop biological evidence for causality, an approach that is assisted by making connections to basic scientists studying the gene of interest, often in the setting of a model organism. Both of these strategies benefit from an open access, online site where individual clinicians and investigators could post genes of interest. To this end, we developed GeneMatcher (http://genematcher.org), a freely accessible Website that enables connections between clinicians and researchers across the world who share an interest in the same gene(s).
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Affiliation(s)
- Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
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160
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Abstract
PURPOSE OF REVIEW Clinical diagnostic sequencing currently focuses on identifying causal mutations in the exome, wherein most disease-causing mutations are known to occur. The rest of the genome is mostly comprised of regulatory elements that control gene expression, but these have remained largely unexplored in clinical diagnostics due to the high cost of whole genome sequencing and interpretive challenges. The purpose of this review is to illustrate examples of diseases caused by mutations in regulatory elements and introduce the diagnostic potential for whole genome sequencing. Different classes of functional elements and chromatin structure are described to provide the clinician with a foundation for understanding the basis of these mutations. RECENT FINDINGS The utilization of whole-genome sequence data, epigenomic maps and induced pluripotent stem (IPS) cell technologies facilitated the discovery that mutations in the pancreas-specific transcription factor 1a enhancer can cause isolated pancreatic agenesis. High resolution array comparative genomic hybridisation (CGH), whole-genome sequencing, maps of 3-D chromatin architecture, and mouse models generated using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas were used to show that disruption of topological-associated domain boundary elements cause limb defects. Structural variants that reposition enhancers in somatic cells have also been described in cancer. SUMMARY Although not ready for diagnostics, new technologies, epigenomic maps, and improved knowledge of chromatin architecture will soon enable a better understanding and diagnostic solutions for currently unexplained genetic disorders.
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161
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Human genotype–phenotype databases: aims, challenges and opportunities. Nat Rev Genet 2015; 16:702-15. [DOI: 10.1038/nrg3932] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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162
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Andelfinger G, Loeys B, Dietz H. A Decade of Discovery in the Genetic Understanding of Thoracic Aortic Disease. Can J Cardiol 2015; 32:13-25. [PMID: 26724507 DOI: 10.1016/j.cjca.2015.10.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/14/2015] [Accepted: 10/18/2015] [Indexed: 12/23/2022] Open
Abstract
Aortic aneurysms are responsible for a significant number of all deaths in Western countries. In this review we provide a perspective on the important progress made over the past decade in the understanding of the genetics of this condition, with an emphasis on the more frequent forms of vascular smooth muscle and transforming growth factor β (TGF-β) signalling alterations. For several nonsyndromic and syndromic forms of thoracic aortic disease, a genetic basis has now been identified, with 3 main pathomechanisms that have emerged: perturbation of the TGF-β signalling pathway, disruption of the vascular smooth muscle cell (VSMC) contractile apparatus, and impairment of extracellular matrix synthesis. Because smooth muscle cells and proteins of the extracellular matrix directly regulate TGF-β signalling, this latter pathway emerges as a key component of thoracic aortic disease initiation and progression. These discoveries have revolutionized our understanding of thoracic aortic disease and provided inroads toward gene-specific stratification of treatment. Last, we outline how these genetic findings are translated into novel pharmaceutical approaches for thoracic aortic disease.
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Affiliation(s)
- Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada.
| | - Bart Loeys
- Centre for Medical Genetics, University Hospital of Antwerp/University of Antwerp, Antwerp, Belgium; Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hal Dietz
- Howard Hughes Medical Institute and Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Division of Pediatric Cardiology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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163
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Sawyer SL, Hartley T, Dyment DA, Beaulieu CL, Schwartzentruber J, Smith A, Bedford HM, Bernard G, Bernier FP, Brais B, Bulman DE, Warman Chardon J, Chitayat D, Deladoëy J, Fernandez BA, Frosk P, Geraghty MT, Gerull B, Gibson W, Gow RM, Graham GE, Green JS, Heon E, Horvath G, Innes AM, Jabado N, Kim RH, Koenekoop RK, Khan A, Lehmann OJ, Mendoza-Londono R, Michaud JL, Nikkel SM, Penney LS, Polychronakos C, Richer J, Rouleau GA, Samuels ME, Siu VM, Suchowersky O, Tarnopolsky MA, Yoon G, Zahir FR, Majewski J, Boycott KM. Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care. Clin Genet 2015; 89:275-84. [PMID: 26283276 PMCID: PMC5053223 DOI: 10.1111/cge.12654] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/14/2015] [Accepted: 08/14/2015] [Indexed: 12/17/2022]
Abstract
An accurate diagnosis is an integral component of patient care for children with rare genetic disease. Recent advances in sequencing, in particular whole‐exome sequencing (WES), are identifying the genetic basis of disease for 25–40% of patients. The diagnostic rate is probably influenced by when in the diagnostic process WES is used. The Finding Of Rare Disease GEnes (FORGE) Canada project was a nation‐wide effort to identify mutations for childhood‐onset disorders using WES. Most children enrolled in the FORGE project were toward the end of the diagnostic odyssey. The two primary outcomes of FORGE were novel gene discovery and the identification of mutations in genes known to cause disease. In the latter instance, WES identified mutations in known disease genes for 105 of 362 families studied (29%), thereby informing the impact of WES in the setting of the diagnostic odyssey. Our analysis of this dataset showed that these known disease genes were not identified prior to WES enrollment for two key reasons: genetic heterogeneity associated with a clinical diagnosis and atypical presentation of known, clinically recognized diseases. What is becoming increasingly clear is that WES will be paradigm altering for patients and families with rare genetic diseases.
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Affiliation(s)
- S L Sawyer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - C L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - A Smith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - H M Bedford
- Genetics Program, North York General Hospital, Toronto, Canada
| | - G Bernard
- Departments of Pediatrics, Neurology and Neurosurgery, Division of Pediatric Neurology, Montréal Children's Hospital, Research Institute of the McGill University Health Centre, Montreal, Canada
| | - F P Bernier
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B Brais
- Neurogenetics of Motion Laboratory, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | - D Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - J Deladoëy
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - B A Fernandez
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - P Frosk
- Departments of Pediatrics and Child Health, University of Manitoba, Winnipeg, Canada
| | - M T Geraghty
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - B Gerull
- Cardiac Sciences and Medical Genetics, University of Calgary, Calgary, Canada
| | - W Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - R M Gow
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - G E Graham
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J S Green
- Disciplines of Genetics and Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - E Heon
- Department of Ophthalmology and Vision Sciences, Program of Genetics and Genomic Biology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G Horvath
- Division of Biochemical Diseases, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, British Columbia, Canada
| | - A M Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - N Jabado
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - R H Kim
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada
| | - R K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Canada
| | - A Khan
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - O J Lehmann
- Departments of Ophthalmology and Medical Genetics, University of Alberta, Edmonton, Canada
| | - R Mendoza-Londono
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - J L Michaud
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - S M Nikkel
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - L S Penney
- Medical Genetics, IWK Health Centre, Halifax, Canada
| | - C Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - J Richer
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - G A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - M E Samuels
- Department of Medicine, Centre de Recherche du CHU Ste-Justine, University of Montreal, Montreal, Canada
| | - V M Siu
- Division of Medical Genetics, Department of Pediatrics, University of Western Ontario, London, Canada
| | - O Suchowersky
- Departments of Medicine, Medical Genetics, and Pediatrics, University of Alberta, Edmonton, Canada
| | - M A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - G Yoon
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - F R Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | | | | - J Majewski
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
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164
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Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, Trang H, Misyura A, Friedman T, Beaulieu C, Bone WP, Links AE, Washington NL, Haendel MA, Robinson PN, Boerkoel CF, Adams D, Gahl WA, Boycott KM, Brudno M. PhenomeCentral: a portal for phenotypic and genotypic matchmaking of patients with rare genetic diseases. Hum Mutat 2015; 36:931-40. [PMID: 26251998 DOI: 10.1002/humu.22851] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/28/2015] [Indexed: 01/18/2023]
Abstract
The discovery of disease-causing mutations typically requires confirmation of the variant or gene in multiple unrelated individuals, and a large number of rare genetic diseases remain unsolved due to difficulty identifying second families. To enable the secure sharing of case records by clinicians and rare disease scientists, we have developed the PhenomeCentral portal (https://phenomecentral.org). Each record includes a phenotypic description and relevant genetic information (exome or candidate genes). PhenomeCentral identifies similar patients in the database based on semantic similarity between clinical features, automatically prioritized genes from whole-exome data, and candidate genes entered by the users, enabling both hypothesis-free and hypothesis-driven matchmaking. Users can then contact other submitters to follow up on promising matches. PhenomeCentral incorporates data for over 1,000 patients with rare genetic diseases, contributed by the FORGE and Care4Rare Canada projects, the US NIH Undiagnosed Diseases Program, the EU Neuromics and ANDDIrare projects, as well as numerous independent clinicians and scientists. Though the majority of these records have associated exome data, most lack a molecular diagnosis. PhenomeCentral has already been used to identify causative mutations for several patients, and its ability to find matching patients and diagnose these diseases will grow with each additional patient that is entered.
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Affiliation(s)
- Orion J Buske
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Bailey Gallinger
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Heather Trang
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Tal Friedman
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Chandree Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - William P Bone
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Amanda E Links
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Nicole L Washington
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Melissa A Haendel
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Peter N Robinson
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Cornelius F Boerkoel
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - David Adams
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
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165
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A mouse informatics platform for phenotypic and translational discovery. Mamm Genome 2015; 26:413-21. [PMID: 26314589 PMCID: PMC4602054 DOI: 10.1007/s00335-015-9599-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/17/2015] [Indexed: 01/05/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is providing the world's first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers.
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166
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Barclay SF, Rand CM, Borch LA, Nguyen L, Gray PA, Gibson WT, Wilson RJA, Gordon PMK, Aung Z, Berry-Kravis EM, Ize-Ludlow D, Weese-Mayer DE, Bech-Hansen NT. Rapid-Onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD): exome sequencing of trios, monozygotic twins and tumours. Orphanet J Rare Dis 2015; 10:103. [PMID: 26302956 PMCID: PMC4548308 DOI: 10.1186/s13023-015-0314-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 07/29/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Rapid-onset Obesity with Hypothalamic Dysfunction, Hypoventilation, and Autonomic Dysregulation (ROHHAD) is thought to be a genetic disease caused by de novo mutations, though causative mutations have yet to be identified. We searched for de novo coding mutations among a carefully-diagnosed and clinically homogeneous cohort of 35 ROHHAD patients. METHODS We sequenced the exomes of seven ROHHAD trios, plus tumours from four of these patients and the unaffected monozygotic (MZ) twin of one (discovery cohort), to identify constitutional and somatic de novo sequence variants. We further analyzed this exome data to search for candidate genes under autosomal dominant and recessive models, and to identify structural variations. Candidate genes were tested by exome or Sanger sequencing in a replication cohort of 28 ROHHAD singletons. RESULTS The analysis of the trio-based exomes found 13 de novo variants. However, no two patients had de novo variants in the same gene, and additional patient exomes and mutation analysis in the replication cohort did not provide strong genetic evidence to implicate any of these sequence variants in ROHHAD. Somatic comparisons revealed no coding differences between any blood and tumour samples, or between the two discordant MZ twins. Neither autosomal dominant nor recessive analysis yielded candidate genes for ROHHAD, and we did not identify any potentially causative structural variations. CONCLUSIONS Clinical exome sequencing is highly unlikely to be a useful diagnostic test in patients with true ROHHAD. As ROHHAD has a high risk for fatality if not properly managed, it remains imperative to expand the search for non-exomic genetic risk factors, as well as to investigate other possible mechanisms of disease. In so doing, we will be able to confirm objectively the ROHHAD diagnosis and to contribute to our understanding of obesity, respiratory control, hypothalamic function, and autonomic regulation.
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Affiliation(s)
- Sarah F Barclay
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Casey M Rand
- Center for Autonomic Medicine in Pediatrics (CAMP) in Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago and Stanley Manne Children's Research Institute, Chicago, IL, USA.
| | - Lauren A Borch
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Lisa Nguyen
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Paul A Gray
- Department of Anatomy and Neurobiology, Washington University of Medicine, St Louis, MO, USA.
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia and Child & Family Research Institute, Vancouver, B.C., Canada.
| | - Richard J A Wilson
- Department of Physiology and Pharmacology, Alberta Children's Hospital Research Institute and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Paul M K Gordon
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Zaw Aung
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
| | - Elizabeth M Berry-Kravis
- Departments of Pediatrics, Neurological Sciences, and Biochemistry, Rush University Medical Center, Chicago, IL, USA.
| | - Diego Ize-Ludlow
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Illinois at Chicago, Chicago, IL, USA.
| | - Debra E Weese-Mayer
- Center for Autonomic Medicine in Pediatrics (CAMP) in Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago and Stanley Manne Children's Research Institute, Chicago, IL, USA. .,Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - N Torben Bech-Hansen
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
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167
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Loucks CM, Parboosingh JS, Shaheen R, Bernier FP, McLeod DR, Seidahmed MZ, Puffenberger EG, Ober C, Hegele RA, Boycott KM, Alkuraya FS, Innes AM. Matching two independent cohorts validates DPH1 as a gene responsible for autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies. Hum Mutat 2015. [PMID: 26220823 DOI: 10.1002/humu.22843] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recently, Alazami et al. (2015) identified 33 putative candidate disease genes for neurogenetic disorders. One such gene was DPH1, in which a homozygous missense mutation was associated with a 3C syndrome-like phenotype in four patients from a single extended family. Here, we report a second homozygous missense variant in DPH1, seen in four members of a founder population, and associated with a phenotype initially reminiscent of Sensenbrenner syndrome. This postpublication "match" validates DPH1 as a gene underlying syndromic intellectual disability with short stature and craniofacial and ectodermal anomalies, reminiscent of, but distinct from, 3C and Sensenbrenner syndromes. This validation took several years after the independent discoveries due to the absence of effective methods for sharing both candidate phenotype and genotype data between investigators. Sharing of data via Web-based anonymous data exchange servers will play an increasingly important role toward more efficient identification of the molecular basis for rare Mendelian disorders.
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Affiliation(s)
- Catrina M Loucks
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jillian S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyhadh, 11211, Saudi Arabia
| | - Francois P Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - D Ross McLeod
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Carole Ober
- Department of Human Genetics, and Department of Obstetrics and Gynecology, The University of Chicago, Chicago, Illinois
| | - Robert A Hegele
- Department of Paediatrics, University of Western Ontario, London, Ontario, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyhadh, 11211, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
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168
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van den Veyver IB, Eng CM. Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a023077. [PMID: 26253094 DOI: 10.1101/cshperspect.a023077] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
New sequencing methods capable of rapidly analyzing the genome at increasing resolution have transformed diagnosis of single-gene or oligogenic genetic disorders in pediatric and adult medicine. Targeted tests, consisting of disease-focused multigene panels and diagnostic exome sequencing to interrogate the sequence of the coding regions of nearly all genes, are now clinically offered when there is suspicion for an undiagnosed genetic disorder or cancer in children and adults. Implementation of diagnostic exome and genome sequencing tests on invasively and noninvasively obtained fetal DNA samples for prenatal genetic diagnosis is also being explored. We predict that they will become more widely integrated into prenatal care in the near future. Providers must prepare for the practical, ethical, and societal dilemmas that accompany the capacity to generate and analyze large amounts of genetic information about the fetus during pregnancy.
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Affiliation(s)
- Ignatia B van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, The Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas 77030 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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169
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Chong J, Buckingham K, Jhangiani S, Boehm C, Sobreira N, Smith J, Harrell T, McMillin M, Wiszniewski W, Gambin T, Coban Akdemir Z, Doheny K, Scott A, Avramopoulos D, Chakravarti A, Hoover-Fong J, Mathews D, Witmer P, Ling H, Hetrick K, Watkins L, Patterson K, Reinier F, Blue E, Muzny D, Kircher M, Bilguvar K, López-Giráldez F, Sutton V, Tabor H, Leal S, Gunel M, Mane S, Gibbs R, Boerwinkle E, Hamosh A, Shendure J, Lupski J, Lifton R, Valle D, Nickerson D, Bamshad M, Bamshad MJ. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. Am J Hum Genet 2015; 97:199-215. [PMID: 26166479 DOI: 10.1016/j.ajhg.2015.06.009] [Citation(s) in RCA: 449] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 01/06/2023] Open
Abstract
Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA.
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170
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Alamillo CL, Powis Z, Farwell K, Shahmirzadi L, Weltmer EC, Turocy J, Lowe T, Kobelka C, Chen E, Basel D, Ashkinadze E, D'Augelli L, Chao E, Tang S. Exome sequencing positively identified relevant alterations in more than half of cases with an indication of prenatal ultrasound anomalies. Prenat Diagn 2015; 35:1073-8. [PMID: 26147564 DOI: 10.1002/pd.4648] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Exome sequencing is a successful option for diagnosing individuals with previously uncharacterized genetic conditions, however little has been reported regarding its utility in a prenatal setting. The goal of this study is to describe the results from a cohort of fetuses for which exome sequencing was performed. METHODS We performed a retrospective analysis of the first seven cases referred to our laboratory for exome sequencing following fetal demise or termination of pregnancy. All seven pregnancies had multiple congenital anomalies identified by level II ultrasound. Exome sequencing was performed on trios using cultured amniocytes or products of conception from the affected fetuses. RESULTS Relevant alterations were identified in more than half of the cases (4/7). Three of the four were categorized as 'positive' results, and one of the four was categorized as a 'likely positive' result. The provided diagnoses included osteogenesis imperfecta II (COL1A2), glycogen storage disease IV (GBE1), oral-facial-digital syndrome 1 (OFD1), and RAPSN-associated fetal akinesia deformation sequence. CONCLUSION This data suggests that exome sequencing is likely to be a valuable diagnostic testing option for pregnancies with multiple congenital anomalies detected by prenatal ultrasound; however, additional studies with larger cohorts of affected pregnancies are necessary to confirm these findings.
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Affiliation(s)
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | | | - John Turocy
- Genetics Department, Kaiser Permanente, Clovis, CA, USA
| | - Thomas Lowe
- Thomas Lowe, MD, Private Practice, Boca Raton, FL, USA
| | | | - Emily Chen
- Genetics Department, Kaiser Permanente, San Francisco, CA, USA
| | - Donald Basel
- Division of Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elena Ashkinadze
- Division of Maternal-Fetal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | | | - Elizabeth Chao
- Ambry Genetics, Aliso Viejo, CA, USA.,Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA, USA
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171
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Smedley D, Robinson PN. Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med 2015; 7:81. [PMID: 26229552 PMCID: PMC4520011 DOI: 10.1186/s13073-015-0199-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified. Hundreds of novel disease-associated genes have been characterized by whole exome sequencing in the past five years, yet the identification of disease-causing mutations is often challenging because of the large number of rare variants that are being revealed. Gene prioritization aims to rank the most probable candidate genes towards the top of a list of potentially pathogenic variants. A promising new approach involves the computational comparison of the phenotypic abnormalities of the individual being investigated with those previously associated with human diseases or genetically modified model organisms. In this review, we compare and contrast the strengths and weaknesses of current phenotype-driven computational algorithms, including Phevor, Phen-Gen, eXtasy and two algorithms developed by our groups called PhenIX and Exomiser. Computational phenotype analysis can substantially improve the performance of exome analysis pipelines.
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Affiliation(s)
- Damian Smedley
- />Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter N. Robinson
- />Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- />Max Planck Institute for Molecular Genetics, Ihnestrasse, 14195 Berlin, Germany
- />Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz, 13353 Berlin, Germany
- />Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany
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172
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Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat Genet 2015; 47:717-726. [PMID: 25985138 PMCID: PMC4601524 DOI: 10.1038/ng.3304] [Citation(s) in RCA: 250] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 04/22/2015] [Indexed: 12/12/2022]
Abstract
To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.
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Affiliation(s)
- Jenny C Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hilary C Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stefano Lise
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - John Broxholme
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Andy Rimmer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexander Kanapin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon Fiddy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Allan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Radu Aricescu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David Beeson
- Neurosciences Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Celeste Bento
- Hematology Department, Centro Hospitalar e Universitário de Coimbra, Portugal
| | - Patricia Bignell
- Molecular Haematology Department, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Edward Blair
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Katherine Bull
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Ondrej Cais
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - Helen Chapel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Richard R Copley
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Richard Cornall
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Jude Craft
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Karin Dahan
- Centre de Génétique Humaine, Institut de Génétique et de Pathologie, Gosselies, Belgium
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Calliope Dendrou
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olivier Devuyst
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Aimée L Fenwick
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lars Fugger
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rodney D Gilbert
- University Hospital Southampton NHS Foundation Trust, University of Southampton, Southampton, UK
| | - Anne Goriely
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Anja V Gruszczyk
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert Hastings
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Edouard Hatton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Doug Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adrian Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chris Holmes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Malcolm Howard
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Linda Hughes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Johnson
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Fredrik Karpe
- Oxford Laboratory for Integrative Physiology, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan Krohn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Craig Langman
- Kidney Diseases, Feinberg School of Medicine, Northwestern University and the Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Lorne Lonie
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Joshua Luck
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Davis McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon J McGowan
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Kerry A Miller
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lisa Murray
- Illumina Cambridge Limited, Saffron Walden, UK
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - M Andrew Nesbit
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - David Nutt
- Centre for Neuropsychopharmacology, Division of Brain Sciences, Imperial College, London, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Annette Bang Oturai
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alistair Pagnamenta
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Smita Y Patel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Melanie Percy
- Department of Haematology, Belfast City Hospital, Belfast, UK
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sian E Piret
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Niko Popitsch
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lynn Quek
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter A Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Kathryn Robson
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alexandra Russo
- Department of Pediatrics, University Hospital, Mainz, Germany
| | - Natasha Sahgal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Anna Schuh
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Earl Silverman
- Division of Rheumatology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Per Soelberg Sørensen
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford NHS Regional Molecular Genetics Laboratory, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Ian Tomlinson
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen Rf Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tim Vyse
- Division of Genetics, King's College London, Guy's Hospital, London, UK
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michael P Whyte
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospital for Children, St Louis, Missouri, USA
| | - Lorna Witty
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ben Wright
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - Andrew Om Wilkie
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Abstract
In this commentary, Philip Hieter and Kym Boycott discuss the importance of model organisms for understanding pathogenesis of rare human genetic diseases, and highlight the work of Brooks et al., "Dysfunction of 60S ribosomal protein L10 (RPL10) disrupts neurodevelopment and causes X-linked microcephaly in humans," published in this issue of GENETICS.
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174
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Yavarna T, Al-Dewik N, Al-Mureikhi M, Ali R, Al-Mesaifri F, Mahmoud L, Shahbeck N, Lakhani S, AlMulla M, Nawaz Z, Vitazka P, Alkuraya FS, Ben-Omran T. High diagnostic yield of clinical exome sequencing in Middle Eastern patients with Mendelian disorders. Hum Genet 2015; 134:967-80. [PMID: 26077850 DOI: 10.1007/s00439-015-1575-0] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 05/30/2015] [Indexed: 12/16/2022]
Abstract
Clinical exome sequencing (CES) has become an increasingly popular diagnostic tool in patients with heterogeneous genetic disorders, especially in those with neurocognitive phenotypes. Utility of CES in consanguineous populations has not yet been determined on a large scale. A clinical cohort of 149 probands from Qatar with suspected Mendelian, mainly neurocognitive phenotypes, underwent CES from July 2012 to June 2014. Intellectual disability and global developmental delay were the most common clinical presentations but our cohort displayed other phenotypes, such as epilepsy, dysmorphism, microcephaly and other structural brain anomalies and autism. A pathogenic or likely pathogenic mutation, including pathogenic CNVs, was identified in 89 probands for a diagnostic yield of 60%. Consanguinity and positive family history predicted a higher diagnostic yield. In 5% (7/149) of cases, CES implicated novel candidate disease genes (MANF, GJA9, GLG1, COL15A1, SLC35F5, MAGE4, NEUROG1). CES uncovered two coexisting genetic disorders in 4% (6/149) and actionable incidental findings in 2% (3/149) of cases. Average time to diagnosis was reduced from 27 to 5 months. CES, which already has the highest diagnostic yield among all available diagnostic tools in the setting of Mendelian disorders, appears to be particularly helpful diagnostically in the highly consanguineous Middle Eastern population.
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Affiliation(s)
- Tarunashree Yavarna
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, P.O.BOX. 3050, Doha, Qatar
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175
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Precision Medicine for Continuing Phenotype Expansion of Human Genetic Diseases. BIOMED RESEARCH INTERNATIONAL 2015; 2015:745043. [PMID: 26137492 PMCID: PMC4475565 DOI: 10.1155/2015/745043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/12/2015] [Indexed: 12/20/2022]
Abstract
Determining the exact genetic causes for a patient and providing definite molecular diagnoses are core elements of precision medicine. Individualized patient care is often limited by our current knowledge of disease etiologies and commonly used phenotypic-based diagnostic approach. The broad and incompletely understood phenotypic spectrum of a disease and various underlying genetic heterogeneity also present extra challenges to our clinical practice. With the rapid adaptation of new sequence technology in clinical setting for diagnostic purpose, phenotypic expansions of disease spectrum are becoming increasingly common. Understanding the underlying molecular mechanisms will help us to integrate genomic information into the workup of individualized patient care and make better clinical decisions.
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176
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Blackburn HL, Schroeder B, Turner C, Shriver CD, Ellsworth DL, Ellsworth RE. Management of Incidental Findings in the Era of Next-generation Sequencing. Curr Genomics 2015; 16:159-74. [PMID: 26069456 PMCID: PMC4460220 DOI: 10.2174/1389202916666150317232930] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 02/23/2015] [Accepted: 03/09/2015] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies allow for the generation of whole exome or whole genome sequencing data, which can be used to identify novel genetic alterations associated with defined phenotypes or to expedite discovery of functional variants for improved patient care. Because this robust technology has the ability to identify all mutations within a genome, incidental findings (IF)- genetic alterations associated with conditions or diseases unrelated to the patient's present condition for which current tests are being performed- may have important clinical ramifications. The current debate among genetic scientists and clinicians focuses on the following questions: 1) should any IF be disclosed to patients, and 2) which IF should be disclosed - actionable mutations, variants of unknown significance, or all IF? Policies for disclosure of IF are being developed for when and how to convey these findings and whether adults, minors, or individuals unable to provide consent have the right to refuse receipt of IF. In this review, we detail current NGS technology platforms, discuss pressing issues regarding disclosure of IF, and how IF are currently being handled in prenatal, pediatric, and adult patients.
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Affiliation(s)
| | - Bradley Schroeder
- Clinical Breast Care Project, Windber Research Institute, Windber, PA, USA
| | - Clesson Turner
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Craig D. Shriver
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | | | - Rachel E. Ellsworth
- Clinical Breast Care Project, Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda, MD, USA
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177
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Thaker VV, Esteves KM, Towne MC, Brownstein CA, James PM, Crowley L, Hirschhorn JN, Elsea SH, Beggs AH, Picker J, Agrawal PB. Whole exome sequencing identifies RAI1 mutation in a morbidly obese child diagnosed with ROHHAD syndrome. J Clin Endocrinol Metab 2015; 100:1723-30. [PMID: 25781356 PMCID: PMC4422892 DOI: 10.1210/jc.2014-4215] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CONTEXT The current obesity epidemic is attributed to complex interactions between genetic and environmental factors. However, a limited number of cases, especially those with early-onset severe obesity, are linked to single gene defects. Rapid-onset obesity with hypothalamic dysfunction, hypoventilation and autonomic dysregulation (ROHHAD) is one of the syndromes that presents with abrupt-onset extreme weight gain with an unknown genetic basis. OBJECTIVE To identify the underlying genetic etiology in a child with morbid early-onset obesity, hypoventilation, and autonomic and behavioral disturbances who was clinically diagnosed with ROHHAD syndrome. Design/Setting/Intervention: The index patient was evaluated at an academic medical center. Whole-exome sequencing was performed on the proband and his parents. Genetic variants were validated by Sanger sequencing. RESULTS We identified a novel de novo nonsense mutation, c.3265 C>T (p.R1089X), in the retinoic acid-induced 1 (RAI1) gene in the proband. Mutations in the RAI1 gene are known to cause Smith-Magenis syndrome (SMS). On further evaluation, his clinical features were not typical of either SMS or ROHHAD syndrome. CONCLUSIONS This study identifies a de novo RAI1 mutation in a child with morbid obesity and a clinical diagnosis of ROHHAD syndrome. Although extreme early-onset obesity, autonomic disturbances, and hypoventilation are present in ROHHAD, several of the clinical findings are consistent with SMS. This case highlights the challenges in the diagnosis of ROHHAD syndrome and its potential overlap with SMS. We also propose RAI1 as a candidate gene for children with morbid obesity.
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Affiliation(s)
- Vidhu V Thaker
- Division of Endocrinology (V.V.T., J.N.H.), Newborn Medicine (K.M.E., P.B.A.), and Genetics and Genomics (M.C.T., C.A.B., L.C., A.H.B., J.P., P.B.A.), Department of Medicine, and Gene Discovery Core (M.C.T., C.A.B., L.C., A.H.B., J.P., P.B.A.), The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115; Genetics and Metabolism (P.M.J.), Phoenix Children's Hospital, Phoenix, Arizona 85006; and Department of Molecular and Human Genetics (S.H.E.), Baylor College of Medicine, Houston, Texas 77030
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178
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Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders. Genome Res 2015; 25:948-57. [PMID: 25917818 PMCID: PMC4484392 DOI: 10.1101/gr.186882.114] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/20/2015] [Indexed: 01/24/2023]
Abstract
Spontaneously arising mouse mutations have served as the foundation for understanding gene function for more than 100 years. We have used exome sequencing in an effort to identify the causative mutations for 172 distinct, spontaneously arising mouse models of Mendelian disorders, including a broad range of clinically relevant phenotypes. To analyze the resulting data, we developed an analytics pipeline that is optimized for mouse exome data and a variation database that allows for reproducible, user-defined data mining as well as nomination of mutation candidates through knowledge-based integration of sample and variant data. Using these new tools, putative pathogenic mutations were identified for 91 (53%) of the strains in our study. Despite the increased power offered by potentially unlimited pedigrees and controlled breeding, about half of our exome cases remained unsolved. Using a combination of manual analyses of exome alignments and whole-genome sequencing, we provide evidence that a large fraction of unsolved exome cases have underlying structural mutations. This result directly informs efforts to investigate the similar proportion of apparently Mendelian human phenotypes that are recalcitrant to exome sequencing.
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179
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Ben-Omran T, Fahiminiya S, Sorfazlian N, Almuriekhi M, Nawaz Z, Nadaf J, Abu Khadija K, Zaineddin S, Kamel H, Majewski J, Tropepe V. Nonsense mutation in theWDR73gene is associated with Galloway-Mowat syndrome. J Med Genet 2015; 52:381-90. [DOI: 10.1136/jmedgenet-2014-102707] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/22/2015] [Indexed: 01/10/2023]
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180
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Harel S, Cohen ASA, Hussain K, Flanagan SE, Schlade-Bartusiak K, Patel M, Courtade J, Li JBW, Van Karnebeek C, Kurata H, Ellard S, Chanoine JP, Gibson WT. Alternating hypoglycemia and hyperglycemia in a toddler with a homozygous p.R1419H ABCC8 mutation: an unusual clinical picture. J Pediatr Endocrinol Metab 2015; 28:345-51. [PMID: 25720052 DOI: 10.1515/jpem-2014-0265] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/30/2014] [Indexed: 11/15/2022]
Abstract
BACKGROUND Inheritance of two pathogenic ABCC8 alleles typically causes severe congenital hyperinsulinism. We describe a girl and her father, both homozygous for the same ABCC8 mutation, who presented with unusual phenotypes. METHODS Single nucleotide polymorphism microarray and Sanger sequencing were performed. Western blot, rubidium efflux, and patch clamp recordings interrogated the expression and activity of the mutant protein. RESULTS A 16-month-old girl of consanguineous descent manifested hypoglycemia. She had dysregulation of insulin secretion, with postprandial hyperglycemia followed by hypoglycemia. Microarray revealed homozygosity for the regions encompassing KCNJ11 and ABCC8. Her father had developed diabetes at 28 years of age. Sequencing of ABCC8 identified a homozygous missense mutation, p.R1419H, in both individuals. Functional studies showed absence of working KATP channels. CONCLUSION This is the first description of a homozygous p.R1419H mutation. Our findings highlight that homozygous loss-of-function mutations of ABCC8 do not necessarily translate into early-onset severe hyperinsulinemia.
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181
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Affiliation(s)
- Jane A Evans
- Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Man.
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182
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Nguyen MT, Charlebois K. The clinical utility of whole-exome sequencing in the context of rare diseases - the changing tides of medical practice. Clin Genet 2015; 88:313-9. [PMID: 25421945 DOI: 10.1111/cge.12546] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/30/2014] [Accepted: 11/21/2014] [Indexed: 01/07/2023]
Abstract
Whole-exome sequencing (WES) carries the potential to facilitate the identification of disease causing genes. This is particularly relevant concerning rare diseases, which proves particularly difficult for physicians to diagnose. However, the complexity of this technology renders its applicability onto the clinical setting uncertain. Our study thus aims to understand physicians' perspectives regarding the clinical utility of WES, particularly for providing a diagnosis for patients with rare diseases. Ten semi-structured interviews were conducted with physicians with experience and familiarity with WES, and the major themes that emerged from our interviews were (i) the relevance of WES in diagnosing patients with rare diseases (appropriateness); (ii) the cost-effectiveness of WES (accessibility), (iii) the practical issues related to the clinical implementation of WES (practicability); and (iv) ethical, legal and social issues (acceptability). Our study highlights how the clinical implementation of WES presents additional challenges where rare diseases are taken into consideration.
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Affiliation(s)
- M T Nguyen
- Centre of Genomics and Policy, McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - K Charlebois
- Centre of Genomics and Policy, McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
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Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Tippin Davis B, Baxter RM, Zeng W, Mroske C, Parra MC, Gandomi SK, Lu I, Li X, Lu H, Lu HM, Salvador D, Ruble D, Lao M, Fischbach S, Wen J, Lee S, Elliott A, Dunlop CL, Tang S. Enhanced utility of family-centered diagnostic exome sequencing with inheritance model–based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med 2014; 17:578-86. [DOI: 10.1038/gim.2014.154] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022] Open
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184
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Schwartzentruber J, Buhas D, Majewski J, Sasarman F, Papillon-Cavanagh S, Thiffault I, Thiffaut I, Sheldon KM, Massicotte C, Patry L, Simon M, Zare AS, McKernan KJ, Michaud J, Boles RG, Deal CL, Desilets V, Shoubridge EA, Samuels ME. Mutation in the nuclear-encoded mitochondrial isoleucyl-tRNA synthetase IARS2 in patients with cataracts, growth hormone deficiency with short stature, partial sensorineural deafness, and peripheral neuropathy or with Leigh syndrome. Hum Mutat 2014; 35:1285-9. [PMID: 25130867 DOI: 10.1002/humu.22629] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 07/10/2014] [Indexed: 01/28/2023]
Abstract
Mutations in the nuclear-encoded mitochondrial aminoacyl-tRNA synthetases are associated with a range of clinical phenotypes. Here, we report a novel disorder in three adult patients with a phenotype including cataracts, short-stature secondary to growth hormone deficiency, sensorineural hearing deficit, peripheral sensory neuropathy, and skeletal dysplasia. Using SNP genotyping and whole-exome sequencing, we identified a single likely causal variant, a missense mutation in a conserved residue of the nuclear gene IARS2, encoding mitochondrial isoleucyl-tRNA synthetase. The mutation is homozygous in the affected patients, heterozygous in carriers, and absent in control chromosomes. IARS2 protein level was reduced in skin cells cultured from one of the patients, consistent with a pathogenic effect of the mutation. Compound heterozygous mutations in IARS2 were independently identified in a previously unreported patient with a more severe mitochondrial phenotype diagnosed as Leigh syndrome. This is the first report of clinical findings associated with IARS2 mutations.
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185
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Hypomaturation amelogenesis imperfecta caused by a novel SLC24A4 mutation. Oral Surg Oral Med Oral Pathol Oral Radiol 2014; 119:e77-81. [PMID: 25442250 DOI: 10.1016/j.oooo.2014.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 01/22/2023]
Abstract
In this case report of autosomal recessive pigmented hypomaturation amelogenesis imperfecta (AI), we identify a novel homozygous missense mutation (g.165151 T>G; c.1317 T>G; p.Leu436 Arg) in SLC24A4, a gene encoding a potassium-dependent sodium-calcium exchanger that is critical for hardening dental enamel during tooth development.
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186
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Savarese M, Di Fruscio G, Mutarelli M, Torella A, Magri F, Santorelli FM, Comi GP, Bruno C, Nigro V. MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples. Acta Neuropathol Commun 2014; 2:100. [PMID: 25214167 PMCID: PMC4172906 DOI: 10.1186/s40478-014-0100-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 08/10/2014] [Indexed: 12/30/2022] Open
Abstract
Mutations in ~100 genes cause muscle diseases with complex and often unexplained genotype/phenotype correlations. Next-generation sequencing studies identify a greater-than-expected number of genetic variations in the human genome. This suggests that existing clinical monogenic testing systematically miss very relevant information. We have created a core panel of genes that cause all known forms of nonsyndromic muscle disorders (MotorPlex). It comprises 93 loci, among which are the largest and most complex human genes, such as TTN, RYR1, NEB and DMD. MotorPlex captures at least 99.2% of 2,544 exons with a very accurate and uniform coverage. This quality is highlighted by the discovery of 20-30% more variations in comparison with whole exome sequencing. The coverage homogeneity has also made feasible to apply a cost-effective pooled sequencing strategy while maintaining optimal sensitivity and specificity. We studied 177 unresolved cases of myopathies for which the best candidate genes were previously excluded. We have identified known pathogenic variants in 52 patients and potential causative ones in further 56 patients. We have also discovered 23 patients showing multiple true disease-associated variants suggesting complex inheritance. Moreover, we frequently detected other nonsynonymous variants of unknown significance in the largest muscle genes. Cost-effective combinatorial pools of DNA samples were similarly accurate (97-99%). MotorPlex is a very robust platform that overcomes for power, costs, speed, sensitivity and specificity the gene-by-gene strategy. The applicability of pooling makes this tool affordable for the screening of genetic variability of muscle genes also in a larger population. We consider that our strategy can have much broader applications.
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187
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Dyment DA, Tétreault M, Beaulieu CL, Hartley T, Ferreira P, Chardon JW, Marcadier J, Sawyer SL, Mosca SJ, Innes AM, Parboosingh JS, Bulman DE, Schwartzentruber J, Majewski J, Tarnopolsky M, Boycott KM. Whole-exome sequencing broadens the phenotypic spectrum of rare pediatric epilepsy: a retrospective study. Clin Genet 2014; 88:34-40. [PMID: 25046240 DOI: 10.1111/cge.12464] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/15/2014] [Accepted: 07/15/2014] [Indexed: 01/12/2023]
Abstract
Whole-exome sequencing (WES) has transformed our ability to detect mutations causing rare diseases. FORGE (Finding Of Rare disease GEnes) and Care4Rare Canada are nation-wide projects focused on identifying disease genes using WES and translating this technology to patient care. Rare forms of epilepsy are well-suited for WES and we retrospectively selected FORGE and Care4Rare families with clinical descriptions that included childhood-onset epilepsy or seizures not part of a recognizable syndrome or an early-onset encephalopathy where standard-of-care investigations were unrevealing. Nine families met these criteria and a diagnosis was made in seven, and potentially eight, of the families. In the eight families we identified mutations in genes associated with known neurological and epilepsy disorders: ASAH1, FOLR1, GRIN2A (two families), SCN8A, SYNGAP1 and SYNJ1. A novel and rare mutation was identified in KCNQ2 and was likely responsible for the benign seizures segregating in the family though additional evidence would be required to be definitive. In retrospect, the clinical presentation of four of the patients was considered atypical, thereby broadening the phenotypic spectrum of these conditions. Given the extensive clinical and genetic heterogeneity associated with epilepsy, our findings suggest that WES may be considered when a specific gene is not immediately suspected as causal.
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Affiliation(s)
- D A Dyment
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - M Tétreault
- McGill University and Genome Quebec Innovation Centre, Montréal, Quebec, Canada.,Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - C L Beaulieu
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - T Hartley
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - J W Chardon
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - J Marcadier
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - S L Sawyer
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - A M Innes
- Department of Medical Genetics.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - J S Parboosingh
- Department of Medical Genetics.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - D E Bulman
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - J Schwartzentruber
- McGill University and Genome Quebec Innovation Centre, Montréal, Quebec, Canada
| | - J Majewski
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - M Tarnopolsky
- Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - K M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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188
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Paz-Filho G, Boguszewski MCS, Mastronardi CA, Patel HR, Johar AS, Chuah A, Huttley GA, Boguszewski CL, Wong ML, Arcos-Burgos M, Licinio J. Whole exome sequencing of extreme morbid obesity patients: translational implications for obesity and related disorders. Genes (Basel) 2014; 5:709-25. [PMID: 25158045 PMCID: PMC4198926 DOI: 10.3390/genes5030709] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/23/2014] [Accepted: 08/14/2014] [Indexed: 12/11/2022] Open
Abstract
Whole-exome sequencing (WES) is a new tool that allows the rapid, inexpensive and accurate exploration of Mendelian and complex diseases, such as obesity. To identify sequence variants associated with obesity, we performed WES of family trios of one male teenager and one female child with severe early-onset obesity. Additionally, the teenager patient had hypopituitarism and hyperprolactinaemia. A comprehensive bioinformatics analysis found de novo and compound heterozygote sequence variants with a damaging effect on genes previously associated with obesity in mice (LRP2) and humans (UCP2), among other intriguing mutations affecting ciliary function (DNAAF1). A gene ontology and pathway analysis of genes harbouring mutations resulted in the significant identification of overrepresented pathways related to ATP/ITP (adenosine/inosine triphosphate) metabolism and, in general, to the regulation of lipid metabolism. We discuss the clinical and physiological consequences of these mutations and the importance of these findings for either the clinical assessment or eventual treatment of morbid obesity.
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Affiliation(s)
- Gilberto Paz-Filho
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Margaret C S Boguszewski
- Endocrine Division (SEMPR), Department of Internal Medicine, Federal University of Parana, Avenida Agostinho Leão Junior, 285-Alto da Glória. CEP 80030-110, Curitiba-PR, Brazil.
| | - Claudio A Mastronardi
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Hardip R Patel
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Angad S Johar
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Aaron Chuah
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Gavin A Huttley
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Cesar L Boguszewski
- Endocrine Division (SEMPR), Department of Internal Medicine, Federal University of Parana, Avenida Agostinho Leão Junior, 285-Alto da Glória. CEP 80030-110, Curitiba-PR, Brazil.
| | - Ma-Li Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, and Department of Psychiatry, School of Medicine, Flinders University, PO Box 11060 Adelaide SA 5001, Adelaide, Australia.
| | - Mauricio Arcos-Burgos
- Genome Biology Department, The John Curtin School of Medical Research, The Australian National University, Garran Rd, building 131, Acton, Canberra, ACT 0200, Australia.
| | - Julio Licinio
- Mind and Brain Theme, South Australian Health and Medical Research Institute, and Department of Psychiatry, School of Medicine, Flinders University, PO Box 11060 Adelaide SA 5001, Adelaide, Australia.
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