851
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Jobling R, Stavropoulos DJ, Marshall CR, Cytrynbaum C, Axford MM, Londero V, Moalem S, Orr J, Rossignol F, Lopes FD, Gauthier J, Alos N, Rupps R, McKinnon M, Adam S, Nowaczyk MJM, Walker S, Scherer SW, Nassif C, Hamdan FF, Deal CL, Soucy JF, Weksberg R, Macleod P, Michaud JL, Chitayat D. Chitayat-Hall and Schaaf-Yang syndromes:a common aetiology: expanding the phenotype of MAGEL2-related disorders. J Med Genet 2018; 55:316-321. [DOI: 10.1136/jmedgenet-2017-105222] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 03/02/2018] [Accepted: 03/11/2018] [Indexed: 12/21/2022]
Abstract
BackgroundChitayat-Hall syndrome, initially described in 1990, is a rare condition characterised by distal arthrogryposis, intellectual disability, dysmorphic features and hypopituitarism, in particular growth hormone deficiency. The genetic aetiology has not been identified.Methods and resultsWe identified three unrelated families with a total of six affected patients with the clinical manifestations of Chitayat-Hall syndrome. Through whole exome or whole genome sequencing, pathogenic variants in the MAGEL2 gene were identified in all affected patients. All disease-causing sequence variants detected are predicted to result in a truncated protein, including one complex variant that comprised a deletion and inversion.ConclusionsChitayat-Hall syndrome is caused by pathogenic variants in MAGEL2 and shares a common aetiology with the recently described Schaaf-Yang syndrome. The phenotype of MAGEL2-related disorders is expanded to include growth hormone deficiency as an important and treatable complication.
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852
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Rapid prenatal diagnosis using targeted exome sequencing: a cohort study to assess feasibility and potential impact on prenatal counseling and pregnancy management. Genet Med 2018; 20:1430-1437. [DOI: 10.1038/gim.2018.30] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/16/2018] [Indexed: 02/07/2023] Open
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853
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Zhou Q, Hui X, Ying W, Hou J, Wang W, Liu D, Wang Y, Yu Y, Wang J, Sun J, Zhang Q, Wang X. A Cohort of 169 Chronic Granulomatous Disease Patients Exposed to BCG Vaccination: a Retrospective Study from a Single Center in Shanghai, China (2004-2017). J Clin Immunol 2018; 38:260-272. [PMID: 29560547 DOI: 10.1007/s10875-018-0486-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/09/2018] [Indexed: 12/20/2022]
Abstract
PURPOSE Clinical diagnosis and treatment for chronic granulomatous disease (CGD) have advanced greatly in recent years. However, CGD patients in China have unique clinical features and infection spectrums, which are challenging to their caretakers. Here, we summarized the clinical characteristics, genetic features, treatment, and prognosis of CGD in a single center in Shanghai. METHODS One hundred sixty-nine CGD patients were recruited between January 2004 and May 2017 based on clinical diagnosis. Electronic medical charts were reviewed to collect clinical data. RESULTS Among the 169 patients recruited, CYBB mutations were identified in 150 cases, whereas CYBA mutations were identified in 7 cases, NCF1 in 5, and NCF2 in 7. The medium age at onset was 1 month (interquartile range 1-3). The medium age at diagnosis was 8 months (interquartile range 3-19). The most common infection sites were the lung (95.9%), lymph node (58.5%), skin (45.4%), intestinal (43.1%), and perianal (38.5%). Bacillus Calmette-Guérin (BCG) infections were common (59.2%). In addition, other non-infectious complications were also common, including anemia (55.4%) and impaired liver functions (34.6%). Thirty-one patients received stem cell transplantation. By the end of this study, 83/131 patients survived. CONCLUSIONS Similar to other non-consanguineous populations, X-linked CGD accounted for the majority of the cases in China. However, BCG infections were a clinical challenge unique to China. In addition, severe infections were the major cause of death and the overall mortality was still high in China.
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Affiliation(s)
- Qinhua Zhou
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Xiaoying Hui
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Wenjing Ying
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Jia Hou
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Wenjie Wang
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Danru Liu
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Ying Wang
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yeheng Yu
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Jingyi Wang
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Jinqiao Sun
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Xiaochuan Wang
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
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854
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Bastarache L, Hughey JJ, Hebbring S, Marlo J, Zhao W, Ho WT, Van Driest SL, McGregor TL, Mosley JD, Wells QS, Temple M, Ramirez AH, Carroll R, Osterman T, Edwards T, Ruderfer D, Velez Edwards DR, Hamid R, Cogan J, Glazer A, Wei WQ, Feng Q, Brilliant M, Zhao ZJ, Cox NJ, Roden DM, Denny JC. Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. Science 2018; 359:1233-1239. [PMID: 29590070 PMCID: PMC5959723 DOI: 10.1126/science.aal4043] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 08/25/2017] [Accepted: 01/22/2018] [Indexed: 12/11/2022]
Abstract
Genetic association studies often examine features independently, potentially missing subpopulations with multiple phenotypes that share a single cause. We describe an approach that aggregates phenotypes on the basis of patterns described by Mendelian diseases. We mapped the clinical features of 1204 Mendelian diseases into phenotypes captured from the electronic health record (EHR) and summarized this evidence as phenotype risk scores (PheRSs). In an initial validation, PheRS distinguished cases and controls of five Mendelian diseases. Applying PheRS to 21,701 genotyped individuals uncovered 18 associations between rare variants and phenotypes consistent with Mendelian diseases. In 16 patients, the rare genetic variants were associated with severe outcomes such as organ transplants. PheRS can augment rare-variant interpretation and may identify subsets of patients with distinct genetic causes for common diseases.
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Affiliation(s)
- Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jacob J Hughey
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Joy Marlo
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wanke Zhao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Wanting T Ho
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Sara L Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tracy L McGregor
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan D Mosley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Quinn S Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael Temple
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrea H Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robert Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Travis Osterman
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Todd Edwards
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Douglas Ruderfer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Digna R Velez Edwards
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew Glazer
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - QiPing Feng
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Murray Brilliant
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Zhizhuang J Zhao
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Nancy J Cox
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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855
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Potuijt JWP, Baas M, Sukenik-Halevy R, Douben H, Nguyen P, Venter DJ, Gallagher R, Swagemakers SM, Hovius SER, van Nieuwenhoven CA, Galjaard RJH, van der Spek PJ, Ahituv N, de Klein A. A point mutation in the pre-ZRS disrupts sonic hedgehog expression in the limb bud and results in triphalangeal thumb-polysyndactyly syndrome. Genet Med 2018. [PMID: 29543231 DOI: 10.1038/gim.2018.18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE The zone of polarizing activity regulatory sequence (ZRS) is an enhancer that regulates sonic hedgehog during embryonic limb development. Recently, mutations in a noncoding evolutionary conserved sequence 500 bp upstream of the ZRS, termed the pre-ZRS (pZRS), have been associated with polydactyly in dogs and humans. Here, we report the first case of triphalangeal thumb-polysyndactyly syndrome (TPT-PS) to be associated with mutations in this region and show via mouse enhancer assays how this mutation leads to ectopic expression throughout the developing limb bud. METHODS We used linkage analysis, whole-exome sequencing, Sanger sequencing, fluorescence in situ hybridization, multiplex ligation-dependent probe amplification, single-nucleotide polymorphism array, and a mouse transgenic enhancer assay. RESULTS Ten members of a TPT-PS family were included in this study. The mutation was linked to chromosome 7q36 (LOD score 3.0). No aberrations in the ZRS could be identified. A point mutation in the pZRS (chr7:156585476G>C; GRCh37/hg19) was detected in all affected family members. Functional characterization using a mouse transgenic enhancer essay showed extended ectopic expression dispersed throughout the entire limb bud (E11.5). CONCLUSION Our work describes the first mutation in the pZRS to be associated with TPT-PS and provides functional evidence that this mutation leads to ectopic expression of this enhancer within the developing limb.
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Affiliation(s)
- Jacob W P Potuijt
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Martijn Baas
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rivka Sukenik-Halevy
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California-San Francisco, San Francisco, California, USA.,Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Picard Nguyen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Deon J Venter
- Department of Pathology, Mater Health Services, South Brisbane, Queensland, Australia.,Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, Sydney, Australia.,School of Medicine, University of Wollongong, Wollongong, New South Wales, Australia
| | - Renée Gallagher
- Department of Pathology, Mater Health Services, South Brisbane, Queensland, Australia
| | - Sigrid M Swagemakers
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Steven E R Hovius
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christianne A van Nieuwenhoven
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter J van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, California, USA.,Institute for Human Genetics, University of California-San Francisco, San Francisco, California, USA
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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856
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Ancien F, Pucci F, Godfroid M, Rooman M. Prediction and interpretation of deleterious coding variants in terms of protein structural stability. Sci Rep 2018. [PMID: 29540703 PMCID: PMC5852127 DOI: 10.1038/s41598-018-22531-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The classification of human genetic variants into deleterious and neutral is a challenging issue, whose complexity is rooted in the large variety of biophysical mechanisms that can be responsible for disease conditions. For non-synonymous mutations in structured proteins, one of these is the protein stability change, which can lead to loss of protein structure or function. We developed a stability-driven knowledge-based classifier that uses protein structure, artificial neural networks and solvent accessibility-dependent combinations of statistical potentials to predict whether destabilizing or stabilizing mutations are disease-causing. Our predictor yields a balanced accuracy of 71% in cross validation. As expected, it has a very high positive predictive value of 89%: it predicts with high accuracy the subset of mutations that are deleterious because of stability issues, but is by construction unable of classifying variants that are deleterious for other reasons. Its combination with an evolutionary-based predictor increases the balanced accuracy up to 75%, and allowed predicting more than 1/4 of the variants with 95% positive predictive value. Our method, called SNPMuSiC, can be used with both experimental and modeled structures and compares favorably with other prediction tools on several independent test sets. It constitutes a step towards interpreting variant effects at the molecular scale. SNPMuSiC is freely available at https://soft.dezyme.com/.
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Affiliation(s)
- François Ancien
- Department of BioModeling, BioInformatics & BioProcesses, Université Libre de Bruxelles (ULB), CP 165/61, Roosevelt Avenue 50, 1050, Brussels, Belgium. .,Interuniversity Institute of Bioinformatics in Brussels, ULB, CP 263, Triumph Bld, 1050, Brussels, Belgium.
| | - Fabrizio Pucci
- Department of BioModeling, BioInformatics & BioProcesses, Université Libre de Bruxelles (ULB), CP 165/61, Roosevelt Avenue 50, 1050, Brussels, Belgium. .,Interuniversity Institute of Bioinformatics in Brussels, ULB, CP 263, Triumph Bld, 1050, Brussels, Belgium.
| | - Maxime Godfroid
- Department of BioModeling, BioInformatics & BioProcesses, Université Libre de Bruxelles (ULB), CP 165/61, Roosevelt Avenue 50, 1050, Brussels, Belgium.,Institute of General Microbiology, Kiel University, Am Botanischen Garten 11, 24118, Kiel, Germany
| | - Marianne Rooman
- Department of BioModeling, BioInformatics & BioProcesses, Université Libre de Bruxelles (ULB), CP 165/61, Roosevelt Avenue 50, 1050, Brussels, Belgium. .,Interuniversity Institute of Bioinformatics in Brussels, ULB, CP 263, Triumph Bld, 1050, Brussels, Belgium.
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857
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Biesecker BB, Lewis KL, Umstead KL, Johnston JJ, Turbitt E, Fishler KP, Patton JH, Miller IM, Heidlebaugh AR, Biesecker LG. Web Platform vs In-Person Genetic Counselor for Return of Carrier Results From Exome Sequencing: A Randomized Clinical Trial. JAMA Intern Med 2018; 178:338-346. [PMID: 29356820 PMCID: PMC5885925 DOI: 10.1001/jamainternmed.2017.8049] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
IMPORTANCE A critical bottleneck in clinical genomics is the mismatch between large volumes of results and the availability of knowledgeable professionals to return them. OBJECTIVE To test whether a web-based platform is noninferior to a genetic counselor for educating patients about their carrier results from exome sequencing. DESIGN, SETTING, AND PARTICIPANTS A randomized noninferiority trial conducted in a longitudinal sequencing cohort at the National Institutes of Health from February 5, 2014, to December 16, 2016, was used to compare the web-based platform with a genetic counselor. Among the 571 eligible participants, 1 to 7 heterozygous variants were identified in genes that cause a phenotype that is recessively inherited. Surveys were administered after cohort enrollment, immediately following trial education, and 1 month and 6 months later to primarily healthy postreproductive participants who expressed interest in learning their carrier results. Both intention-to-treat and per-protocol analyses were applied. INTERVENTIONS A web-based platform that integrated education on carrier results with personal test results was designed to directly parallel disclosure education by a genetic counselor. The sessions took a mean (SD) time of 21 (10.6), and 27 (9.3) minutes, respectively. MAIN OUTCOMES AND MEASURES The primary outcomes and noninferiority margins (δNI) were knowledge (0 to 8, δNI = -1), test-specific distress (0 to 30, δNI = +1), and decisional conflict (15 to 75, δNI = +6). RESULTS After 462 participants (80.9%) provided consent and were randomized, all but 3 participants (n = 459) completed surveys following education and counseling; 398 (86.1%) completed 1-month surveys and 392 (84.8%) completed 6-month surveys. Participants were predominantly well-educated, non-Hispanic white, married parents; mean (SD) age was 63 (63.1) years and 246 (53.6%) were men. The web platform was noninferior to the genetic counselor on outcomes assessed at 1 and 6 months: knowledge (mean group difference, -0.18; lower limit of 97.5% CI, -0.63; δNI = -1), test-specific distress (median group difference, 0; upper limit of 97.5% CI, 0; δNI = +1), and decisional conflict about choosing to learn results (mean group difference, 1.18; upper limit of 97.5% CI, 2.66; δNI = +6). There were no significant differences between the genetic counselors and web-based platform detected between modes of education delivery in disclosure rates to spouses (151 vs 159; relative risk [RR], 1.04; 95% CI, 0.64-1.69; P > .99), children (103 vs 117; RR, 1.07; 95% CI, 0.85-1.36; P = .59), or siblings (91 vs 78; RR, 1.17; 95% CI, 0.94-1.46; P = .18). CONCLUSIONS AND RELEVANCE This trial demonstrates noninferiority of web-based return of carrier results among postreproductive, mostly healthy adults. Replication studies among younger and more diverse populations are needed to establish generalizability. Yet return of results via a web-based platform may be sufficient for subsets of test results, reserving genetic counselors for return of results with a greater health threat. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00410241.
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Affiliation(s)
- Barbara B Biesecker
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Katie L Lewis
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Kendall L Umstead
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Jennifer J Johnston
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Erin Turbitt
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Kristen P Fishler
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - John H Patton
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ilana M Miller
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Alexis R Heidlebaugh
- Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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858
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Liu T, Ish‐Shalom S, Torng W, Lafita A, Bock C, Mort M, Cooper DN, Bliven S, Capitani G, Mooney SD, Altman RB. Biological and functional relevance of CASP predictions. Proteins 2018; 86 Suppl 1:374-386. [PMID: 28975675 PMCID: PMC5820171 DOI: 10.1002/prot.25396] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/12/2017] [Accepted: 10/03/2017] [Indexed: 02/06/2023]
Abstract
Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo-sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo-sites), and Ten sites containing important motifs, loops, or key residues with important disease-associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best-ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand-binding sites, most prediction methods have higher performance on apo-sites than holo-sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein-protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein-protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template.
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Affiliation(s)
- Tianyun Liu
- Department of BioengineeringStanford UniversityStanfordCalifornia
| | - Shirbi Ish‐Shalom
- Biomedical Informatics Training Program, Stanford UniversityStanfordCalifornia
| | - Wen Torng
- Department of BioengineeringStanford UniversityStanfordCalifornia
| | - Aleix Lafita
- Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
- Department of Biosystems Science and EngineeringETH Zurich4058BaselSwitzerland
| | - Christian Bock
- Department of Biomedical Informatics and Medical EducationUniversity of WashingtonSeattleWashington
- Heidelberg UniversityHeidelbergGermany
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff UniversityUnited Kingdom
| | - David N Cooper
- Institute of Medical Genetics, Cardiff UniversityUnited Kingdom
| | - Spencer Bliven
- Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
- National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaMaryland
| | - Guido Capitani
- Laboratory of Biomolecular ResearchPaul Scherrer InstituteVilligenSwitzerland
- Department of BiologyETH ZurichZurichSwitzerland
| | - Sean D. Mooney
- Department of Biomedical Informatics and Medical EducationUniversity of WashingtonSeattleWashington
| | - Russ B. Altman
- Department of BioengineeringStanford UniversityStanfordCalifornia
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859
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Periodic reanalysis of whole-genome sequencing data enhances the diagnostic advantage over standard clinical genetic testing. Eur J Hum Genet 2018; 26:740-744. [PMID: 29453418 DOI: 10.1038/s41431-018-0114-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/11/2017] [Accepted: 01/23/2018] [Indexed: 12/20/2022] Open
Abstract
Whole-genome sequencing (WGS) as a first-tier diagnostic test could transform medical genetic assessments, but there are limited data regarding its clinical use. We previously showed that WGS could feasibly be deployed as a single molecular test capable of a higher diagnostic rate than current practices, in a prospectively recruited cohort of 100 children meeting criteria for chromosomal microarray analysis. In this study, we report on the added diagnostic yield with re-annotation and reanalysis of these WGS data ~2 years later. Explanatory variants have been discovered in seven (10.9%) of 64 previously undiagnosed cases, in emerging disease genes like HMGA2. No new genetic diagnoses were made by any other method in the interval period as part of ongoing clinical care. The results increase the cumulative diagnostic yield of WGS in the study cohort to 41%. This represents a greater than 5-fold increase over the chromosomal microarrays, and a greater than 3-fold increase over all the clinical genetic testing ordered in practice. These findings highlight periodic reanalysis as yet another advantage of genomic sequencing in heterogeneous disorders. We recommend reanalysis of an individual's genome-wide sequencing data every 1-2 years until diagnosis, or sooner if their phenotype evolves.
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860
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Maron MS, Xin W, Sims KB, Butler R, Haas TS, Rowin EJ, Desnick RJ, Maron BJ. Identification of Fabry Disease in a Tertiary Referral Cohort of Patients with Hypertrophic Cardiomyopathy. Am J Med 2018; 131:200.e1-200.e8. [PMID: 28943383 DOI: 10.1016/j.amjmed.2017.09.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/01/2017] [Accepted: 09/01/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Fabry disease is an X-linked lysosomal storage disorder caused by the deficient activity of α-galactosidase A due to mutations in the GLA gene, which may be associated with increased left ventricular wall thickness and mimic the morphologic features of hypertrophic cardiomyopathy. Management strategies for these 2 diseases diverge, with Fabry disease-specific treatment utilizing recombinant α-galactosidase A enzyme replacement therapy. METHODS We studied a prospectively assembled consecutive cohort of 585 patients (71% male) from 2 hypertrophic cardiomyopathy tertiary referral centers by screening for low α-galactosidase A activity in dried blood spots. Male patients with low α-galactosidase A activity levels and all females were tested for mutations in the GLA gene. RESULTS In 585 patients previously diagnosed with hypertrophic cardiomyopathy, we identified 2 unrelated patients (0.34%), both with the GLA mutation encoding P.N215S, the most common mutation causing later-onset Fabry disease phenotype. These patients were both asymptomatic, a man aged 53 years and a woman aged 69 years, and demonstrated a mild cardiac phenotype with symmetric distribution of left ventricular hypertrophy. After family screening, a total of 27 new Fabry disease patients aged 2-81 years were identified in the 2 families, including 12 individuals who are now receiving enzyme replacement therapy. CONCLUSIONS These observations support consideration for routine prospective screening for Fabry disease in all patients without a definitive etiology for left ventriclar hypertrophy. This strategy would likely result, through cascade family testing, in the earlier identification of new Fabry disease-affected males and female heterozygotes who may benefit from monitoring and/or enzyme replacement therapy.
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Affiliation(s)
- Martin S Maron
- Hypertrophic Cardiomyopathy Institute, Division of Cardiology, Tufts Medical Center, Boston, Mass.
| | - Winnie Xin
- Neurogenetics DNA Diagnostic Laboratory and Center for Human Genetic Research and Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Katherine B Sims
- Neurogenetics DNA Diagnostic Laboratory and Center for Human Genetic Research and Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Rita Butler
- Hypertrophic Cardiomyopathy Institute, Division of Cardiology, Tufts Medical Center, Boston, Mass
| | - Tammy S Haas
- Hypertrophic Cardiomyopathy Center, Minneapolis Heart Institute Foundation, Minn
| | - Ethan J Rowin
- Hypertrophic Cardiomyopathy Institute, Division of Cardiology, Tufts Medical Center, Boston, Mass
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY
| | - Barry J Maron
- Hypertrophic Cardiomyopathy Institute, Division of Cardiology, Tufts Medical Center, Boston, Mass
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861
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Pasipoularides A. Implementing genome-driven personalized cardiology in clinical practice. J Mol Cell Cardiol 2018; 115:142-157. [PMID: 29343412 PMCID: PMC5820118 DOI: 10.1016/j.yjmcc.2018.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/04/2018] [Accepted: 01/12/2018] [Indexed: 12/18/2022]
Abstract
Genomics designates the coordinated investigation of a large number of genes in the context of a biological process or disease. It may be long before we attain comprehensive understanding of the genomics of common complex cardiovascular diseases (CVDs) such as inherited cardiomyopathies, valvular diseases, primary arrhythmogenic conditions, congenital heart syndromes, hypercholesterolemia and atherosclerotic heart disease, hypertensive syndromes, and heart failure with preserved/reduced ejection fraction. Nonetheless, as genomics is evolving rapidly, it is constructive to survey now pertinent concepts and breakthroughs. Today, clinical multimodal electronic medical/health records (EMRs/EHRs) incorporating genomic information establish a continuously-learning, vast knowledge-network with seamless cycling between clinical application and research. It can inform insights into specific pathogenetic pathways, guide biomarker-assisted precise diagnoses and individualized treatments, and stratify prognoses. Complex CVDs blend multiple interacting genomic variants, epigenetics, and environmental risk-factors, engendering progressions of multifaceted disease-manifestations, including clinical symptoms and signs. There is no straight-line linkage between genetic cause(s) or causal gene-variant(s) and disease phenotype(s). Because of interactions involving modifier-gene influences, (micro)-environmental, and epigenetic effects, the same variant may actually produce dissimilar abnormalities in different individuals. Implementing genome-driven personalized cardiology in clinical practice reveals that the study of CVDs at the level of molecules and cells can yield crucial clinical benefits. Complementing evidence-based medicine guidelines from large ("one-size fits all") randomized controlled trials, genomics-based personalized or precision cardiology is a most-creditable paradigm: It provides customizable approaches to prevent, diagnose, and manage CVDs with treatments directly/precisely aimed at causal defects identified by high-throughput genomic technologies. They encompass stem cell and gene therapies exploiting CRISPR-Cas9-gene-editing, and metabolomic-pharmacogenomic therapeutic modalities, precisely fine-tuned for the individual patient. Following the Human Genome Project, many expected genomics technology to provide imminent solutions to intractable medical problems, including CVDs. This eagerness has reaped some disappointment that advances have not yet materialized to the degree anticipated. Undoubtedly, personalized genetic/genomics testing is an emergent technology that should not be applied without supplementary phenotypic/clinical information: Genotype≠Phenotype. However, forthcoming advances in genomics will naturally build on prior attainments and, combined with insights into relevant epigenetics and environmental factors, can plausibly eradicate intractable CVDs, improving human health and well-being.
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Affiliation(s)
- Ares Pasipoularides
- Consulting Professor of Surgery, Emeritus Faculty of Surgery and of Biomedical Engineering, Duke University School of Medicine and Graduate School, Durham, NC 27710, USA.
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862
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Villate O, Ibarluzea N, Fraile-Bethencourt E, Valenzuela A, Velasco EA, Grozeva D, Raymond FL, Botella MP, Tejada MI. Functional Analyses of a Novel Splice Variant in the CHD7 Gene, Found by Next Generation Sequencing, Confirm Its Pathogenicity in a Spanish Patient and Diagnose Him with CHARGE Syndrome. Front Genet 2018; 9:7. [PMID: 29434620 PMCID: PMC5790995 DOI: 10.3389/fgene.2018.00007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/08/2018] [Indexed: 01/30/2023] Open
Abstract
Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosis. A splice donor variant in CHD7 (c.5665 + 1G > T) was identified. To study its potential pathogenicity, exons and flanking intronic sequences were amplified from patient DNA and cloned into the pSAD® splicing vector. HeLa cells were transfected with this construct and a wild-type minigene and functional analysis were performed. The construct with the c.5665 + 1G > T variant produced an aberrant transcript with an insert of 63 nucleotides of intron 28 creating a premature termination codon (TAG) 25 nucleotides downstream. This would lead to the insertion of 8 new amino acids and therefore a truncated 1896 amino acid protein. As a result of this, the patient was diagnosed with CHARGE syndrome. Functional analyses underline their usefulness for studying the pathogenicity of variants found by NGS and therefore its application to accurately diagnose patients.
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Affiliation(s)
- Olatz Villate
- Biocruces Health Research Institute, Barakaldo, Spain.,Molecular Genetics Laboratory, Genetics Service, Cruces University Hospital, Barakaldo, Spain
| | | | - Eugenia Fraile-Bethencourt
- Splicing and Cancer Laboratory, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Alberto Valenzuela
- Splicing and Cancer Laboratory, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Eladio A Velasco
- Splicing and Cancer Laboratory, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Detelina Grozeva
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - F L Raymond
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - María P Botella
- Department of Pediatrics, Araba University Hospital, Vitoria, Spain
| | - María-Isabel Tejada
- Biocruces Health Research Institute, Barakaldo, Spain.,Molecular Genetics Laboratory, Genetics Service, Cruces University Hospital, Barakaldo, Spain.,Clinical Group, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
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863
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Cao B, Zeng Y, Wu F, Liu J, Shuang Z, Xu X, Guo J. Novel TRERF1 mutations in Chinese patients with ovarian endometriosis. Mol Med Rep 2018; 17:5435-5439. [PMID: 29393434 DOI: 10.3892/mmr.2018.8510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/20/2017] [Indexed: 11/06/2022] Open
Abstract
Endometriosis is an estrogen-dependent precancerous lesion exhibiting frequently perturbed level of steroid hormones and transcriptional‑regulating factor 1 (TRERF1) has a crucial role in the production of steroid hormones including estrogen. Endometriosis has previously been revealed to be a precancerous lesion that harbors somatic mutations in cancer‑associated genes. Therefore, the authors of the present study hypothesize that TRERF1 aberrations may be involved in the development of endometriosis. In the present study, endometriotic lesions and paired blood samples from 92 individuals with ovarian endometriosis were analyzed for the potential presence of TRERF1 mutations by sequencing the entire coding region and the corresponding intron‑exon boundaries of the TRERF1 gene. Two heterozygous missense somatic mutations [c.3166A>C (p.K1056Q) and c.3187 G>A (p.G1063R)] in the TRERF1 gene were identified in two out of 92 ectopic endometria (2.2%), to the best of our knowledge, these mutations have not been previously reported. From the two samples with TRERF1 mutations, one sample was from a 42‑year‑old patient also diagnosed with uterine leiomyoma and the other mutation was identified in a 36‑year‑old woman exhibiting no other apparent gynecological conditions. The evolutionary conservation analysis and in silico prediction of these TRERF1 mutations suggested that they may be pathogenic. To the best of our knowledge, the present study was the first to identify 2 novel, potentially 'disease‑causing' TRERF1 somatic mutations in the endometriotic lesions in 2 out of 92 patients with ovarian endometriosis; therefore, TRERF1 mutations may be involved in the pathogenesis of ovarian endometriosis.
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Affiliation(s)
- Bianna Cao
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Yuanfeng Zeng
- Department of Pathology, Jiangxi Provincial People's Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Fei Wu
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Jun Liu
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Zeliang Shuang
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Xiaoyun Xu
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Jiubai Guo
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
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864
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Lata S, Marasa M, Li Y, Fasel DA, Groopman E, Jobanputra V, Rasouly H, Mitrotti A, Westland R, Verbitsky M, Nestor J, Slater LM, D'Agati V, Zaniew M, Materna-Kiryluk A, Lugani F, Caridi G, Rampoldi L, Mattoo A, Newton CA, Rao MK, Radhakrishnan J, Ahn W, Canetta PA, Bomback AS, Appel GB, Antignac C, Markowitz GS, Garcia CK, Kiryluk K, Sanna-Cherchi S, Gharavi AG. Whole-Exome Sequencing in Adults With Chronic Kidney Disease: A Pilot Study. Ann Intern Med 2018; 168:100-109. [PMID: 29204651 PMCID: PMC5947852 DOI: 10.7326/m17-1319] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The utility of whole-exome sequencing (WES) for the diagnosis and management of adult-onset constitutional disorders has not been adequately studied. Genetic diagnostics may be advantageous in adults with chronic kidney disease (CKD), in whom the cause of kidney failure often remains unknown. OBJECTIVE To study the diagnostic utility of WES in a selected referral population of adults with CKD. DESIGN Observational cohort. SETTING A major academic medical center. PATIENTS 92 adults with CKD of unknown cause or familial nephropathy or hypertension. MEASUREMENTS The diagnostic yield of WES and its potential effect on clinical management. RESULTS Whole-exome sequencing provided a diagnosis in 22 of 92 patients (24%), including 9 probands with CKD of unknown cause and encompassing 13 distinct genetic disorders. Among these, loss-of-function mutations were identified in PARN in 2 probands with tubulointerstitial fibrosis. PARN mutations have been implicated in a short telomere syndrome characterized by lung, bone marrow, and liver fibrosis; these findings extend the phenotype of PARN mutations to renal fibrosis. In addition, review of the American College of Medical Genetics actionable genes identified a pathogenic BRCA2 mutation in a proband who was diagnosed with breast cancer on follow-up. The results affected clinical management in most identified cases, including initiation of targeted surveillance, familial screening to guide donor selection for transplantation, and changes in therapy. LIMITATION The small sample size and recruitment at a tertiary care academic center limit generalizability of findings among the broader CKD population. CONCLUSION Whole-exome sequencing identified diagnostic mutations in a substantial number of adults with CKD of many causes. Further study of the utility of WES in the evaluation and care of patients with CKD in additional settings is warranted. PRIMARY FUNDING SOURCE New York State Empire Clinical Research Investigator Program, Renal Research Institute, and National Human Genome Research Institute of the National Institutes of Health.
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Affiliation(s)
- Sneh Lata
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Maddalena Marasa
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Yifu Li
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - David A Fasel
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Emily Groopman
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Vaidehi Jobanputra
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Hila Rasouly
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Adele Mitrotti
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Rik Westland
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Miguel Verbitsky
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Jordan Nestor
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Lindsey M Slater
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Vivette D'Agati
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Marcin Zaniew
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Anna Materna-Kiryluk
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Francesca Lugani
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Gianluca Caridi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Luca Rampoldi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Aditya Mattoo
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Chad A Newton
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Maya K Rao
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Jai Radhakrishnan
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Wooin Ahn
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Pietro A Canetta
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Andrew S Bomback
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Gerald B Appel
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Corinne Antignac
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Glen S Markowitz
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Christine K Garcia
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Krzysztof Kiryluk
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Simone Sanna-Cherchi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
| | - Ali G Gharavi
- From Columbia University, New York, New York; VU University Medical Center, Amsterdam, the Netherlands; Nephrology Associates, Newark, Delaware; Krysiewicza Children's Hospital, Poznań, Poland; Poznań University of Medical Sciences and Center for Medical Genetics GENESIS, Poznań, Poland; IRCCS Giannina Gaslini Children's Hospital, Genova, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy; New York University School of Medicine, New York, New York; University of Texas Southwestern Medical Center, Dallas, Texas; and French Institute of Health and Medical Research (INSERM) U1163, Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, and Necker Hospital, Paris, France
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865
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Doheny D, Srinivasan R, Pagant S, Chen B, Yasuda M, Desnick RJ. Fabry Disease: prevalence of affected males and heterozygotes with pathogenic GLA mutations identified by screening renal, cardiac and stroke clinics, 1995-2017. J Med Genet 2018; 55:261-268. [PMID: 29330335 DOI: 10.1136/jmedgenet-2017-105080] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/29/2017] [Accepted: 12/11/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Fabry Disease (FD), an X linked lysosomal storage disease due to pathogenic α-galactosidase A (GLA) mutations, results in two major subtypes, the early-onset Type 1 'Classic' and the Type 2 'Later-Onset' phenotypes. To identify previously unrecognised patients, investigators screened cardiac, renal and stroke clinics by enzyme assays. However, some screening studies did not perform confirmatory GLA mutation analyses, and many included recently recognised 'benign/likely-benign' variants, thereby inflating prevalence estimates. METHODS Online databases were searched for all FD screening studies in high-risk clinics (1995-2017). Studies reporting GLA mutations were re-analysed for pathogenic mutations, sex and phenotype. Phenotype-specific and sex-specific prevalence rates were determined. RESULTS Of 67 studies, 63 that screened 51363patients (33943M and 17420F) and provided GLA mutations were reanalysed for disease-causing mutations. Of reported GLA mutations, benign variants occurred in 47.9% of males and 74.1% of females. The following were the revised prevalence estimates: among 36820 (23954M and 12866F) haemodialysis screenees, 0.21% males and 0.15% females; among 3074 (2031M and 1043F) renal transplant screenees, 0.25% males and no females; among 5491 (4054M and 1437F) cardiac screenees, 0.94% males and 0.90% females; and among 5978 (3904M and 2074F) stroke screenees, 0.13% males and 0.14% females. Among male and female screenees with pathogenic mutations, the type 1 Classic phenotype was predominant (~60%), except more male cardiac patients (75%) had type 2 Later-Onset phenotype. CONCLUSIONS Compared with previous findings, reanalysis of 63 studies increased the screenee numbers (~3.4-fold), eliminated 20 benign/likely benign variants, and provided more accurate sex-specific and phenotype-specific prevalence estimates, ranging from ~0.13% of stroke to ~0.9% of cardiac male or female screenees.
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Affiliation(s)
- Dana Doheny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ram Srinivasan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Silvere Pagant
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Brenden Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Makiko Yasuda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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866
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Ishida K, Xu H, Sasakawa N, Lung MSY, Kudryashev JA, Gee P, Hotta A. Site-specific randomization of the endogenous genome by a regulatable CRISPR-Cas9 piggyBac system in human cells. Sci Rep 2018; 8:310. [PMID: 29321585 PMCID: PMC5762678 DOI: 10.1038/s41598-017-18568-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/14/2017] [Indexed: 12/26/2022] Open
Abstract
Randomized mutagenesis at an endogenous chromosomal locus is a promising approach for protein engineering, functional assessment of regulatory elements, and modeling genetic variations. In mammalian cells, however, it is challenging to perform site-specific single-nucleotide substitution with single-stranded oligodeoxynucleotide (ssODN) donor templates due to insufficient homologous recombination and the infeasibility of positive selection. Here, we developed a DNA transposon based CRISPR-Cas9 regulated transcription and nuclear shuttling (CRONUS) system that enables the stable transduction of CRISPR-Cas9/sgRNA in broad cell types, but avoids undesired genome cleavage in the absence two chemical inducing molecules. Highly efficient single nucleotide alterations induced randomization of desired codons (up to 4 codons) at a defined genomic locus in various human cell lines, including human iPS cells. Thus, CRONUS provides a novel platform for modeling diseases and genetic variations.
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Affiliation(s)
- Kentaro Ishida
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Huaigeng Xu
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Noriko Sasakawa
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Mandy Siu Yu Lung
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | | | - Peter Gee
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
| | - Akitsu Hotta
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
- Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
- Institute for integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan.
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867
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Lin Y, Zheng Z, Sun W, Fu Q. A novel compound heterozygous variant identified in GLDC gene in a Chinese family with non-ketotic hyperglycinemia. BMC MEDICAL GENETICS 2018; 19:5. [PMID: 29304759 PMCID: PMC5755286 DOI: 10.1186/s12881-017-0517-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/22/2017] [Indexed: 12/23/2022]
Abstract
Background Non-ketotic hyperglycinemia (NKH) is a rare, devastating autosomal recessive disorder of glycine metabolism with a very poor prognosis. Currently, few studies have reported genetic profiling of Chinese NKH patients. This study aimed to identify the genetic mutations in a Chinese family with NKH. Methods A Chinese family of Han ethnicity, with three siblings with NKH was studied. Sanger sequencing and multiplex ligation-dependent probe amplification combined with SYBR green real-time quantitative PCR was used to identify potential mutations in the GLDC, AMT and GCSH genes. The potential pathogenicity of the identified missense mutation was analyzed using SIFT, PolyPhen-2, PROVEAN and MutationTaster software. Results All patients exhibited severe and progressive clinical symptoms, including lethargy, hypotonia and seizures, and had greatly elevated glycine levels in their plasma and CSF. Molecular genetic analysis identified compound heterozygous variants in the GLDC gene in these three siblings, including a novel missense variant c.2680A > G (p.Thr894Ala) in exon 23 and a heterozygous deletion of exon 3, which were inherited respectively from their parents. In silico analysis, using several different types of bioinformatic software, predicted that the novel variant c.2680A > G in the GLDC gene was pathogenic. Moreover, the deletion of exon 3 was identified for the first time in a Chinese population. Conclusions A novel missense variant and a previously reported deletion in GLDC gene were identified. The two variants of GLDC gene identified probably underlie the pathogenesis of non-ketotic hyperglycinemia in this family, and also enrich the mutational spectrum of GLDC gene. Electronic supplementary material The online version of this article (10.1186/s12881-017-0517-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Zhenzhu Zheng
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Wenjia Sun
- Genuine Diagnostics Company Limited, 859 Shixiang West Road, Hangzhou, Zhejiang Province, 310007, China.
| | - Qingliu Fu
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China.
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868
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Dingerdissen HM, Torcivia-Rodriguez J, Hu Y, Chang TC, Mazumder R, Kahsay R. BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. Nucleic Acids Res 2018; 46:D1128-D1136. [PMID: 30053270 PMCID: PMC5753215 DOI: 10.1093/nar/gkx907] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/21/2017] [Accepted: 09/26/2017] [Indexed: 12/29/2022] Open
Abstract
Single-nucleotide variation and gene expression of disease samples represent important resources for biomarker discovery. Many databases have been built to host and make available such data to the community, but these databases are frequently limited in scope and/or content. BioMuta, a database of cancer-associated single-nucleotide variations, and BioXpress, a database of cancer-associated differentially expressed genes and microRNAs, differ from other disease-associated variation and expression databases primarily through the aggregation of data across many studies into a single source with a unified representation and annotation of functional attributes. Early versions of these resources were initiated by pilot funding for specific research applications, but newly awarded funds have enabled hardening of these databases to production-level quality and will allow for sustained development of these resources for the next few years. Because both resources were developed using a similar methodology of integration, curation, unification, and annotation, we present BioMuta and BioXpress as allied databases that will facilitate a more comprehensive view of gene associations in cancer. BioMuta and BioXpress are hosted on the High-performance Integrated Virtual Environment (HIVE) server at the George Washington University at https://hive.biochemistry.gwu.edu/biomuta and https://hive.biochemistry.gwu.edu/bioxpress, respectively.
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Affiliation(s)
- Hayley M Dingerdissen
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, USA
| | - John Torcivia-Rodriguez
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, USA
| | - Yu Hu
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, USA
| | - Ting-Chia Chang
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, USA
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, USA
- McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Robel Kahsay
- The Department of Biochemistry & Molecular Medicine, The George Washington University Medical Center, Washington, DC 20037, USA
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869
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Li J, Shi L, Zhang K, Zhang Y, Hu S, Zhao T, Teng H, Li X, Jiang Y, Ji L, Sun Z. VarCards: an integrated genetic and clinical database for coding variants in the human genome. Nucleic Acids Res 2018; 46:D1039-D1048. [PMID: 29112736 PMCID: PMC5753295 DOI: 10.1093/nar/gkx1039] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/24/2022] Open
Abstract
A growing number of genomic tools and databases were developed to facilitate the interpretation of genomic variants, particularly in coding regions. However, these tools are separately available in different online websites or databases, making it challenging for general clinicians, geneticists and biologists to obtain the first-hand information regarding some particular variants and genes of interest. Starting with coding regions and splice sties, we artificially generated all possible single nucleotide variants (n = 110 154 363) and cataloged all reported insertion and deletions (n = 1 223 370). We then annotated these variants with respect to functional consequences from more than 60 genomic data sources to develop a database, named VarCards (http://varcards.biols.ac.cn/), by which users can conveniently search, browse and annotate the variant- and gene-level implications of given variants, including the following information: (i) functional effects; (ii) functional consequences through different in silico algorithms; (iii) allele frequencies in different populations; (iv) disease- and phenotype-related knowledge; (v) general meaningful gene-level information; and (vi) drug-gene interactions. As a case study, we successfully employed VarCards in interpretation of de novo mutations in autism spectrum disorders. In conclusion, VarCards provides an intuitive interface of necessary information for researchers to prioritize candidate variations and genes.
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Affiliation(s)
- Jinchen Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Leisheng Shi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Shanshan Hu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Tingting Zhao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianfeng Li
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Jiang
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Liying Ji
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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870
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Verhoeven W, Egger J, Räkers E, van Erkelens A, Pfundt R, Willemsen MH. Phenotypic characterization of an older adult male with late-onset epilepsy and a novel mutation in ASXL3 shows overlap with the associated Bainbridge-Ropers syndrome. Neuropsychiatr Dis Treat 2018; 14:867-870. [PMID: 29628764 PMCID: PMC5877499 DOI: 10.2147/ndt.s153511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The additional sex combs like 3 gene is considered to be causative for the rare Bainbridge-Ropers syndrome (BRPS), which is characterized by severe intellectual disability, neonatal hypotonia, nearly absent development of speech and language as well as several facial dysmorphisms. Apart from disruptive autistiform behaviors, sleep disturbances and epileptic phenomena may be present. Here, a 47-year-old severely intellectually disabled male is described in whom exome sequencing disclosed a novel heterozygous frameshift mutation in the ASXL3 gene leading to a premature stopcodon in the last part of the last exon. Mutations in this very end 3' of the gene have not been reported before in BRPS. The phenotypical presentation of the patient including partially therapy-resistant epilepsy starting in later adulthood shows overlap with BRPS, and it was therefore concluded that the phenotype is likely explained by the identified mutation in ASXL3.
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Affiliation(s)
- Willem Verhoeven
- Vincent van Gogh Institute for Psychiatry, Centre of Excellence for Neuropsychiatry, Venray, the Netherlands.,Department of Psychiatry, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jos Egger
- Vincent van Gogh Institute for Psychiatry, Centre of Excellence for Neuropsychiatry, Venray, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Emmy Räkers
- ASVZ, Centre for People with Intellectual Disabilities, Sliedrecht, the Netherlands
| | - Arjen van Erkelens
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
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871
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Hunt SE, McLaren W, Gil L, Thormann A, Schuilenburg H, Sheppard D, Parton A, Armean IM, Trevanion SJ, Flicek P, Cunningham F. Ensembl variation resources. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5255129. [PMID: 30576484 PMCID: PMC6310513 DOI: 10.1093/database/bay119] [Citation(s) in RCA: 278] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022]
Abstract
The major goal of sequencing humans and many other species is to understand the link between genomic variation, phenotype and disease. There are numerous valuable and well-established variation resources, but collating and making sense of non-homogeneous, often large-scale data sets from disparate sources remains a challenge. Without a systematic catalogue of these data and appropriate query and annotation tools, understanding the genome sequence of an individual and assessing their disease risk is impossible. In Ensembl, we substantially solve this problem: we develop methods to facilitate data integration and broad access; aggregate information in a consistent manner and make it available a variety of standard formats, both visually and programmatically; build analysis pipelines to compare variants to comprehensive genomic annotation sets; and make all tools and data publicly available.
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Affiliation(s)
- Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dan Sheppard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew Parton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Irina M Armean
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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872
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Campuzano O, Sanchez-Molero O, Fernandez A, Iglesias A, Brugada R. Muerte súbita cardiaca de origen arrítmico: valor del análisis genético post mortem. REVISTA ESPAÑOLA DE MEDICINA LEGAL 2018; 44:32-37. [DOI: 10.1016/j.reml.2017.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
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873
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Sun R, Cui C, Zhou Y, Cui Q. AGD: Aneurysm Gene Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5107030. [PMID: 30256987 PMCID: PMC6157070 DOI: 10.1093/database/bay100] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022]
Abstract
An aneurysm is an outward bulge on an arterial wall. Aneurysms are becoming a serious public health concern as the worldwide population ages. Unfortunately, no effective drugs have been developed for aneurysms to date. In addition, aneurysms may be associated with grave prognosis due to conditions such as ruptures and recurrence. Altogether, these factors make earlier aneurysm prevention, diagnosis and intervention strategies even more important. A bioinformatics resource for aneurysm-associated molecules would be helpful for addressing the above issues; however, such a tool is not yet available. In this study, we developed Aneurysm Gene Database (AGD) for the above purpose. AGD contains 1472 aneurysm-gene associations, including 29 types of aneurysms, 967 protein-coding genes, 29 miRNAs, 6 lncRNAs and several other types of molecules. Users can search, browse and download content in AGD. We believe that AGD is a valuable resource that can help us better understand aneurysms and discover novel treatment targets.
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Affiliation(s)
- Ruya Sun
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Chunmei Cui
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yuan Zhou
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Qinghua Cui
- Department of Biomedical Informatics, Department of Physiology and Pathophysiology, Center for Noncoding RNA Medicine, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University, Beijing, China.,Center of Bioinformatics, Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
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874
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Best S, Wou K, Vora N, Van der Veyver IB, Wapner R, Chitty LS. Promises, pitfalls and practicalities of prenatal whole exome sequencing. Prenat Diagn 2018; 38:10-19. [PMID: 28654730 PMCID: PMC5745303 DOI: 10.1002/pd.5102] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/16/2017] [Accepted: 06/22/2017] [Indexed: 12/17/2022]
Abstract
Prenatal genetic diagnosis provides information for pregnancy and perinatal decision-making and management. In several small series, prenatal whole exome sequencing (WES) approaches have identified genetic diagnoses when conventional tests (karyotype and microarray) were not diagnostic. Here, we review published prenatal WES studies and recent conference abstracts. Thirty-one studies were identified, with diagnostic rates in series of five or more fetuses varying between 6.2% and 80%. Differences in inclusion criteria and trio versus singleton approaches to sequencing largely account for the wide range of diagnostic rates. The data suggest that diagnostic yields will be greater in fetuses with multiple anomalies or in cases preselected following genetic review. Beyond its ability to improve diagnostic rates, we explore the potential of WES to improve understanding of prenatal presentations of genetic disorders and lethal fetal syndromes. We discuss prenatal phenotyping limitations, counselling challenges regarding variants of uncertain significance, incidental and secondary findings, and technical problems in WES. We review the practical, ethical, social and economic issues that must be considered before prenatal WES could become part of routine testing. Finally, we reflect upon the potential future of prenatal genetic diagnosis, including a move towards whole genome sequencing and non-invasive whole exome and whole genome testing. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sunayna Best
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Karen Wou
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Neeta Vora
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ignatia B. Van der Veyver
- Departments of Obstetrics and Gynecology and Molecular and Human Genetics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Division of Reproductive Genetics, Columbia University, New York, NY, USA
| | - Lyn S. Chitty
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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875
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del Castillo FJ, del Castillo I. DFNB1 Non-syndromic Hearing Impairment: Diversity of Mutations and Associated Phenotypes. Front Mol Neurosci 2017; 10:428. [PMID: 29311818 PMCID: PMC5743749 DOI: 10.3389/fnmol.2017.00428] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/07/2017] [Indexed: 02/02/2023] Open
Abstract
The inner ear is a very complex sensory organ whose development and function depend on finely balanced interactions among diverse cell types. The many different kinds of inner ear supporting cells play the essential roles of providing physical and physiological support to sensory hair cells and of maintaining cochlear homeostasis. Appropriately enough, the gene most commonly mutated among subjects with hereditary hearing impairment (HI), GJB2, encodes the connexin-26 (Cx26) gap-junction channel protein that underlies both intercellular communication among supporting cells and homeostasis of the cochlear fluids, endolymph and perilymph. GJB2 lies at the DFNB1 locus on 13q12. The specific kind of HI associated with this locus is caused by recessively-inherited mutations that inactivate the two alleles of the GJB2 gene, either in homozygous or compound heterozygous states. We describe the many diverse classes of genetic alterations that result in DFNB1 HI, such as large deletions that either destroy the GJB2 gene or remove a regulatory element essential for GJB2 expression, point mutations that interfere with promoter function or splicing, and small insertions or deletions and nucleotide substitutions that target the GJB2 coding sequence. We focus on how these alterations disrupt GJB2 and Cx26 functions and on their different effects on cochlear development and physiology. We finally discuss the diversity of clinical features of DFNB1 HI as regards severity, age of onset, inner ear malformations and vestibular dysfunction, highlighting the areas where future research should be concentrated.
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Affiliation(s)
- Francisco J. del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
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876
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Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW. Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Med 2017; 9:113. [PMID: 29254494 PMCID: PMC5735928 DOI: 10.1186/s13073-017-0509-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods.
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Affiliation(s)
| | - Peter W Rose
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA
| | - Andreas Prlić
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.,RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA
| | | | - José M Duarte
- RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA
| | - Andrew S Hoffman
- Human Centered Design & Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Geoffrey J Barton
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Timothy Bergquist
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Christian Bock
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Elizabeth Brunk
- University of California San Diego, La Jolla, CA, 92093, USA
| | - Marija Buljan
- Institute of Molecular Systems Biology, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Stephen K Burley
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, 98093, USA.,RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Binghuang Cai
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Hannah Carter
- University of California San Diego, La Jolla, CA, 92093, USA
| | - JianJiong Gao
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Adam Godzik
- SBP Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Michael Heuer
- AMPLab, University of California, Berkeley, CA, 94720, USA
| | | | - Thomas Hrabe
- SBP Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA.,Department of Oncology, Johns Hopkins Medicine, Baltimore, MD, 21287, USA
| | - Julia Koehler Leman
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY, 10010, USA.,Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Lydie Lane
- SIB Swiss Institute of Bioinformatics and University of Geneva, CH-1211, Geneva, Switzerland
| | - David L Masica
- Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, WA, 98109, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Frances Pearl
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Vikas Pejaver
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA.,The University of Washington eScience Institute, Seattle, WA, 98195, USA
| | | | - Ariel Rokem
- The University of Washington eScience Institute, Seattle, WA, 98195, USA
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics and Biozentrum University of Basel, CH-4056, Basel, Switzerland
| | - Sicheng Song
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, 98109, USA
| | - Hagen Tilgner
- Brain and Mind Research Institute, Weill Cornell Medicine, New York City, NY, 10021, USA
| | - Yana Valasatava
- RCSB Protein Data Bank, University of California San Diego, La Jolla, CA, 98093, USA
| | - Yang Zhang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
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877
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Menezes J, Ventura C, Costa JM, Parreira E, Romão L, Gonçalves J. PROS1 novel splice-site variant decreases protein S expression in patients from two families with thrombotic disease. Clin Case Rep 2017; 5:2062-2065. [PMID: 29225857 PMCID: PMC5715601 DOI: 10.1002/ccr3.1226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/04/2017] [Accepted: 09/19/2017] [Indexed: 11/11/2022] Open
Abstract
Our results prove that c.1871-14T>G is causative of type I PS deficiency, highlighting the importance of performing mRNA-based studies in order to evaluate variants pathogenicity. We evidence the increased risk of venous thromboembolism associated with this cryptic splice-site variant if present in patients with PS deficiency.
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Affiliation(s)
- Juliane Menezes
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal.,Gene Expression and Regulation Group Biosystems & Integrative Sciences Institute (BioISI) Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Célia Ventura
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal
| | - João Matos Costa
- Third Department of Internal Medicine Hospital Distrital de Santarém Santarém Portugal
| | | | - Luísa Romão
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal.,Gene Expression and Regulation Group Biosystems & Integrative Sciences Institute (BioISI) Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - João Gonçalves
- Department of Human Genetics Instituto Nacional de Saúde Doutor Ricardo Jorge Lisbon Portugal.,Centre for Toxicogenomics and Human Health (ToxOmics) Genetics, Oncology and Human Toxicology Nova Medical School Universidade Nova de Lisboa Lisbon Portugal
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878
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Bosch B, Itan Y, Meyts I. Whole-exome sequencing for detecting inborn errors of immunity: overview and perspectives. F1000Res 2017; 6:2056. [PMID: 29225788 PMCID: PMC5710381 DOI: 10.12688/f1000research.12365.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/19/2022] Open
Abstract
The study of inborn errors of immunity is based on a comprehensive clinical description of the patient’s phenotype and the elucidation of the underlying molecular mechanisms and their genetic etiology. Deciphering the pathogenesis is key to genetic counseling and the development of targeted therapy. This review shows the power of whole-exome sequencing in detecting inborn errors of immunity along five central steps taken in whole-exome sequencing analysis. In parallel, we highlight the challenges for the clinical and scientific use of the method and how these hurdles are currently being addressed. We end by ruminating on major areas in the field open to future research.
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Affiliation(s)
- Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,St. Giles Laboratory of the Human Genetics of Infectious Disease, Rockefeller University, New York, USA
| | - Yuval Itan
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Isabelle Meyts
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium.,Childhood Immunology, KULeuven, Leuven, Belgium
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879
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Vona B, Maroofian R, Mendiratta G, Croken M, Peng S, Ye X, Rezazadeh J, Bahena P, Lekszas C, Haaf T, Edelmann L, Shi L. Dual Diagnosis of Ellis-van Creveld Syndrome and Hearing Loss in a Consanguineous Family. Mol Syndromol 2017; 9:5-14. [PMID: 29456477 PMCID: PMC5803684 DOI: 10.1159/000480458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2017] [Indexed: 11/19/2022] Open
Abstract
Multilocus analysis of rare or genetically heterogeneous diseases is a distinct advantage of next-generation sequencing (NGS) over conventional single-gene investigations. Recent studies have begun to uncover an under-recognized prevalence of dual molecular diagnoses in patients with a "blended" phenotype that is the result of 2 clinical diagnoses involving 2 separate genetic loci. This blended phenotype could be mistakenly interpreted as a novel clinical extension of a single-gene disorder. In this study, we ascertained a proband from a large consanguineous Iranian family who manifests postlingual, progressive, moderate hearing loss in addition to suspected Ellis-van Creveld syndrome phenotype. NGS with a customized skeletal dysplasia panel containing over 370 genes and subsequent bioinformatics analysis disclosed 2 homozygous mutations in EVC2 (c.2653C>T; p.Arg885*) and COL11A2 (c.966dup; p.Thr323Hisfs*19), respectively. This study highlights a dual molecular diagnosis in a patient with a blending of 2 distinct phenotypes and illustrates the advantage and importance of this staple technology to facilitate rapid and comprehensive genetic dissection of a heterogeneous phenotype. The differentiation between phenotypic expansion of a genetic disorder and a blended phenotype that is due to more than one distinct genetic aberration is essential in order to reduce the diagnostic odyssey endured by patients.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Reza Maroofian
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Geetu Mendiratta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Croken
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Siwu Peng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaoqian Ye
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Dentistry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jamileh Rezazadeh
- Genetic Counselling and Rehabilitation Unit, Welfare Organization, South Khorasan, Iran
| | - Paulina Bahena
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Caroline Lekszas
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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880
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Christie KA, Courtney DG, DeDionisio LA, Shern CC, De Majumdar S, Mairs LC, Nesbit MA, Moore CBT. Towards personalised allele-specific CRISPR gene editing to treat autosomal dominant disorders. Sci Rep 2017; 7:16174. [PMID: 29170458 PMCID: PMC5701044 DOI: 10.1038/s41598-017-16279-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/09/2017] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 holds immense potential to treat a range of genetic disorders. Allele-specific gene disruption induced by non-homologous end-joining (NHEJ) DNA repair offers a potential treatment option for autosomal dominant disease. Here, we successfully delivered a plasmid encoding S. pyogenes Cas9 and sgRNA to the corneal epithelium by intrastromal injection and acheived long-term knockdown of a corneal epithelial reporter gene, demonstrating gene disruption via NHEJ in vivo. In addition, we used TGFBI corneal dystrophies as a model of autosomal dominant disease to assess the use of CRISPR/Cas9 in two allele-specific systems, comparing cleavage using a SNP-derived PAM to a guide specific approach. In vitro, cleavage via a SNP-derived PAM was found to confer stringent allele-specific cleavage, while a guide-specific approach lacked the ability to distinguish between the wild-type and mutant alleles. The failings of the guide-specific approach highlights the necessity for meticulous guide design and assessment, as various degrees of allele-specificity are achieved depending on the guide sequence employed. A major concern for the use of CRISPR/Cas9 is its tendency to cleave DNA non-specifically at “off-target” sites. Confirmation that S. pyogenes Cas9 lacks the specificity to discriminate between alleles differing by a single base-pair regardless of the position in the guide is demonstrated.
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Affiliation(s)
- Kathleen A Christie
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - David G Courtney
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | | | | | - Shyamasree De Majumdar
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - Laura C Mairs
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - M Andrew Nesbit
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK
| | - C B Tara Moore
- Biomedical Sciences Research Institute, Ulster University, Coleraine, Northern Ireland, BT52 1SA, UK. .,Avellino Laboratories, Menlo Park, California, CA, 94025, USA.
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881
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Rohanizadegan M, Abdo SM, O'Donnell-Luria A, Mihalek I, Chen P, Sanders M, Leeman K, Cho M, Hung C, Bodamer O. Utility of rapid whole-exome sequencing in the diagnosis of Niemann-Pick disease type C presenting with fetal hydrops and acute liver failure. Cold Spring Harb Mol Case Stud 2017; 3:mcs.a002147. [PMID: 28802248 PMCID: PMC5701306 DOI: 10.1101/mcs.a002147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/02/2017] [Indexed: 01/07/2023] Open
Abstract
Rapid whole-exome sequencing (rWES) is used in critically ill newborn infants to inform about diagnosis, clinical management, and prognosis. Here we report a male newborn infant with hydrops, pancytopenia, and acute liver failure who was listed for liver transplantation. Given the acuity of the presentation, the procedure-related morbidity and mortality, and lack of diagnosis, we used rWES in the proband and both parents with a turnaround time of 10 business days. rWES returned one maternally inherited, likely pathogenic and one paternally inherited, likely pathogenic variant in NPC1, suggestive of a diagnosis of Niemann–Pick disease type C (NPC). Interestingly, a diagnosis of NPC was entertained prior to rWES, but deemed unlikely in light of absent cholesterol storage on liver biopsy and near-normal oxysterol levels in dried blood. The diagnosis of NPC was confirmed on filipin stain in fibroblasts demonstrating defective cholesterol trafficking. NPC is a slowly progressive neurodegenerative disorder that may also affect the liver with overall poor prognosis. It was decided to take the infant off the transplant list and transfer to palliative care, where he died after 4 wk. This case highlights the utility of rWES in an acute clinical setting for several domains of precision medicine including (1) diagnosis, (2) prognosis and outcome, (3) management and therapy, and (4) utilization of resources.
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Affiliation(s)
- Mersedeh Rohanizadegan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sara M Abdo
- Division of Biochemistry, Faculty of Science, Helwan University, Cairo, Egypt
| | - Anne O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Ivana Mihalek
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peggy Chen
- Department of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut 06106, USA
| | - Marilyn Sanders
- Department of Neonatology, Connecticut Children's Medical Center, Hartford, Connecticut 06106, USA
| | - Kristen Leeman
- Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Megan Cho
- GeneDx, Gaithersburg, Maryland 20877, USA
| | - Christina Hung
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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882
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Zhao ZY, Jiang YL, Li BR, Yang F, Li J, Jin XW, Ning SB, Sun SH. Sanger sequencing in exonic regions of STK11 gene uncovers a novel de-novo germline mutation (c.962_963delCC) associated with Peutz-Jeghers syndrome and elevated cancer risk: case report of a Chinese patient. BMC MEDICAL GENETICS 2017; 18:130. [PMID: 29141581 PMCID: PMC5688745 DOI: 10.1186/s12881-017-0471-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/27/2017] [Indexed: 01/24/2023]
Abstract
Background Peutz-Jeghers syndrome (PJS) is caused by mutations in the tumor suppressor gene, STK11, and is characterized by gastrointestinal hamartomas, melanin spots on the lips and the extremities, and an increased risk of developing cancer. Case presentation We reported an isolated PJS patient who died of colon cancer, whose blood sample was collected together with all the available family members’. The entire coding region of the STK11 gene was amplified by PCR and analyzed by Sanger sequencing, through which, a novel mutation, c.962_963delCC in exon 8 was identified in this patient. This mutation causes a frameshift mutation and a premature termination at codon 358. Protein structure prediction by Swiss-Model indicated a dramatic change and partial loss of the C-terminal domain. We did not observe this mutation in both parents of the proband. Therefore, it is considered a novel de-novo mutation. Furthermore, the mutation was not found in 50 unrelated healthy people. Conclusions The novel mutation we reported here had not been recorded in databases or literature, and the patient who possessed it suffered from PJS and colon cancer. So our results enlarge the spectrum of STK11 variants in PJS patients. This mutation is most likely responsible for development of the PJS phenotype, especially the cancer occurrence. Electronic supplementary material The online version of this article (10.1186/s12881-017-0471-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zi-Ye Zhao
- Department of Medical Genetics, Naval Medical University, 800 Xiangyin Rd, Shanghai, 200433, China
| | - Yu-Liang Jiang
- Hebei North University, 11 South Zuanshi Rd., Zhangjiakou, Hebei Province, 075061, China.,Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Bai-Rong Li
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Fu Yang
- Department of Medical Genetics, Naval Medical University, 800 Xiangyin Rd, Shanghai, 200433, China
| | - Jing Li
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Xiao-Wei Jin
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China
| | - Shou-Bin Ning
- Department of Gastroenterology, Airforce General Hospital of PLA, 30 Fucheng Rd, Beijing, 100142, China.
| | - Shu-Han Sun
- Department of Medical Genetics, Naval Medical University, 800 Xiangyin Rd, Shanghai, 200433, China.
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883
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A 23-Nucleotide Deletion in STK11 Gene Causes Peutz-Jeghers Syndrome and Malignancy in a Chinese Patient Without a Positive Family History. Dig Dis Sci 2017; 62:3014-3020. [PMID: 28986664 DOI: 10.1007/s10620-017-4741-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/28/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND AND AIMS Peutz-Jeghers syndrome (PJS) is an autosomal-dominant genetic disease caused by mutations in the tumor suppressor gene, STK11, which is characterized by gastrointestinal hamartomas, melanin spots on the lips and the extremities, and an increased risk of developing both gastrointestinal and extraintestinal malignancies. METHODS AND RESULTS We treated a PJS patient without a positive family history, who possessed typical clinical manifestations including polyp canceration. In order to explore the genotype of this patient, blood samples were collected from all the available family members. The whole coding region and the flanking regions of the STK11 gene were amplified by polymerase chain reaction and analyzed by Sanger sequencing. Molecular analysis of the STK11 gene here revealed a 23-nucleotide deletion (c.426-448delCGTGCCGGAGAAGCGTTTCCCAG) in exon 3, resulting in a change of 13 codons and a truncating protein (p.S142SfsX13). This mutation was not found in normal individuals in this family including her parents or in 100 control individuals. Protein structure prediction indicated a dramatic loss of the kinase domain and complete loss of the C-terminal regulatory domain. CONCLUSIONS The results presented here enlarge the spectrum of STK11 mutation both disease-causing and malignancy-causing.
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884
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Ludwig NF, Velho RV, Sperb-Ludwig F, Acosta AX, Ribeiro EM, Kim CA, Gandelman Horovitz DD, Boy R, Rodovalho-Doriqui MJ, Lourenço CM, Santos ES, Braulke T, Pohl S, Schwartz IVD. GNPTAB missense mutations cause loss of GlcNAc-1-phosphotransferase activity in mucolipidosis type II through distinct mechanisms. Int J Biochem Cell Biol 2017; 92:90-94. [DOI: 10.1016/j.biocel.2017.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/12/2017] [Indexed: 01/08/2023]
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885
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Aggarwal S, Nayek A, Pradhan D, Verma R, Yadav M, Ponnusamy K, Jain AK. dbGAPs: A comprehensive database of genes and genetic markers associated with psoriasis and its subtypes. Genomics 2017; 110:S0888-7543(17)30115-5. [PMID: 29031638 DOI: 10.1016/j.ygeno.2017.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 01/12/2023]
Abstract
Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data. The database contains annotation for 202 manually curated genes associated with psoriasis and its subtypes with cross-references. Functional enrichment of these genes, in context of Gene Ontology and pathways, provide insight into their important role in psoriasis etiology and pathogenesis. The dbGAPs interface is enriched with an interactive search engine for data retrieval along with unique customized tools for Single Nucleotide Polymorphism (SNP)/indel detection and SNP/indel annotations. dbGAPs is accessible at http://www.bmicnip.in/dbgaps/.
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Affiliation(s)
- Shweta Aggarwal
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Arnab Nayek
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Dibyabhaba Pradhan
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Rashi Verma
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | - Monika Yadav
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India
| | | | - Arun Kumar Jain
- Biomedical Informatics Centre, National Institute of Pathology - ICMR, New Delhi, India.
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886
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Ferlaino M, Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C. An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. BMC Bioinformatics 2017; 18:442. [PMID: 28985712 PMCID: PMC5955213 DOI: 10.1186/s12859-017-1862-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/02/2017] [Indexed: 11/30/2022] Open
Abstract
Background Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of mutations associated with complex traits are located outside the exome, it is crucial to investigate the potential pathogenic impact of indels in non-coding regions of the human genome. Results We present FATHMM-indel, an integrative approach to predict the functional effect, pathogenic or neutral, of indels in non-coding regions of the human genome. Our method exploits various genomic annotations in addition to sequence data. When validated on benchmark data, FATHMM-indel significantly outperforms CADD and GAVIN, state of the art models in assessing the pathogenic impact of non-coding variants. FATHMM-indel is available via a web server at indels.biocompute.org.uk. Conclusions FATHMM-indel can accurately predict the functional impact and prioritise small indels throughout the whole non-coding genome. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1862-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Ferlaino
- Big Data Institute, University of Oxford, Oxford, OX3 7LF, UK. .,Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, OX3 9DU, UK.
| | - Mark F Rogers
- Intelligent Systems Laboratory, University of Bristol, Bristol, BS8 1UB, UK
| | - Hashem A Shihab
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Colin Campbell
- Intelligent Systems Laboratory, University of Bristol, Bristol, BS8 1UB, UK
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887
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Bastida JM, Lozano ML, Benito R, Janusz K, Palma-Barqueros V, Del Rey M, Hernández-Sánchez JM, Riesco S, Bermejo N, González-García H, Rodriguez-Alén A, Aguilar C, Sevivas T, López-Fernández MF, Marneth AE, van der Reijden BA, Morgan NV, Watson SP, Vicente V, Hernández-Rivas JM, Rivera J, González-Porras JR. Introducing high-throughput sequencing into mainstream genetic diagnosis practice in inherited platelet disorders. Haematologica 2017; 103:148-162. [PMID: 28983057 PMCID: PMC5777202 DOI: 10.3324/haematol.2017.171132] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/29/2017] [Indexed: 12/30/2022] Open
Abstract
Inherited platelet disorders are a heterogeneous group of rare diseases, caused by inherited defects in platelet production and/or function. Their genetic diagnosis would benefit clinical care, prognosis and preventative treatments. Until recently, this diagnosis has usually been performed via Sanger sequencing of a limited number of candidate genes. High-throughput sequencing is revolutionizing the genetic diagnosis of diseases, including bleeding disorders. We have designed a novel high-throughput sequencing platform to investigate the unknown molecular pathology in a cohort of 82 patients with inherited platelet disorders. Thirty-four (41.5%) patients presented with a phenotype strongly indicative of a particular type of platelet disorder. The other patients had clinical bleeding indicative of platelet dysfunction, but with no identifiable features. The high-throughput sequencing test enabled a molecular diagnosis in 70% of these patients. This sensitivity increased to 90% among patients suspected of having a defined platelet disorder. We found 57 different candidate variants in 28 genes, of which 70% had not previously been described. Following consensus guidelines, we qualified 68.4% and 26.3% of the candidate variants as being pathogenic and likely pathogenic, respectively. In addition to establishing definitive diagnoses of well-known inherited platelet disorders, high-throughput sequencing also identified rarer disorders such as sitosterolemia, filamin and actinin deficiencies, and G protein-coupled receptor defects. This included disease-causing variants in DIAPH1 (n=2) and RASGRP2 (n=3). Our study reinforces the feasibility of introducing high-throughput sequencing technology into the mainstream laboratory for the genetic diagnostic practice in inherited platelet disorders.
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Affiliation(s)
- José M Bastida
- Servicio de Hematología, Hospital Universitario de Salamanca-IBSAL-USAL, Spain .,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - María L Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain.,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - Rocío Benito
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - Kamila Janusz
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - Verónica Palma-Barqueros
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain
| | | | | | - Susana Riesco
- Servicio de Pediatría, Hospital Universitario de Salamanca-IBSAL, Spain
| | - Nuria Bermejo
- Servicio de Hematología, Complejo Hospitalario San Pedro Alcántara, Cáceres, Spain
| | | | - Agustín Rodriguez-Alén
- Servicio de Hematología y Hemoterapia, Hospital Virgen de la Salud, Complejo Hospitalario de Toledo, Spain
| | - Carlos Aguilar
- Servicio de Hematología, Complejo Asistencial de Soria, Spain
| | - Teresa Sevivas
- Serviço de Imunohemoterapia, Sangue e Medicina Transfusional do Centro Hospitalar e Universitário de Coimbra, EPE, Portugal
| | | | - Anna E Marneth
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Neil V Morgan
- Birmingham Platelet Group, Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Steve P Watson
- Birmingham Platelet Group, Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Vicente Vicente
- On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - Jesús M Hernández-Rivas
- Servicio de Hematología, Hospital Universitario de Salamanca-IBSAL-USAL, Spain.,IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - José Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain.,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
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888
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Comander J, Weigel-DiFranco C, Maher M, Place E, Wan A, Harper S, Sandberg MA, Navarro-Gomez D, Pierce EA. The Genetic Basis of Pericentral Retinitis Pigmentosa-A Form of Mild Retinitis Pigmentosa. Genes (Basel) 2017; 8:genes8100256. [PMID: 28981474 PMCID: PMC5664106 DOI: 10.3390/genes8100256] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/06/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022] Open
Abstract
Pericentral retinitis pigmentosa (RP) is an atypical form of RP that affects the near-peripheral retina first and tends to spare the far periphery. This study was performed to further define the genetic basis of this phenotype. We identified a cohort of 43 probands with pericentral RP based on a comprehensive analysis of their retinal phenotype. Genetic analyses of DNA samples from these patients were performed using panel-based next-generation sequencing, copy number variations, and whole exome sequencing (WES). Mutations provisionally responsible for disease were found in 19 of the 43 families (44%) analyzed. These include mutations in RHO (five patients), USH2A (four patients), and PDE6B (two patients). Of 28 putatively pathogenic alleles, 15 (54%) have been previously identified in patients with more common forms of typical RP, while the remaining 13 mutations (46%) were novel. Burden testing of WES data successfully identified HGSNAT as a cause of pericentral RP in at least two patients, suggesting it is also a relatively common cause of pericentral RP. While additional sequencing might uncover new genes specifically associated with pericentral RP, the current results suggest that genetically pericentral RP is not a separate clinical entity, but rather is part of the spectrum of mild RP phenotypes.
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Affiliation(s)
- Jason Comander
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Carol Weigel-DiFranco
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Matthew Maher
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Emily Place
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Aliete Wan
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Shyana Harper
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Michael A Sandberg
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Eric A Pierce
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
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889
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Deng H, Xiao H. The role of the ATP2C1 gene in Hailey-Hailey disease. Cell Mol Life Sci 2017; 74:3687-3696. [PMID: 28551824 PMCID: PMC11107712 DOI: 10.1007/s00018-017-2544-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/27/2017] [Accepted: 05/18/2017] [Indexed: 12/24/2022]
Abstract
Hailey-Hailey disease (HHD) is a rare autosomal dominant acantholytic dermatosis, characterized by a chronic course of repeated and exacerbated skin lesions in friction regions. The pathogenic gene of HHD was reported to be the ATPase calcium-transporting type 2C member 1 gene (ATP2C1) located on chromosome 3q21-q24. Its function is to maintain normal intracellular concentrations of Ca2+/Mn2+ by transporting Ca2+/Mn2+ into the Golgi apparatus. ATP2C1 gene mutations are reportedly responsible for abnormal cytosolic Ca2+/Mn2+ levels and the clinical manifestations of HHD. Environmental factors and genetic modifiers may also affect the clinical variability of HHD. This article aims to critically discuss the clinical and pathological features of HHD, differential diagnoses, and genetic and functional studies of the ATP2C1 gene in HHD. Further understanding the role of the ATP2C1 gene in the pathogenesis of HHD by genetic, molecular, and animal studies may contribute to a better clinical diagnosis and provide new strategies for the treatment and prevention of HHD.
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Affiliation(s)
- Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Tongzipo Road 138, Changsha, 410013, Hunan, People's Republic of China.
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, People's Republic of China.
| | - Heng Xiao
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Tongzipo Road 138, Changsha, 410013, Hunan, People's Republic of China
- Department of Pathology, The Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, People's Republic of China
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890
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Ghouse J, Skov MW, Bigseth RS, Ahlberg G, Kanters JK, Olesen MS. Distinguishing pathogenic mutations from background genetic noise in cardiology: The use of large genome databases for genetic interpretation. Clin Genet 2017; 93:459-466. [PMID: 28589536 DOI: 10.1111/cge.13066] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/15/2022]
Abstract
Advances in clinical genetic testing have led to increased insight into the human genome, including how challenging it is to interpret rare genetic variation. In some cases, the ability to detect genetic mutations exceeds the ability to understand their clinical impact, limiting the advantage of these technologies. Obstacles in genomic medicine are many and include: understanding the level of certainty/uncertainty behind pathogenicity determination, the numerous different variant interpretation-guidelines used by clinical laboratories, delivering the certain or uncertain result to the patient, helping patients evaluate medical decisions in light of uncertainty regarding the consequence of the findings. Through publication of large publicly available exome/genome databases, researchers and physicians are now able to highlight dubious variants previously associated with different cardiac traits. Also, continuous efforts through data sharing, international collaborative efforts to develop disease-gene-specific guidelines, and computational analyses using large data, will indubitably assist in better variant interpretation and classification. This article discusses the current, and quickly changing, state of variant interpretation resources within cardiovascular genetic research, e.g., publicly available databases and ways of how cardiovascular genetic counselors and geneticists can aid in improving variant interpretation in cardiology.
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Affiliation(s)
- J Ghouse
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - M W Skov
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - R S Bigseth
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - G Ahlberg
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J K Kanters
- Laboratory of Experimental Cardiology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - M S Olesen
- Laboratory of Molecular Cardiology, Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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891
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Fassio AV, Martins PM, Guimarães SDS, Junior SSA, Ribeiro VS, de Melo-Minardi RC, Silveira SDA. Vermont: a multi-perspective visual interactive platform for mutational analysis. BMC Bioinformatics 2017; 18:403. [PMID: 28929973 PMCID: PMC5606220 DOI: 10.1186/s12859-017-1789-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease association and effects on protein structure and function. Therefore, reliable computational approaches are needed to support the understanding of mutations and their impacts. Here, we present VERMONT 2.0, a visual interactive platform that combines sequence and structural parameters with interactive visualizations to make the impact of protein point mutations more understandable. RESULTS We aimed to contribute a novel visual analytics oriented method to analyze and gain insight on the impact of protein point mutations. To assess the ability of VERMONT to do this, we visually examined a set of mutations that were experimentally characterized to determine if VERMONT could identify damaging mutations and why they can be considered so. CONCLUSIONS VERMONT allowed us to understand mutations by interpreting position-specific structural and physicochemical properties. Additionally, we note some specific positions we believe have an impact on protein function/structure in the case of mutation.
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Affiliation(s)
- Alexandre V Fassio
- Department of Computer Science, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil. .,Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil.
| | - Pedro M Martins
- Department of Computer Science, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil.,Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Samuel da S Guimarães
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
| | - Sócrates S A Junior
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
| | - Vagner S Ribeiro
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
| | - Raquel C de Melo-Minardi
- Department of Computer Science, Universidade Federal de Minas Gerais, 6627, Antônio Carlos avenue, Pampulha, Belo Horizonte, 31270-901, Brazil
| | - Sabrina de A Silveira
- Department of Computer Science, Universidade Federal de Viçosa, Peter Henry Rolfs avenue, Campus Universitário, Viçosa, 36570-900, Brazil
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892
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Álvarez-Satta M, Castro-Sánchez S, Valverde D. Bardet-Biedl Syndrome as a Chaperonopathy: Dissecting the Major Role of Chaperonin-Like BBS Proteins (BBS6-BBS10-BBS12). Front Mol Biosci 2017; 4:55. [PMID: 28824921 PMCID: PMC5534436 DOI: 10.3389/fmolb.2017.00055] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/13/2017] [Indexed: 01/01/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a rare genetic disorder that belongs to the group of ciliopathies, defined as diseases caused by defects in cilia structure and/or function. The six diagnostic features considered for this syndrome include retinal dystrophy, obesity, polydactyly, cognitive impairment and renal and urogenital anomalies. Furthermore, three of the 21 genes currently known to be involved in BBS encode chaperonin-like proteins (MKKS/BBS6, BBS10, and BBS12), so BBS can be also considered a member of the growing group of chaperonopathies. Remarkably, up to 50% of clinically-diagnosed BBS families can harbor disease-causing variants in these three genes, which highlights the importance of chaperone defects as pathogenic factors even for genetically heterogeneous syndromes such as BBS. In addition, it is interesting to note that BBS families with deleterious variants in MKKS/BBS6, BBS10 or BBS12 genes generally display more severe phenotypes than families with changes in other BBS genes. The chaperonin-like BBS proteins have structural homology to the CCT family of group II chaperonins, although they are believed to conserve neither the ATP-dependent folding activity of canonical CCT chaperonins nor the ability to form CCT-like oligomeric complexes. Thus, they play an important role in the initial steps of assembly of the BBSome, which is a multiprotein complex essential for mediating the ciliary trafficking activity. In this review, we present a comprehensive review of those genetic, functional and evolutionary aspects concerning chaperonin-like BBS proteins, trying to provide a new perspective that expands the classical conception of BBS only from a ciliary point of view.
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Affiliation(s)
- María Álvarez-Satta
- Grupo de Biomarcadores Moleculares, Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de VigoVigo, Spain.,Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGOVigo, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia 2016-2019), Universidad de VigoVigo, Spain
| | - Sheila Castro-Sánchez
- Grupo de Biomarcadores Moleculares, Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de VigoVigo, Spain.,Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGOVigo, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia 2016-2019), Universidad de VigoVigo, Spain
| | - Diana Valverde
- Grupo de Biomarcadores Moleculares, Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de VigoVigo, Spain.,Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGOVigo, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia 2016-2019), Universidad de VigoVigo, Spain
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893
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Pagel KA, Pejaver V, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics 2017; 33:i389-i398. [PMID: 28882004 PMCID: PMC5870554 DOI: 10.1093/bioinformatics/btx272] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Loss-of-function genetic variants are frequently associated with severe clinical phenotypes, yet many are present in the genomes of healthy individuals. The available methods to assess the impact of these variants rely primarily upon evolutionary conservation with little to no consideration of the structural and functional implications for the protein. They further do not provide information to the user regarding specific molecular alterations potentially causative of disease. RESULTS To address this, we investigate protein features underlying loss-of-function genetic variation and develop a machine learning method, MutPred-LOF, for the discrimination of pathogenic and tolerated variants that can also generate hypotheses on specific molecular events disrupted by the variant. We investigate a large set of human variants derived from the Human Gene Mutation Database, ClinVar and the Exome Aggregation Consortium. Our prediction method shows an area under the Receiver Operating Characteristic curve of 0.85 for all loss-of-function variants and 0.75 for proteins in which both pathogenic and neutral variants have been observed. We applied MutPred-LOF to a set of 1142 de novo vari3ants from neurodevelopmental disorders and find enrichment of pathogenic variants in affected individuals. Overall, our results highlight the potential of computational tools to elucidate causal mechanisms underlying loss of protein function in loss-of-function variants. AVAILABILITY AND IMPLEMENTATION http://mutpred.mutdb.org. CONTACT predrag@indiana.edu.
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Affiliation(s)
- Kymberleigh A Pagel
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
| | - Vikas Pejaver
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
| | - Guan Ning Lin
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Hyun-Jun Nam
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Beyster Center for Psychiatric Genomics, Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Sean D Mooney
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Predrag Radivojac
- Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA
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894
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Rehm HL. A new era in the interpretation of human genomic variation. Genet Med 2017; 19:1092-1095. [PMID: 28703787 DOI: 10.1038/gim.2017.90] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/10/2017] [Indexed: 01/19/2023] Open
Affiliation(s)
- Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Brigham &Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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895
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Livingstone M, Folkman L, Yang Y, Zhang P, Mort M, Cooper DN, Liu Y, Stantic B, Zhou Y. Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants. Hum Mutat 2017. [DOI: 10.1002/humu.23283] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark Livingstone
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
| | - Lukas Folkman
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
| | - Yuedong Yang
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
- Institute for Glycomics; Griffith University; Southport Queensland 4222 Australia
| | - Ping Zhang
- Menzies Health Institute; Griffith University; Southport Queensland 4222 Australia
| | - Matthew Mort
- Institute of Medical Genetics; Cardiff University; Cardiff CF144XN United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics; Cardiff University; Cardiff CF144XN United Kingdom
| | - Yunlong Liu
- Department of Medical and Molecular Genetics; Indiana University; Indianapolis Indiana 46202
| | - Bela Stantic
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
| | - Yaoqi Zhou
- School of Information and Communication Technology; Griffith University; Southport Queensland 4222 Australia
- Institute for Glycomics; Griffith University; Southport Queensland 4222 Australia
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896
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Khan SA, Peracha H, Ballhausen D, Wiesbauer A, Rohrbach M, Gautschi M, Mason RW, Giugliani R, Suzuki Y, Orii KE, Orii T, Tomatsu S. Epidemiology of mucopolysaccharidoses. Mol Genet Metab 2017; 121:227-240. [PMID: 28595941 PMCID: PMC5653283 DOI: 10.1016/j.ymgme.2017.05.016] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 12/15/2022]
Abstract
The aim of this study was to obtain data about the epidemiology of the different types of mucopolysaccharidoses in Japan and Switzerland and to compare with similar data from other countries. Data for Japan was collected between 1982 and 2009, and 467 cases with MPS were identified. The combined birth prevalence was 1.53 per 100,000 live births. The highest birth prevalence was 0.84 for MPS II, accounting for 55% of all MPS. MPS I, III, and IV accounted for 15, 16, and 10%, respectively. MPS VI and VII were more rare and accounted for 1.7 and 1.3%, respectively. A retrospective epidemiological data collection was performed in Switzerland between 1975 and 2008 (34years), and 41 living MPS patients were identified. The combined birth prevalence was 1.56 per 100,000 live births. The highest birth prevalence was 0.46 for MPS II, accounting for 29% of all MPS. MPS I, III, and IV accounted for 12, 24, and 24%, respectively. As seen in the Japanese population, MPS VI and VII were more rare and accounted for 7.3 and 2.4%, respectively. The high birth prevalence of MPS II in Japan was comparable to that seen in other East Asian countries where this MPS accounted for approximately 50% of all forms of MPS. Birth prevalence was also similar in some European countries (Germany, Northern Ireland, Portugal and the Netherlands) although the prevalence of other forms of MPS is also reported to be higher in these countries. Birth prevalence of MPS II in Switzerland and other European countries is comparatively lower. The birth prevalence of MPS III and IV in Switzerland is higher than in Japan but comparable to that in most other European countries. Moreover, the birth prevalence of MPS VI and VII was very low in both, Switzerland and Japan. Overall, the frequency of MPS varies for each population due to differences in ethnic backgrounds and/or founder effects that affect the birth prevalence of each type of MPS, as seen for other rare genetic diseases. Methods for identification of MPS patients are not uniform across all countries, and consequently, if patients are not identified, recorded prevalence rates will be aberrantly low.
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Affiliation(s)
- Shaukat A Khan
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
| | - Hira Peracha
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
| | - Diana Ballhausen
- Centre for Molecular Diseases, Service for Genetic Medicine, University Hospital Lausanne, Switzerland
| | - Alfred Wiesbauer
- Institute of Social and Preventive Medicine, University of Bern, Switzerland
| | - Marianne Rohrbach
- Division of Metabolism and Children's Research Centre (CRC), University Children's Hospital, Zurich, Switzerland
| | - Matthias Gautschi
- Division of Endocrinology, Diabetology and Metabolism, University Children's Hospital, University Institute of Clinical Chemistry, Inselspital, University of Bern, Bern, Switzerland
| | - Robert W Mason
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States
| | - Roberto Giugliani
- Medical Genetics Service, HCPA, Dep. Genetics, UFRGS, and INAGEMP, Porto Alegre, Brazil
| | | | - Kenji E Orii
- Department of Pediatrics, Gifu University, Gifu, Japan
| | - Tadao Orii
- Department of Pediatrics, Gifu University, Gifu, Japan
| | - Shunji Tomatsu
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States; Department of Pediatrics, Gifu University, Gifu, Japan; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, United States.
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897
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Martínez-Ulloa PL, Vallejo M, Corral I, García-Barragán N, Alcazar A, Martínez-Alonso E, Martínez-Poles J, Pian H, Jiménez-Escrig A. A novel ATTR L32V mutation causes familial amyloid polyneuropathy in a Bolivian family. J Peripher Nerv Syst 2017. [PMID: 28646538 DOI: 10.1111/jns.12227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report a new transthyretin (ATTR) gene c.272C>G mutation and variant protein, p.Leu32Val, in a kindred of Bolivian origin with a rapid progressive peripheral neuropathy and cardiomyopathy. Three individuals from a kindred with peripheral nerve and cardiac amyloidosis were examined. Analysis of the TTR gene was performed by Sanger direct sequencing. Neuropathologic examination was obtained on the index patient with mass spectrometry study of the ATTR deposition. Direct DNA sequence analysis of exons 2, 3, and 4 of the TTR gene demonstrated a c.272 C>G mutation in exon 2 (p.L32V). Sural nerve biopsy revealed massive amyloid deposition in the perineurium, endoneurium and vasa nervorum. Mass spectrometric analyses of ATTR immunoprecipitated from nerve biopsy showed the presence of both wild-type and variant proteins. The observed mass results for the wild-type and variant proteins were consistent with the predicted values calculated from the genetic analysis data. The ATTR L32V is associated with a severe course. This has implications for treatment of affected individuals and counseling of family members.
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Affiliation(s)
| | - Manuela Vallejo
- Neurobiología, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain
| | - Iñigo Corral
- Department of Neurology, Hospital Ramón y Cajal, Madrid, Spain
| | | | - Alberto Alcazar
- Departmento de Investigación, IRYCIS, Hospital Ramón y Cajal, Madrid, Spain
| | | | | | - Hector Pian
- Department of Pathology, Hospital Ramón y Cajal, Madrid, Spain
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898
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Abstract
Background Neurofibromatosis type 1 (NF1: Online Mendelian Inheritance in Man (OMIM) #162200) is an autosomal dominantly inherited tumour predisposition syndrome. Heritable constitutional mutations in the NF1 gene result in dysregulation of the RAS/MAPK pathway and are causative of NF1. The major known function of the NF1 gene product neurofibromin is to downregulate RAS. NF1 exhibits variable clinical expression and is characterized by benign cutaneous lesions including neurofibromas and café-au-lait macules, as well as a predisposition to various types of malignancy, such as breast cancer and leukaemia. However, acquired somatic mutations in NF1 are also found in a wide variety of malignant neoplasms that are not associated with NF1. Main body Capitalizing upon the availability of next-generation sequencing data from cancer genomes and exomes, we review current knowledge of somatic NF1 mutations in a wide variety of tumours occurring at a number of different sites: breast, colorectum, urothelium, lung, ovary, skin, brain and neuroendocrine tissues, as well as leukaemias, in an attempt to understand their broader role and significance, and with a view ultimately to exploiting this in a diagnostic and therapeutic context. Conclusion As neurofibromin activity is a key to regulating the RAS/MAPK pathway, NF1 mutations are important in the acquisition of drug resistance, to BRAF, EGFR inhibitors, tamoxifen and retinoic acid in melanoma, lung and breast cancers and neuroblastoma. Other curiosities are observed, such as a high rate of somatic NF1 mutation in cutaneous melanoma, lung cancer, ovarian carcinoma and glioblastoma which are not usually associated with neurofibromatosis type 1. Somatic NF1 mutations may be critical drivers in multiple cancers. The mutational landscape of somatic NF1 mutations should provide novel insights into our understanding of the pathophysiology of cancer. The identification of high frequency of somatic NF1 mutations in sporadic tumours indicates that neurofibromin is likely to play a critical role in development, far beyond that evident in the tumour predisposition syndrome NF1.
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899
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The landscape of genetic diseases in Saudi Arabia based on the first 1000 diagnostic panels and exomes. Hum Genet 2017; 136:921-939. [PMID: 28600779 PMCID: PMC5502059 DOI: 10.1007/s00439-017-1821-8] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 06/05/2017] [Indexed: 12/13/2022]
Abstract
In this study, we report the experience of the only reference clinical next-generation sequencing lab in Saudi Arabia with the first 1000 families who span a wide-range of suspected Mendelian phenotypes. A total of 1019 tests were performed in the period of March 2016–December 2016 comprising 972 solo (index only), 14 duo (parents or affected siblings only), and 33 trio (index and parents). Multigene panels accounted for 672 tests, while whole exome sequencing (WES) represented the remaining 347 tests. Pathogenic or likely pathogenic variants that explain the clinical indications were identified in 34% (27% in panels and 43% in exomes), spanning 279 genes and including 165 novel variants. While recessive mutations dominated the landscape of solved cases (71% of mutations, and 97% of which are homozygous), a substantial minority (27%) were solved on the basis of dominant mutations. The highly consanguineous nature of the study population also facilitated homozygosity for many private mutations (only 32.5% of the recessive mutations are founder), as well as the first instances of recessive inheritance of previously assumed strictly dominant disorders (involving ITPR1, VAMP1, MCTP2, and TBP). Surprisingly, however, dual molecular diagnosis was only observed in 1.5% of cases. Finally, we have encountered candidate variants in 75 genes (ABHD6, ACY3, ADGRB2, ADGRG7, AGTPBP1, AHNAK2, AKAP6, ASB3, ATXN1L, C17orf62, CABP1, CCDC186, CCP110, CLSTN2, CNTN3, CNTN5, CTNNA2, CWC22, DMAP1, DMKN, DMXL1, DSCAM, DVL2, ECI1, EP400, EPB41L5, FBXL22, GAP43, GEMIN7, GIT1, GRIK4, GRSF1, GTRP1, HID1, IFNL1, KCNC4, LRRC52, MAP7D3, MCTP2, MED26, MPP7, MRPS35, MTDH, MTMR9, NECAP2, NPAT, NRAP, PAX7, PCNX, PLCH2, PLEKHF1, PTPN12, QKI, RILPL2, RIMKLA, RIMS2, RNF213, ROBO1, SEC16A, SIAH1, SIRT2, SLAIN2, SLC22A20, SMDT1, SRRT, SSTR1, ST20, SYT9, TSPAN6, UBR4, VAMP4, VPS36, WDR59, WDYHV1, and WHSC1) not previously linked to human phenotypes and these are presented to accelerate post-publication matchmaking. Two of these genes were independently mutated in more than one family with similar phenotypes, which substantiates their link to human disease (AKAP6 in intellectual disability and UBR4 in early dementia). If the novel candidate disease genes in this cohort are independently confirmed, the yield of WES will have increased to 83%, which suggests that most “negative” clinical exome tests are unsolved due to interpretation rather than technical limitations.
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900
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Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A, Harrow J. Genome annotation for clinical genomic diagnostics: strengths and weaknesses. Genome Med 2017; 9:49. [PMID: 28558813 PMCID: PMC5448149 DOI: 10.1186/s13073-017-0441-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis.
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Affiliation(s)
- Charles A Steward
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR, UK. .,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | | | - Berge A Minassian
- Department of Pediatrics (Neurology), University of Texas Southwestern, Dallas, TX, USA.,Program in Genetics and Genome Biology and Department of Paediatrics (Neurology), The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, WC1N 3BG, UK.,Chalfont Centre for Epilepsy, Chesham Lane, Chalfont St Peter, Buckinghamshire, SL9 0RJ, UK
| | - Adam Frankish
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer Harrow
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Illumina Inc, Great Chesterford, Essex, CB10 1XL, UK
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