351
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Burdick KJ, Cogan JD, Rives LC, Robertson AK, Koziura ME, Brokamp E, Duncan L, Hannig V, Pfotenhauer J, Vanzo R, Paul MS, Bican A, Morgan T, Duis J, Newman JH, Hamid R, Phillips JA. Limitations of exome sequencing in detecting rare and undiagnosed diseases. Am J Med Genet A 2020; 182:1400-1406. [PMID: 32190976 DOI: 10.1002/ajmg.a.61558] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/28/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
Abstract
While exome sequencing (ES) is commonly the final diagnostic step in clinical genetics, it may miss diagnoses. To clarify the limitations of ES, we investigated the diagnostic yield of genetic tests beyond ES in our Undiagnosed Diseases Network (UDN) participants. We reviewed the yield of additional genetic testing including genome sequencing (GS), copy number variant (CNV), noncoding variant (NCV), repeat expansion (RE), or methylation testing in UDN cases with nondiagnostic ES results. Overall, 36/54 (67%) of total diagnoses were based on clinical findings and coding variants found by ES and 3/54 (6%) were based on clinical findings only. The remaining 15/54 (28%) required testing beyond ES. Of these, 7/15 (47%) had NCV, 6/15 (40%) CNV, and 2/15 (13%) had a RE or a DNA methylation disorder. Thus 18/54 (33%) of diagnoses were not solved exclusively by ES. Several methods were needed to detect and/or confirm the functional effects of the variants missed by ES, and in some cases by GS. These results indicate that tests to detect elusive variants should be considered after nondiagnostic preliminary steps. Further studies are needed to determine the cost-effectiveness of tests beyond ES that provide diagnoses and insights to possible treatment.
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Affiliation(s)
- Kendall J Burdick
- University of Massachusetts of Medical School, Worcester, Massachusetts, USA
| | - Joy D Cogan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lynette C Rives
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Amy K Robertson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary E Koziura
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura Duncan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Vickie Hannig
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jean Pfotenhauer
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rena Vanzo
- Lineagen Inc., Salt Lake City, Utah, USA
| | | | - Anna Bican
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Thomas Morgan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jessica Duis
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John H Newman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rizwan Hamid
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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352
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Genomic Landscape and Mutational Spectrum of ADAMTS Family Genes in Mendelian Disorders Based on Gene Evidence Review for Variant Interpretation. Biomolecules 2020; 10:biom10030449. [PMID: 32183147 PMCID: PMC7175297 DOI: 10.3390/biom10030449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 01/17/2023] Open
Abstract
ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) are a family of multidomain extracellular protease enzymes with 19 members. A growing number of ADAMTS family gene variants have been identified in patients with various hereditary diseases. To understand the genomic landscape and mutational spectrum of ADAMTS family genes, we evaluated all reported variants in the ClinVar database and Human Gene Mutation Database (HGMD), as well as recent literature on Mendelian hereditary disorders associated with ADAMTS family genes. Among 1089 variants in 14 genes reported in public databases, 307 variants previously suggested for pathogenicity in Mendelian diseases were comprehensively re-evaluated using the American College of Medical Genetics and Genomics (ACMG) 2015 guideline. A total of eight autosomal recessive genes were annotated as being strongly associated with specific Mendelian diseases, including two recently discovered genes (ADAMTS9 and ADAMTS19) for their causality in congenital diseases (nephronophthisis-related ciliopathy and nonsyndromic heart valve disease, respectively). Clinical symptoms and affected organs were extremely heterogeneous among hereditary diseases caused by ADAMTS family genes, indicating phenotypic heterogeneity despite their structural and functional similarity. ADAMTS6 was suggested as presenting undiscovered pathogenic mutations responsible for novel Mendelian disorders. Our study is the first to highlight the genomic landscape of ADAMTS family genes, providing an appropriate genetic approach for clinical use.
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353
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Myers L, Anderlid BM, Nordgren A, Lundin K, Kuja-Halkola R, Tammimies K, Bölte S. Clinical versus automated assessments of morphological variants in twins with and without neurodevelopmental disorders. Am J Med Genet A 2020; 182:1177-1189. [PMID: 32162839 DOI: 10.1002/ajmg.a.61545] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/05/2019] [Accepted: 02/14/2020] [Indexed: 12/28/2022]
Abstract
Physical examinations are recommended as part of a comprehensive evaluation for individuals with neurodevelopmental disorders (NDDs), such as autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder. These examinations should include assessment for morphological variants. Previous studies have shown an increase in morphological variants in individuals with NDDs, particularly ASD, and that these variants may be present in greater amounts in individuals with genetic alterations. Unfortunately, assessment for morphological variants can be subjective and time-consuming, and require a high degree of clinical expertise. Therefore, objective, automated methods of morphological assessment are desirable. This study compared the use of Face2Gene, an automated tool to explore facial morphological variants, to clinical consensus assessment, using a cohort of N = 290 twins enriched for NDDs (n = 135 with NDD diagnoses). Agreement between automated and clinical assessments were satisfactory to complete (78.3-100%). In our twin sample, individuals with NDDs did not have greater numbers of facial morphological variants when compared to those with typical development, nor when controlling for shared genetic and environmental factors within twin pairs. Common facial morphological variants in those with and without NDDs were similar and included thick upper lip vermilion, abnormality of the nasal tip, long face, and upslanted palpebral fissure. We conclude that although facial morphological variants can be assessed reliably in NDDs with automated tools like Face2Gene, clinical utility is limited when just exploring the facial region. Therefore, currently, automated assessments may best complement, rather than replace, in-person clinical assessments.
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Affiliation(s)
- Lynnea Myers
- Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Centre for Psychiatry Research; Department of Women's and Children's Health, Karolinska Institutet, Stockholm Health Care Services, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Karl Lundin
- Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Centre for Psychiatry Research; Department of Women's and Children's Health, Karolinska Institutet, Stockholm Health Care Services, Stockholm, Sweden
| | - Ralf Kuja-Halkola
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Centre for Psychiatry Research; Department of Women's and Children's Health, Karolinska Institutet, Stockholm Health Care Services, Stockholm, Sweden
| | - Sven Bölte
- Center of Neurodevelopmental Disorders (KIND), Division of Neuropsychiatry, Centre for Psychiatry Research; Department of Women's and Children's Health, Karolinska Institutet, Stockholm Health Care Services, Stockholm, Sweden.,Child and Adolescent Psychiatry, Stockholm Health Care Services, Stockholm, Sweden.,Curtin Autism Research Group, School of Occupational Therapy, Social Work and Speech Pathology, Curtin University, Perth, Western Australia
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354
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Garcia-Giordano L, Paraiso-Medina S, Alonso-Calvo R, Fernández-Martínez FJ, Maojo V. genoDraw: A Web Tool for Developing Pedigree Diagrams Using the Standardized Human Pedigree Nomenclature Integrated with Biomedical Vocabularies. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2020; 2019:457-466. [PMID: 32308839 PMCID: PMC7153108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The integration of genetic information in current clinical routine has raised a need for tools to exploit family genetic knowledge. On the clinical side, an application for managing and visualizing pedigree diagrams could provide genetics specialists with an integrated environment with potential positive impact on their current practice. This article presents a web tool (genoDraw) that provides clinical practitioners with the ability to create, maintain and visualize patients' and their families' information in the form of pedigree diagrams. genoDraw implements a graph-based three-step process for generating diagrams according to a de facto standard in the area and clinical terminologies. It also complies with five characteristics identified as indispensable for the next-generation of pedigree drawing software: comprehensiveness, data-drivenness, automation, interactivity and compatibility with biomedical vocabularies. The platform was implemented and tested, confirming its potential interest to clinical routine.
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Affiliation(s)
- Luciano Garcia-Giordano
- Biomedical Informatics Group, DIA & DLSIIS, ETSI Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, Spain
| | - Sergio Paraiso-Medina
- Biomedical Informatics Group, DIA & DLSIIS, ETSI Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, Spain
| | - Raul Alonso-Calvo
- Biomedical Informatics Group, DIA & DLSIIS, ETSI Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, Spain
| | | | - Victor Maojo
- Biomedical Informatics Group, DIA & DLSIIS, ETSI Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, Spain
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355
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Bioinformatic framework for analysis of transcription factor changes as the molecular link between replicative cellular senescence signaling pathways and carcinogenesis. Biogerontology 2020; 21:357-366. [PMID: 32100207 DOI: 10.1007/s10522-020-09866-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/22/2020] [Indexed: 01/10/2023]
Abstract
Cellular senescence is a natural condition of irreversible cell cycle arrest and apoptotic resistance that occurs in cells exposed to various stress factors, such as replicative stress or overexpression of oncogenes. Unraveling the complex regulation of senescence in cells is essential to strengthen senescence-related therapeutic approaches in cancer, as cellular senescence plays a dual role in tumorigenesis, having both anti- and pro-tumorigenic effects. In our study we created a model of replicative cellular senescence, based on transcriptomic data, including an extra intermediate time-point prior to cells entering senescence, to elucidate the interplay of networks governing cellular senescence with networks involved in tumorigenesis. We reveal specific changes that occur in transcription factor activity at different timepoints before and after cells entering senescence and model the signaling networks that govern these changes.
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356
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Rahit KMTH, Tarailo-Graovac M. Genetic Modifiers and Rare Mendelian Disease. Genes (Basel) 2020; 11:E239. [PMID: 32106447 PMCID: PMC7140819 DOI: 10.3390/genes11030239] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022] Open
Abstract
Despite advances in high-throughput sequencing that have revolutionized the discovery of gene defects in rare Mendelian diseases, there are still gaps in translating individual genome variation to observed phenotypic outcomes. While we continue to improve genomics approaches to identify primary disease-causing variants, it is evident that no genetic variant acts alone. In other words, some other variants in the genome (genetic modifiers) may alleviate (suppress) or exacerbate (enhance) the severity of the disease, resulting in the variability of phenotypic outcomes. Thus, to truly understand the disease, we need to consider how the disease-causing variants interact with the rest of the genome in an individual. Here, we review the current state-of-the-field in the identification of genetic modifiers in rare Mendelian diseases and discuss the potential for future approaches that could bridge the existing gap.
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Affiliation(s)
- K. M. Tahsin Hassan Rahit
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
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357
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Pascual-Alonso A, Blasco L, Vidal S, Gean E, Rubio P, O'Callaghan M, Martínez-Monseny AF, Castells AA, Xiol C, Català V, Brandi N, Pacheco P, Ros C, Del Campo M, Guillén E, Ibañez S, Sánchez MJ, Lapunzina P, Nevado J, Santos F, Lloveras E, Ortigoza-Escobar JD, Tejada MI, Maortua H, Martínez F, Orellana C, Roselló M, Mesas MA, Obón M, Plaja A, Fernández-Ramos JA, Tizzano E, Marín R, Peña-Segura JL, Alcántara S, Armstrong J. Molecular characterization of Spanish patients with MECP2 duplication syndrome. Clin Genet 2020; 97:610-620. [PMID: 32043567 DOI: 10.1111/cge.13718] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022]
Abstract
MECP2 duplication syndrome (MDS) is an X-linked neurodevelopmental disorder characterized by a severe to profound intellectual disability, early onset hypotonia and diverse psycho-motor and behavioural features. To date, fewer than 200 cases have been published. We report the clinical and molecular characterization of a Spanish MDS cohort that included 19 boys and 2 girls. Clinical suspicions were confirmed by array comparative genomic hybridization and multiplex ligation-dependent probe amplification (MLPA). Using, a custom in-house MLPA assay, we performed a thorough study of the minimal duplicated region, from which we concluded a complete duplication of both MECP2 and IRAK1 was necessary for a correct MDS diagnosis, as patients with partial MECP2 duplications lacked some typical clinical traits present in other MDS patients. In addition, the duplication location may be related to phenotypic severity. This observation may provide a new approach for genotype-phenotype correlations, and thus more personalized genetic counselling.
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Affiliation(s)
- Ainhoa Pascual-Alonso
- Fundación San Juan de Dios, Servicio de Medicina Genética y Molecular, Barcelona, Spain
| | - Laura Blasco
- Fundación San Juan de Dios, Servicio de Medicina Genética y Molecular, Barcelona, Spain
| | - Silvia Vidal
- Fundación San Juan de Dios, Servicio de Medicina Genética y Molecular, Barcelona, Spain
| | - Esther Gean
- Departamento de Medicina Genética y Molecular, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - Patricia Rubio
- Departamento de Medicina Genética y Molecular, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - Mar O'Callaghan
- Departamento de Neurología Pediátrica, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - Antonio F Martínez-Monseny
- Departamento de Medicina Genética y Molecular, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - Alba Aina Castells
- Fundación San Juan de Dios, Servicio de Medicina Genética y Molecular, Barcelona, Spain.,Neural Development Lab, Departament de Patologia i Terapèutica Experimental, Institut de Neurociències, Universitat de Barcelona, IDIBELL, l'Hospitalet de Llobregat, Barcelona, Spain
| | - Clara Xiol
- Fundación San Juan de Dios, Servicio de Medicina Genética y Molecular, Barcelona, Spain
| | - Vicenç Català
- Unitad de Biología Celular y Genética Médica, Departament of BCFyI, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Nuria Brandi
- Servicio de Medicina Genètica i Molecular, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - Paola Pacheco
- Servicio de Medicina Genètica i Molecular, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - Carlota Ros
- Servicio de Medicina Genètica i Molecular, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - Miguel Del Campo
- Pediatrics, Genetic Epidemiology, Hospital Valle Hebrón, Barcelona, Spain
| | - Encarna Guillén
- Unidad de Genética, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - Salva Ibañez
- Unidad de Genética, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - María J Sánchez
- Unidad de Genética, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain.,CIBERER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III, Madrid, Spain
| | - Julián Nevado
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain.,CIBERER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Santos
- Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain
| | | | - Juan D Ortigoza-Escobar
- Departamento de Neurología Pediátrica, Hospital Universitario San Juan de Dios, Barcelona, Spain
| | - María I Tejada
- CIBERER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III, Madrid, Spain.,Laboratorio de Genética Molecular, Servicio de Genética, Instituto de Investigación Sanitaria Biocruces, Hospital Universitario de Cruces, Barakaldo, Spain
| | - Hiart Maortua
- CIBERER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III, Madrid, Spain.,Laboratorio de Genética Molecular, Servicio de Genética, Instituto de Investigación Sanitaria Biocruces, Hospital Universitario de Cruces, Barakaldo, Spain
| | - Francisco Martínez
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Carmen Orellana
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Mónica Roselló
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - María Obón
- Area de Genètica Clínica i Consell Genètic, Laboratoris ICS, Girona, Spain
| | - Alberto Plaja
- Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Eduardo Tizzano
- Area Genética Clínica y Molecular, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Rosario Marín
- Hospital Universitario Puerta del Mar Unidad de Genética, Cádiz, Spain
| | - José L Peña-Segura
- Unidad de Neuropediatría, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Soledad Alcántara
- Neural Development Lab, Departament de Patologia i Terapèutica Experimental, Institut de Neurociències, Universitat de Barcelona, IDIBELL, l'Hospitalet de Llobregat, Barcelona, Spain
| | - Judith Armstrong
- Servicio de Medicina Genètica i Molecular, Hospital Universitario San Juan de Dios, Barcelona, Spain.,CIBERER (Biomedical Network Research Center for Rare Diseases), Instituto de Salud Carlos III, Madrid, Spain.,Institut de Recerca Pediàtrica, Hospital Sant Joan de Déu, Barcelona, Spain
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358
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Kumar R, Palmer E, Gardner AE, Carroll R, Banka S, Abdelhadi O, Donnai D, Elgersma Y, Curry CJ, Gardham A, Suri M, Malla R, Brady LI, Tarnopolsky M, Azmanov DN, Atkinson V, Black M, Baynam G, Dreyer L, Hayeems RZ, Marshall CR, Costain G, Wessels MW, Baptista J, Drummond J, Leffler M, Field M, Gecz J. Expanding Clinical Presentations Due to Variations in THOC2 mRNA Nuclear Export Factor. Front Mol Neurosci 2020; 13:12. [PMID: 32116545 PMCID: PMC7026477 DOI: 10.3389/fnmol.2020.00012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/15/2020] [Indexed: 12/31/2022] Open
Abstract
Multiple TREX mRNA export complex subunits (e.g., THOC1, THOC2, THOC5, THOC6, THOC7) have now been implicated in neurodevelopmental disorders (NDDs), neurodegeneration and cancer. We previously implicated missense and splicing-defective THOC2 variants in NDDs and a broad range of other clinical features. Here we report 10 individuals from nine families with rare missense THOC2 variants including the first case of a recurrent variant (p.Arg77Cys), and an additional individual with an intragenic THOC2 microdeletion (Del-Ex37-38). Ex vivo missense variant testing and patient-derived cell line data from current and published studies show 9 of the 14 missense THOC2 variants result in reduced protein stability. The splicing-defective and deletion variants result in a loss of small regions of the C-terminal THOC2 RNA binding domain (RBD). Interestingly, reduced stability of THOC2 variant proteins has a flow-on effect on the stability of the multi-protein TREX complex; specifically on the other NDD-associated THOC subunits. Our current, expanded cohort refines the core phenotype of THOC2 NDDs to language disorder and/or ID, with a variable severity, and disorders of growth. A subset of affected individuals' has severe-profound ID, persistent hypotonia and respiratory abnormalities. Further investigations to elucidate the pathophysiological basis for this severe phenotype are warranted.
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Affiliation(s)
- Raman Kumar
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Elizabeth Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
- School of Women’s and Children’s Health, University of New South Wales, Randwick, NSW, Australia
| | - Alison E. Gardner
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Renee Carroll
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Siddharth Banka
- Faculty of Biology, Medicine and Health, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Ola Abdelhadi
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Dian Donnai
- Faculty of Biology, Medicine and Health, Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, United Kingdom
| | - Ype Elgersma
- Department of Neuroscience, Erasmus MC University Medical Center, Rotterdam, Netherlands
- ENCORE Expertise Centre for Neurodevelopmental Disorders, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Cynthia J. Curry
- Genetic Medicine, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States
| | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, United Kingdom
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, and the 100,000 Genomes Project and the Genomics England Research Consortium, Nottingham, United Kingdom
| | - Rishikesh Malla
- Division of Pediatric Neurology, Medical University of South Carolina, Charleston, SC, United States
| | - Lauren Ilana Brady
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, ON, Canada
| | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, ON, Canada
| | - Dimitar N. Azmanov
- Department of Diagnostic Genomics, PathWest, Nedlands, WA, Australia
- Division of Pathology and Laboratory Medicine, Medical School, University of Western Australia, Crawley, WA, Australia
| | - Vanessa Atkinson
- Department of Diagnostic Genomics, PathWest, Nedlands, WA, Australia
- Division of Pathology and Laboratory Medicine, Medical School, University of Western Australia, Crawley, WA, Australia
| | - Michael Black
- Department of Diagnostic Genomics, PathWest, Nedlands, WA, Australia
- Division of Pathology and Laboratory Medicine, Medical School, University of Western Australia, Crawley, WA, Australia
| | - Gareth Baynam
- Faculty of Health and Medical Sciences, University of Western Australia Medical School, Perth, WA, Australia
| | - Lauren Dreyer
- Genetic Services of Western Australia, Undiagnosed Diseases Program, Department of Health, Government of Western Australia, Perth, WA, Australia
- Linear Clinical Research, Perth, WA, Australia
| | - Robin Z. Hayeems
- Child Health Evaluative Sciences, Research Institute, The Hospital for Sick Children, and Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Christian R. Marshall
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marja W. Wessels
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Julia Baptista
- Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - James Drummond
- Neuroradiology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
- Childhood Disability Prevention, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
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359
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Carmody LC, Blau H, Danis D, Zhang XA, Gourdine JP, Vasilevsky N, Krawitz P, Thompson MD, Robinson PN. Significantly different clinical phenotypes associated with mutations in synthesis and transamidase+remodeling glycosylphosphatidylinositol (GPI)-anchor biosynthesis genes. Orphanet J Rare Dis 2020; 15:40. [PMID: 32019583 PMCID: PMC7001271 DOI: 10.1186/s13023-020-1313-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Defects in the glycosylphosphatidylinositol (GPI) biosynthesis pathway can result in a group of congenital disorders of glycosylation known as the inherited GPI deficiencies (IGDs). To date, defects in 22 of the 29 genes in the GPI biosynthesis pathway have been identified in IGDs. The early phase of the biosynthetic pathway assembles the GPI anchor (Synthesis stage) and the late phase transfers the GPI anchor to a nascent peptide in the endoplasmic reticulum (ER) (Transamidase stage), stabilizes the anchor in the ER membrane using fatty acid remodeling and then traffics the GPI-anchored protein to the cell surface (Remodeling stage). RESULTS We addressed the hypothesis that disease-associated variants in either the Synthesis stage or Transamidase+Remodeling-stage GPI pathway genes have distinct phenotypic spectra. We reviewed clinical data from 58 publications describing 152 individual patients and encoded the phenotypic information using the Human Phenotype Ontology (HPO). We showed statistically significant differences between the Synthesis and Transamidase+Remodeling Groups in the frequencies of phenotypes in the musculoskeletal system, cleft palate, nose phenotypes, and cognitive disability. Finally, we hypothesized that phenotypic defects in the IGDs are likely to be at least partially related to defective GPI anchoring of their target proteins. Twenty-two of one hundred forty-two proteins that receive a GPI anchor are associated with one or more Mendelian diseases and 12 show some phenotypic overlap with the IGDs, represented by 34 HPO terms. Interestingly, GPC3 and GPC6, members of the glypican family of heparan sulfate proteoglycans bound to the plasma membrane through a covalent GPI linkage, are associated with 25 of these phenotypic abnormalities. CONCLUSIONS IGDs associated with Synthesis and Transamidase+Remodeling stages of the GPI biosynthesis pathway have significantly different phenotypic spectra. GPC2 and GPC6 genes may represent a GPI target of general disruption to the GPI biosynthesis pathway that contributes to the phenotypes of some IGDs.
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Affiliation(s)
- Leigh C Carmody
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Hannah Blau
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Xingman A Zhang
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | | | | | - Peter Krawitz
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Miles D Thompson
- Department of Pediatrics, UCSD School of Medicine, La Jolla, CA, 92093, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA.
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Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes. Int J Mol Sci 2020; 21:ijms21031042. [PMID: 32033219 PMCID: PMC7038094 DOI: 10.3390/ijms21031042] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/01/2020] [Accepted: 02/02/2020] [Indexed: 12/19/2022] Open
Abstract
Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS.
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Affiliation(s)
- Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Ángela Ascaso
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Laura Trujillano
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Marta Gil-Salvador
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Maria Arnedo
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Cristina Lucia-Campos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Rebeca Antoñanzas-Pérez
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), E-28049 Madrid, Spain;
- Bioscience Research Institute, School of Experimental Sciences, Universidad Francisco de Vitoria, UFV, E-28223 Pozuelo de Alarcón, Spain
| | - Ilaria Parenti
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany; (I.P.); (F.J.K.)
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Gloria Bueno-Lozano
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, I-56124 Pisa, Italy;
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Frank J. Kaiser
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany; (I.P.); (F.J.K.)
- Institute for Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Feliciano J. Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), E-28049 Madrid, Spain;
- Correspondence: (J.P.); (P.G.-P.); Tel.: +34-976-761677 (J.P.); +34-91-1964663 (P.G.-P.)
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
- Correspondence: (J.P.); (P.G.-P.); Tel.: +34-976-761677 (J.P.); +34-91-1964663 (P.G.-P.)
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Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D. Human and mouse essentiality screens as a resource for disease gene discovery. Nat Commun 2020; 11:655. [PMID: 32005800 PMCID: PMC6994715 DOI: 10.1038/s41467-020-14284-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.
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Grants
- UM1 HG008900 NHGRI NIH HHS
- UM1 HG006504 NHGRI NIH HHS
- MC_UP_1502/1 Medical Research Council
- UM1 HG006542 NHGRI NIH HHS
- UM1 OD023221 NIH HHS
- MC_U142684171 Medical Research Council
- MR/S006753/1 Medical Research Council
- UM1 HG006370 NHGRI NIH HHS
- UM1 HG006493 NHGRI NIH HHS
- U54 HG006370 NHGRI NIH HHS
- U54 HG006364 NHGRI NIH HHS
- MC_U142684172 Medical Research Council
- UM1 HG006348 NHGRI NIH HHS
- U42 OD011174 NIH HHS
- U42 OD011175 NIH HHS
- Wellcome Trust
- This work was supported by NIH grant U54 HG006370. IMPC-related mouse production and phenotyping was funded by the Government of Canada through Genome Canada and Ontario Genomics (OGI-051) for NorCOMM2 (C.M.) and the National Institutes of Health and OD, NCRR, NIDDK and NHLBI for KOMP and KOMP2 Projects U42 OD011175 and UM1OD023221 (C.M., K.C.K.L), Infrafrontier grant 01KX1012, EU Horizon2020: IPAD-MD funding 653961 (M.H.d.A); EUCOMM: LSHM-CT-2005-018931, EUCOMMTOOLS: FP7-HEALTH-F4-2010-261492 (W.G.W). UM1 HG006348; U42 OD011174; U54 HG005348 (A.L.B), NIH U54706HG006364 (A.L.B). Wellcome Trust grants WT098051 and WT206194 (D.A). The French National Centre for Scientific Research (CNRS), the French National Institute of Health and Medical Research (INSERM), the University of Strasbourg and the “Centre Europeen de Recherche en Biomedecine”, and the French state funds through the “Agence Nationale de la Recherche” under the frame programme Investissements d’Avenir labelled (ANR-10-IDEX-0002-02, ANR-10-LABX-0030-INRT, ANR-10-INBS-07 PHENOMIN (J.H.). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. We are also grateful for the data access provided by the DDD and CMG projects. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. The Centers for Mendelian Genomics are funded by the National Human Genome Research Institute, the National Heart, Lung, and Blood Institute, and the National Eye Institute. Broad Institute (UM1 HG008900), Johns Hopkins University School of Medicine/Baylor College of Medicine (UM1 HG006542), University of Washington (UM1 HG006493), Yale University (UM1 HG006504).
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Affiliation(s)
- Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Mary E Dickinson
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | | | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ann M Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tomasz Konopka
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Chih-Wei Hsu
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Audrey Christiansen
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Denise G Lanza
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404, Illkirch, France
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tertius Hough
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
- Department of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85764, Neuherberg, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336, Munich, Germany
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John R Seavitt
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | | | - Colin McKerlie
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404, Illkirch, France
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA, 95618, USA
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
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362
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Konopka T, Smedley D. Incremental data integration for tracking genotype-disease associations. PLoS Comput Biol 2020; 16:e1007586. [PMID: 31986132 PMCID: PMC7004389 DOI: 10.1371/journal.pcbi.1007586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/06/2020] [Accepted: 12/03/2019] [Indexed: 12/30/2022] Open
Abstract
Functional annotation of genes remains a challenge in fundamental biology and is a limiting factor for translational medicine. Computational approaches have been developed to process heterogeneous data into meaningful metrics, but often do not address how findings might be updated when new evidence comes to light. To address this challenge, we describe requirements for a framework for incremental data integration and propose an implementation based on phenotype ontologies and Bayesian probability updates. We apply the framework to quantify similarities between gene annotations and disease profiles. Within this scope, we categorize human diseases according to how well they can be recapitulated by animal models and quantify similarities between human diseases and mouse models produced by the International Mouse Phenotyping Consortium. The flexibility of the approach allows us to incorporate negative phenotypic data to better prioritize candidate genes, and to stratify disease mapping using sex-dependent phenotypes. All our association scores can be updated and we exploit this feature to showcase integration with curated annotations from high-precision assays. Incremental integration is thus a suitable framework for tracking functional annotations and linking to complex human pathology. Human diseases are often caused or influenced by genetic factors. The link between a particular gene and a specific disease is well-established in some cases. However, the roles of many genes are still unclear and many diseases do not have an understood genetic mechanism. Dissecting such interactions requires using a range of experimental approaches and assessing the results in a holistic manner. Computational methods already exist for comparing phenotypes observed in models and patients, and they work well when the phenotypes are detailed. In this work we argue that algorithms should also be able to report meaningful assessments based on preliminary data, and to update reports in a coherent manner when new information comes to light. These requirements lead to specific mathematical properties, which define incremental integration. We implement these requirements in a computational framework. We study the extent individual rare human diseases might be recapitulated by animal models. We compute gene-disease associations using data from public resources, including previously unused negative data. Altogether, these examples illustrate the framework can use observations in model systems to track gene-disease associations in the human context.
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Affiliation(s)
- Tomasz Konopka
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- * E-mail: (TK); (DS)
| | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London, United Kingdom
- * E-mail: (TK); (DS)
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Kasak L, Laan M. Monogenic causes of non-obstructive azoospermia: challenges, established knowledge, limitations and perspectives. Hum Genet 2020; 140:135-154. [DOI: 10.1007/s00439-020-02112-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/05/2020] [Indexed: 02/07/2023]
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364
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Levine AP, Chan MMY, Sadeghi-Alavijeh O, Wong EKS, Cook HT, Ashford S, Carss K, Christian MT, Hall M, Harris CL, McAlinden P, Marchbank KJ, Marks SD, Maxwell H, Megy K, Penkett CJ, Mozere M, Stirrups KE, Tuna S, Wessels J, Whitehorn D, Johnson SA, Gale DP. Large-Scale Whole-Genome Sequencing Reveals the Genetic Architecture of Primary Membranoproliferative GN and C3 Glomerulopathy. J Am Soc Nephrol 2020; 31:365-373. [PMID: 31919107 DOI: 10.1681/asn.2019040433] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/03/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Primary membranoproliferative GN, including complement 3 (C3) glomerulopathy, is a rare, untreatable kidney disease characterized by glomerular complement deposition. Complement gene mutations can cause familial C3 glomerulopathy, and studies have reported rare variants in complement genes in nonfamilial primary membranoproliferative GN. METHODS We analyzed whole-genome sequence data from 165 primary membranoproliferative GN cases and 10,250 individuals without the condition (controls) as part of the National Institutes of Health Research BioResource-Rare Diseases Study. We examined copy number, rare, and common variants. RESULTS Our analysis included 146 primary membranoproliferative GN cases and 6442 controls who were unrelated and of European ancestry. We observed no significant enrichment of rare variants in candidate genes (genes encoding components of the complement alternative pathway and other genes associated with the related disease atypical hemolytic uremic syndrome; 6.8% in cases versus 5.9% in controls) or exome-wide. However, a significant common variant locus was identified at 6p21.32 (rs35406322) (P=3.29×10-8; odds ratio [OR], 1.93; 95% confidence interval [95% CI], 1.53 to 2.44), overlapping the HLA locus. Imputation of HLA types mapped this signal to a haplotype incorporating DQA1*05:01, DQB1*02:01, and DRB1*03:01 (P=1.21×10-8; OR, 2.19; 95% CI, 1.66 to 2.89). This finding was replicated by analysis of HLA serotypes in 338 individuals with membranoproliferative GN and 15,614 individuals with nonimmune renal failure. CONCLUSIONS We found that HLA type, but not rare complement gene variation, is associated with primary membranoproliferative GN. These findings challenge the paradigm of complement gene mutations typically causing primary membranoproliferative GN and implicate an underlying autoimmune mechanism in most cases.
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Affiliation(s)
- Adam P Levine
- Department of Renal Medicine, University College London, London, United Kingdom
| | - Melanie M Y Chan
- Department of Renal Medicine, University College London, London, United Kingdom
| | | | - Edwin K S Wong
- Renal Department, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.,Faculty of Medical Sciences, Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.,The National Renal Complement Therapeutics Centre, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - H Terence Cook
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, London, United Kingdom
| | - Sofie Ashford
- National Institute of Health Research BioResource, Cambridge University Hospitals, Cambridge, United Kingdom
| | - Keren Carss
- National Institute of Health Research BioResource, Cambridge University Hospitals, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Martin T Christian
- Children's Renal and Urology Unit, Nottingham Children's Hospital, Queen's Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Matthew Hall
- Department of Nephrology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Claire Louise Harris
- Faculty of Medical Sciences, Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paul McAlinden
- Renal Department, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Kevin J Marchbank
- Faculty of Medical Sciences, Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.,The National Renal Complement Therapeutics Centre, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Stephen D Marks
- Department of Paediatric Nephrology, Great Ormond Street Hospital and University College London Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre, London, United Kingdom
| | - Heather Maxwell
- Department of Paediatric Nephrology, Royal Hospital for Children, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Karyn Megy
- National Institute of Health Research BioResource, Cambridge University Hospitals, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Christopher J Penkett
- National Institute of Health Research BioResource, Cambridge University Hospitals, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Monika Mozere
- Department of Renal Medicine, University College London, London, United Kingdom
| | - Kathleen E Stirrups
- National Institute of Health Research BioResource, Cambridge University Hospitals, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Salih Tuna
- National Institute of Health Research BioResource, Cambridge University Hospitals, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Julie Wessels
- Renal Department, University Hospitals of North Midlands NHS Trust, Stoke-on-Trent, United Kingdom
| | - Deborah Whitehorn
- National Institute of Health Research BioResource, Cambridge University Hospitals, Cambridge, United Kingdom.,Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Sally A Johnson
- Faculty of Medical Sciences, Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.,The National Renal Complement Therapeutics Centre, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom.,Department of Paediatric Nephrology, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; and
| | - Daniel P Gale
- Department of Renal Medicine, University College London, London, United Kingdom;
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365
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Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J, Zaugg JB. Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. Nat Commun 2020; 11:124. [PMID: 31913281 PMCID: PMC6949242 DOI: 10.1038/s41467-019-13888-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/28/2019] [Indexed: 11/25/2022] Open
Abstract
Recent high-throughput transcription factor (TF) binding assays revealed that TF cooperativity is a widespread phenomenon. However, a global mechanistic and functional understanding of TF cooperativity is still lacking. To address this, here we introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data. We identify DNA shape as driver for cooperativity, with a particularly strong effect for Forkhead-Ets pairs. Follow-up experiments reveal a local shape preference at the Ets-DNA-Forkhead interface and decreased cooperativity upon loss of the interaction. Additionally, we discover many functional associations for cooperatively bound TFs. Examination of the link between FOXO1:ETV6 and lymphomas reveals that their joint expression levels improve patient clinical outcome stratification. Altogether, our results demonstrate that inter-family cooperative TF binding is driven by position-specific DNA readout mechanisms, which provides an additional regulatory layer for downstream biological functions. Although transcription factor (TF) cooperativity is widespread, a global mechanistic understanding of the role of TF cooperativity is still lacking. Here the authors introduce a statistical learning framework that provides structural insight into TF cooperativity and its functional consequences based on next generation sequencing data and provide mechanistic insights into TF cooperativity and its impact on protein-phenotype interactions.
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Affiliation(s)
- Ignacio L Ibarra
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Nele M Hollmann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Bernd Klaus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sandra Augsten
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Britta Velten
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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366
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Beck T, Shorter T, Brookes AJ. GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies. Nucleic Acids Res 2020; 48:D933-D940. [PMID: 31612961 PMCID: PMC7145571 DOI: 10.1093/nar/gkz895] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/31/2022] Open
Abstract
The GWAS Central resource provides a toolkit for integrative access and visualization of a uniquely extensive collection of genome-wide association study data, while ensuring safe open access to prevent research participant identification. GWAS Central is the world's most comprehensive openly accessible repository of summary-level GWAS association information, providing over 70 million P-values for over 3800 studies investigating over 1400 unique phenotypes. The database content comprises direct submissions received from GWAS authors and consortia, in addition to actively gathered data sets from various public sources. GWAS data are discoverable from the perspective of genetic markers, genes, genome regions or phenotypes, via graphical visualizations and detailed downloadable data reports. Tested genetic markers and relevant genomic features can be visually interrogated across up to sixteen multiple association data sets in a single view using the integrated genome browser. The semantic standardization of phenotype descriptions with Medical Subject Headings and the Human Phenotype Ontology allows the precise identification of genetic variants associated with diseases, phenotypes and traits of interest. Harmonization of the phenotype descriptions used across several GWAS-related resources has extended the phenotype search capabilities to enable cross-database study discovery using a range of ontologies. GWAS Central is updated regularly and available at https://www.gwascentral.org.
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Affiliation(s)
- Tim Beck
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Health Data Research UK, University of Leicester, Leicester LE1 7RH, UK
| | - Tom Shorter
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Health Data Research UK, University of Leicester, Leicester LE1 7RH, UK
| | - Anthony J Brookes
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Health Data Research UK, University of Leicester, Leicester LE1 7RH, UK
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367
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Harris TW, Arnaboldi V, Cain S, Chan J, Chen WJ, Cho J, Davis P, Gao S, Grove CA, Kishore R, Lee RYN, Muller HM, Nakamura C, Nuin P, Paulini M, Raciti D, Rodgers FH, Russell M, Schindelman G, Auken KV, Wang Q, Williams G, Wright AJ, Yook K, Howe KL, Schedl T, Stein L, Sternberg PW. WormBase: a modern Model Organism Information Resource. Nucleic Acids Res 2020; 48:D762-D767. [PMID: 31642470 PMCID: PMC7145598 DOI: 10.1093/nar/gkz920] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 01/16/2023] Open
Abstract
WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.
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Affiliation(s)
- Todd W Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sibyl Gao
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Christian A Grove
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Raymond Y N Lee
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cecilia Nakamura
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Faye H Rodgers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Matthew Russell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gary Schindelman
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kimberly V Auken
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qinghua Wang
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gary Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam J Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering 156–29, California Institute of Technology, Pasadena, CA 91125, USA
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Mubungu G, Lumaka A, Mvuama N, Tshika D, Makay P, Tshilobo PL, Devriendt K. Morphological characterization of newborns in Kinshasa, DR Congo: Common variants, minor, and major anomalies. Am J Med Genet A 2020; 182:632-639. [DOI: 10.1002/ajmg.a.61477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/28/2019] [Accepted: 12/16/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Gerrye Mubungu
- Faculty of Medicine, Centre for Human GeneticsUniversity of Kinshasa Kinshasa DR Congo
- Faculty of Medicine, Department of PediatricsUniversity of Kinshasa Kinshasa DR Congo
- Centre for Human Genetics, University HospitalsUniversity of Leuven Leuven Belgium
| | - Aimé Lumaka
- Faculty of Medicine, Centre for Human GeneticsUniversity of Kinshasa Kinshasa DR Congo
- Faculty of Medicine, Department of PediatricsUniversity of Kinshasa Kinshasa DR Congo
- Département des Sciences Biomédicales et Précliniques, GIGA‐R, Laboratoire de Génétique HumaineUniversity of Liège Liège Belgium
- Institut National de Recherche Biomédicale Kinshasa DR Congo
| | - Nono Mvuama
- Department of Health EnvironmentKinshasa School of Public Health Kinshasa DR Congo
| | - Dahlie Tshika
- Faculty of Medicine, Centre for Human GeneticsUniversity of Kinshasa Kinshasa DR Congo
- Faculty of Medicine, Department of PediatricsUniversity of Kinshasa Kinshasa DR Congo
| | - Prince Makay
- Faculty of Medicine, Centre for Human GeneticsUniversity of Kinshasa Kinshasa DR Congo
- Faculty of Medicine, Department of PediatricsUniversity of Kinshasa Kinshasa DR Congo
| | - Prosper Lukusa Tshilobo
- Faculty of Medicine, Centre for Human GeneticsUniversity of Kinshasa Kinshasa DR Congo
- Faculty of Medicine, Department of PediatricsUniversity of Kinshasa Kinshasa DR Congo
- Centre for Human Genetics, University HospitalsUniversity of Leuven Leuven Belgium
- Institut National de Recherche Biomédicale Kinshasa DR Congo
| | - Koenraad Devriendt
- Centre for Human Genetics, University HospitalsUniversity of Leuven Leuven Belgium
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369
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Cardoso C, Sousa RT, Köhler S, Pesquita C. A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain. Database (Oxford) 2020; 2020:baaa078. [PMID: 33181823 PMCID: PMC7661097 DOI: 10.1093/database/baaa078] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/13/2020] [Accepted: 08/24/2020] [Indexed: 01/12/2023]
Abstract
The ability to compare entities within a knowledge graph is a cornerstone technique for several applications, ranging from the integration of heterogeneous data to machine learning. It is of particular importance in the biomedical domain, where semantic similarity can be applied to the prediction of protein-protein interactions, associations between diseases and genes, cellular localization of proteins, among others. In recent years, several knowledge graph-based semantic similarity measures have been developed, but building a gold standard data set to support their evaluation is non-trivial. We present a collection of 21 benchmark data sets that aim at circumventing the difficulties in building benchmarks for large biomedical knowledge graphs by exploiting proxies for biomedical entity similarity. These data sets include data from two successful biomedical ontologies, Gene Ontology and Human Phenotype Ontology, and explore proxy similarities calculated based on protein sequence similarity, protein family similarity, protein-protein interactions and phenotype-based gene similarity. Data sets have varying sizes and cover four different species at different levels of annotation completion. For each data set, we also provide semantic similarity computations with state-of-the-art representative measures. Database URL: https://github.com/liseda-lab/kgsim-benchmark.
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Affiliation(s)
- Carlota Cardoso
- Departamento de informática, LASIGE Faculdade de Ciências da Universidade de Lisboa, 1749 - 016 Lisboa, Portugal
| | - Rita T Sousa
- Departamento de informática, LASIGE Faculdade de Ciências da Universidade de Lisboa, 1749 - 016 Lisboa, Portugal
| | | | - Catia Pesquita
- Departamento de informática, LASIGE Faculdade de Ciências da Universidade de Lisboa, 1749 - 016 Lisboa, Portugal
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370
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Méjécase C, Malka S, Guan Z, Slater A, Arno G, Moosajee M. Practical guide to genetic screening for inherited eye diseases. Ther Adv Ophthalmol 2020; 12:2515841420954592. [PMID: 33015543 PMCID: PMC7513416 DOI: 10.1177/2515841420954592] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/29/2020] [Indexed: 12/16/2022] Open
Abstract
Genetic eye diseases affect around one in 1000 people worldwide for which the molecular aetiology remains unknown in the majority. The identification of disease-causing gene variant(s) allows a better understanding of the disorder and its inheritance. There is now an approved retinal gene therapy for autosomal recessive RPE65-retinopathy, and numerous ocular gene/mutation-targeted clinical trials underway, highlighting the importance of establishing a genetic diagnosis so patients can fully access the latest research developments and treatment options. In this review, we will provide a practical guide to managing patients with these conditions including an overview of inheritance patterns, required pre- and post-test genetic counselling, different types of cytogenetic and genetic testing available, with a focus on next generation sequencing using targeted gene panels, whole exome and genome sequencing. We will expand on the pros and cons of each modality, variant interpretation and options for family planning for the patient and their family. With the advent of genomic medicine, genetic screening will soon become mainstream within all ophthalmology subspecialties for prevention of disease and provision of precision therapeutics.
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Affiliation(s)
- Cécile Méjécase
- Institute of Ophthalmology, University College
London, London, UK
| | - Samantha Malka
- Institute of Ophthalmology, University College
London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
| | - Zeyu Guan
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
| | - Amy Slater
- Royal Brompton and Harefield NHS Foundation
Trust, London, UK
| | - Gavin Arno
- Institute of Ophthalmology, University College
London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Trust, London, UK
| | - Mariya Moosajee
- Professor, Institute of Ophthalmology,
University College London, 11-43 Bath Street, London EC1V 9EL, UK
- Moorfields Eye Hospital NHS Foundation Trust,
London, UK
- Great Ormond Street Hospital for Children NHS
Trust, London, UK
- The Francis Crick Institute, London, UK
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371
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Singh V, Kalliolias GD, Ostaszewski M, Veyssiere M, Pilalis E, Gawron P, Mazein A, Bonnet E, Petit-Teixeira E, Niarakis A. RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database (Oxford) 2020; 2020:baaa017. [PMID: 32311035 PMCID: PMC7170216 DOI: 10.1093/database/baaa017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/21/2020] [Accepted: 02/13/2020] [Indexed: 02/07/2023]
Abstract
Rheumatoid arthritis (RA) is a progressive, inflammatory autoimmune disease of unknown aetiology. The complex mechanism of aetiopathogenesis, progress and chronicity of the disease involves genetic, epigenetic and environmental factors. To understand the molecular mechanisms underlying disease phenotypes, one has to place implicated factors in their functional context. However, integration and organization of such data in a systematic manner remains a challenging task. Molecular maps are widely used in biology to provide a useful and intuitive way of depicting a variety of biological processes and disease mechanisms. Recent large-scale collaborative efforts such as the Disease Maps Project demonstrate the utility of such maps as versatile tools to organize and formalize disease-specific knowledge in a comprehensive way, both human and machine-readable. We present a systematic effort to construct a fully annotated, expert validated, state-of-the-art knowledge base for RA in the form of a molecular map. The RA map illustrates molecular and signalling pathways implicated in the disease. Signal transduction is depicted from receptors to the nucleus using the Systems Biology Graphical Notation (SBGN) standard representation. High-quality manual curation, use of only human-specific studies and focus on small-scale experiments aim to limit false positives in the map. The state-of-the-art molecular map for RA, using information from 353 peer-reviewed scientific publications, comprises 506 species, 446 reactions and 8 phenotypes. The species in the map are classified to 303 proteins, 61 complexes, 106 genes, 106 RNA entities, 2 ions and 7 simple molecules. The RA map is available online at ramap.elixir-luxembourg.org as an open-access knowledge base allowing for easy navigation and search of molecular pathways implicated in the disease. Furthermore, the RA map can serve as a template for omics data visualization.
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Affiliation(s)
- Vidisha Singh
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
| | - George D Kalliolias
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021, USA
- Weill Cornell Medical Center, Weill Department of Medicine, 525 East 68th Street, New York, NY 10065, USA
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Maëva Veyssiere
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
| | - Eleftherios Pilalis
- eNIOS Applications P.C., R&D department, Alexandrou Pantou 25, 17671, Kallithea-Athens, Greece
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Eric Bonnet
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, 2 rue Gaston Crémieux, CP5706 91057 EVRY-GENOPOLE cedex, Evry, France
| | - Elisabeth Petit-Teixeira
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
| | - Anna Niarakis
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
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372
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Dahary D, Golan Y, Mazor Y, Zelig O, Barshir R, Twik M, Iny Stein T, Rosner G, Kariv R, Chen F, Zhang Q, Shen Y, Safran M, Lancet D, Fishilevich S. Genome analysis and knowledge-driven variant interpretation with TGex. BMC Med Genomics 2019; 12:200. [PMID: 31888639 PMCID: PMC6937949 DOI: 10.1186/s12920-019-0647-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/15/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The clinical genetics revolution ushers in great opportunities, accompanied by significant challenges. The fundamental mission in clinical genetics is to analyze genomes, and to identify the most relevant genetic variations underlying a patient's phenotypes and symptoms. The adoption of Whole Genome Sequencing requires novel capacities for interpretation of non-coding variants. RESULTS We present TGex, the Translational Genomics expert, a novel genome variation analysis and interpretation platform, with remarkable exome analysis capacities and a pioneering approach of non-coding variants interpretation. TGex's main strength is combining state-of-the-art variant filtering with knowledge-driven analysis made possible by VarElect, our highly effective gene-phenotype interpretation tool. VarElect leverages the widely used GeneCards knowledgebase, which integrates information from > 150 automatically-mined data sources. Access to such a comprehensive data compendium also facilitates TGex's broad variant annotation, supporting evidence exploration, and decision making. TGex has an interactive, user-friendly, and easy adaptive interface, ACMG compliance, and an automated reporting system. Beyond comprehensive whole exome sequence capabilities, TGex encompasses innovative non-coding variants interpretation, towards the goal of maximal exploitation of whole genome sequence analyses in the clinical genetics practice. This is enabled by GeneCards' recently developed GeneHancer, a novel integrative and fully annotated database of human enhancers and promoters. Examining use-cases from a variety of TGex users world-wide, we demonstrate its high diagnostic yields (42% for single exome and 50% for trios in 1500 rare genetic disease cases) and critical actionable genetic findings. The platform's support for integration with EHR and LIMS through dedicated APIs facilitates automated retrieval of patient data for TGex's customizable reporting engine, establishing a rapid and cost-effective workflow for an entire range of clinical genetic testing, including rare disorders, cancer predisposition, tumor biopsies and health screening. CONCLUSIONS TGex is an innovative tool for the annotation, analysis and prioritization of coding and non-coding genomic variants. It provides access to an extensive knowledgebase of genomic annotations, with intuitive and flexible configuration options, allows quick adaptation, and addresses various workflow requirements. It thus simplifies and accelerates variant interpretation in clinical genetics workflows, with remarkable diagnostic yield, as exemplified in the described use cases. TGex is available at http://tgex.genecards.org/.
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Affiliation(s)
- Dvir Dahary
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA.
| | - Yaron Golan
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Yaron Mazor
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Ofer Zelig
- Clinical Genetics, LifeMap Sciences Inc., Marshfield, MA, 02050, USA
| | - Ruth Barshir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Guy Rosner
- Department of Gastroenterology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Revital Kariv
- Department of Gastroenterology, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Qiang Zhang
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Birth Defect Prevention Research Institute, Maternal and Child Health Hospital, Children's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530002, China.,Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.,Department of Neurology, Harvard Medical School, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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373
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Pfeffer TJ, Schlothauer S, Pietzsch S, Schaufelberger M, Auber B, Ricke-Hoch M, List M, Berliner D, Abou Moulig V, König T, Arany Z, Sliwa K, Bauersachs J, Hilfiker-Kleiner D. Increased Cancer Prevalence in Peripartum Cardiomyopathy. JACC: CARDIOONCOLOGY 2019; 1:196-205. [PMID: 34396183 PMCID: PMC8352111 DOI: 10.1016/j.jaccao.2019.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
Objectives This study was designed to analyze the prevalence and potential genetic basis of cancer and heart failure in peripartum cardiomyopathy (PPCM). Background PPCM manifests as heart failure late in pregnancy or postpartum in women without previous heart disease. Methods Clinical history and cancer prevalence were evaluated in a cohort of 236 PPCM patients from Germany and Sweden. Exome sequencing assessed variants in 133 genes associated with cancer predisposition syndromes (CPS) and in 115 genes associated with dilated/hypertrophic cardiomyopathy (DCM/HCM) in 14 PPCM patients with a history of cancer, and in 6 PPCM patients without a history of cancer. Results The prevalence of cancer was 16-fold higher (8.9%, 21 of 236 patients) in PPCM patients compared to age-matched women (German cancer registry, Robert-Koch-Institute: 0.59%; p < 0.001). Cancer before PPCM occurred in 12 of 21 patients of whom 11 obtained cardiotoxic cancer therapies. Of those, 17% fully recovered cardiac function by 7 ± 2 months of follow-up compared to 55% of PPCM patients without cancer (p = 0.015). Cancer occurred after PPCM in 10 of 21 patients; 80% had left ventricular ejection fraction of ≥50% after cancer therapy. Whole-exome sequencing in 14 PPCM patients with cancer revealed that 43% (6 of 14 patients) carried likely pathogenic (Class IV) or pathogenic (Class V) gene variants associated with DCM/HCM in CPT2, DSP, MYH7, TTN, and/or with CPS in ATM, ERCC5, NBN, RECQL4, and SLX4. All CPS variants affected DNA damage response genes. Conclusions Cardiotoxic cancer therapy before PPCM is associated with delayed full recovery. The high cancer prevalence in PPCM is linked to likely pathogenic/pathogenic gene variants associated with DCM/HCM and/or CPS/DNA damage response-related cancer risk. This may warrant genetic testing and screening for heart failure in pregnant women with a cancer history and screening for cancer in PPCM patients.
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Key Words
- ATM, ataxia telangiectasia mutated
- BMBF, Bundesministerium für Bildung und Forschung
- BRCA1, breast cancer 1
- CPS, cancer predisposition syndrome
- DCM, dilated cardiomyopathy
- DDR, DNA damage response
- DFG, Deutsche Forschungsgesellschaft
- ERCC5, excision repair cross-complementing rodent repair deficiency
- FANCA, Fanconi anemia, complementation group
- FKRP, fukutin-related protein
- HCM, hypertrophic cardiomyopathy
- HTX, heart transplantation
- LVAD, left ventricular assist device
- LVEF, left ventricular ejection fraction
- PPCM, peripartum cardiomyopathy
- RECQL4, ATP-dependent DNA helicase Q4
- RYR1, ryanodine receptor 1
- SLX4, structure-specific endonuclease subunit SLX4
- TXNRD2, thioredoxin reductase 2
- VUS, variants of unknown significance
- cancer
- cardiotoxicity
- genetics
- peripartum cardiomyopathy
- whole-exome sequencing
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Affiliation(s)
- Tobias J Pfeffer
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Stella Schlothauer
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Stefan Pietzsch
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Maria Schaufelberger
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Melanie Ricke-Hoch
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Manuel List
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Dominik Berliner
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Valeska Abou Moulig
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Tobias König
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Zolt Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karen Sliwa
- Hatter Institute for Cardiovascular Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Johann Bauersachs
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
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374
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Middelkamp S, Vlaar JM, Giltay J, Korzelius J, Besselink N, Boymans S, Janssen R, de la Fonteijne L, van Binsbergen E, van Roosmalen MJ, Hochstenbach R, Giachino D, Talkowski ME, Kloosterman WP, Cuppen E. Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants. Genome Med 2019; 11:79. [PMID: 31801603 PMCID: PMC6894143 DOI: 10.1186/s13073-019-0692-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown. METHODS We applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with multiple congenital abnormalities and/or intellectual disability harboring apparent de novo SVs, most with an inconclusive diagnosis after regular genetic testing. RESULTS In 7 of these cases (18%), whole-genome sequencing analysis revealed disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict the effects on genes directly affected by SVs and on genes indirectly affected likely due to the changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In 8 cases, evidence was found for the involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to two cohorts containing a total of 379 patients with previously detected and classified de novo SVs and identified candidate driver genes in 189 cases (50%), including 40 cases whose SVs were previously not classified as pathogenic. Pathogenic position effects were predicted in 28% of all studied cases with balanced SVs and in 11% of the cases with copy number variants. CONCLUSIONS These results demonstrate an integrated computational and experimental approach to predict driver genes based on analyses of WGS data with phenotype association and chromatin organization datasets. These analyses nominate new pathogenic loci and have strong potential to improve the molecular diagnosis of patients with de novo SVs.
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Affiliation(s)
- Sjors Middelkamp
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Judith M Vlaar
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Jacques Giltay
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Jerome Korzelius
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Lisanne de la Fonteijne
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ron Hochstenbach
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wigard P Kloosterman
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands.
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375
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Thompson MD, Knaus AA, Barshop BA, Caliebe A, Muhle H, Nguyen TTM, Baratang NV, Kinoshita T, Percy ME, Campeau PM, Murakami Y, Cole DE, Krawitz PM, Mabry CC. A post glycosylphosphatidylinositol (GPI) attachment to proteins, type 2 (PGAP2) variant identified in Mabry syndrome index cases: Molecular genetics of the prototypical inherited GPI disorder. Eur J Med Genet 2019; 63:103822. [PMID: 31805394 DOI: 10.1016/j.ejmg.2019.103822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/12/2019] [Accepted: 11/30/2019] [Indexed: 10/25/2022]
Abstract
We report that recessive inheritance of a post-GPI attachment to proteins 2 (PGAP2) gene variant results in the hyperphosphatasia with neurologic deficit (HPMRS) phenotype described by Mabry et al., in 1970. HPMRS, or Mabry syndrome, is now known to be one of 21 inherited glycosylphosphatidylinositol (GPI) deficiencies (IGDs), or GPI biosynthesis defects (GPIBDs). Bi-allelic mutations in at least six genes result in HPMRS phenotypes. Disruption of four phosphatidylinositol glycan (PIG) biosynthesis genes, PIGV, PIGO, PIGW and PIGY, expressed in the endoplasmic reticulum, result in HPMRS 1, 2, 5 and 6; disruption of the PGAP2 and PGAP3 genes, necessary for stabilizing the association of GPI anchored proteins (AP) with the Golgi membrane, result in HPMRS 3 and 4. We used exome sequencing to identify a novel homozygous missense PGAP2 variant NM_014489.3:c.881C > T, p.Thr294Met in two index patients and targeted sequencing to identify this variant in an unrelated patient. Rescue assays were conducted in two PGAP2 deficient cell lines, PGAP2 KO cells generated by CRISPR/Cas9 and PGAP2 deficient CHO cells, in order to examine the pathogenicity of the PGAP2 variant. First, we used the CHO rescue assay to establish that the wild type PGAP2 isoform 1, translated from transcript 1, is less active than the wild type PGAP2 isoform 8, translated from transcript 12 (alternatively spliced to omit exon 3). As a result, in our variant rescue assays, we used the more active NM_001256240.2:c.698C > T, p.Thr233Met isoform 8 instead of NM_014489.3:c.881C > T, p.Thr294Met isoform 1. Flow cytometric analysis showed that restoration of cell surface CD59 and CD55 with variant PGAP2 isoform 8, driven by the weak (pTA FLAG) promoter, was less efficient than wild type isoform 8. Therefore, we conclude that recessive inheritance of c.881C > T PGAP2, expressed as the hypomorphic PGAP2 c.698C > T, p.Thr233Met isoform 8, results in prototypical Mabry phenotype, HPMRS3 (GPIBD 8 [MIM: 614207]). This study highlights the need for long-term follow up of individuals with rare diseases in order to ensure that they benefit from innovations in diagnosis and treatment.
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Affiliation(s)
- Miles D Thompson
- Department of Pediatrics, UCSD School of Medicine, United States.
| | - Alexej A Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - Bruce A Barshop
- Department of Pediatrics, UCSD School of Medicine, United States
| | - Almuth Caliebe
- Department of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts-University, Kiel, Germany
| | - Hiltrud Muhle
- Department of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel, Christian-Albrechts-University, Kiel, Germany
| | - Thi Tuyet Mai Nguyen
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Canada
| | - Nissan V Baratang
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Canada
| | - Taroh Kinoshita
- Research Institute for Microbial Diseases, Osaka University, Japan
| | - Maire E Percy
- Department of Physiology, University of Toronto, Canada; Department of Obstetrics and Gynaecology, University of Toronto, Canada
| | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte Justine Research Center, University of Montreal, Canada
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, Japan
| | - David E Cole
- Laboratory Medicine and Pathobiology, University of Toronto, Canada
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - C Charlton Mabry
- Department of Pediatrics, College of Medicine, University of Kentucky, United States
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376
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Bizon C, Cox S, Balhoff J, Kebede Y, Wang P, Morton K, Fecho K, Tropsha A. ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources. J Chem Inf Model 2019; 59:4968-4973. [DOI: 10.1021/acs.jcim.9b00683] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27517, United States
| | - Steven Cox
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27517, United States
| | - James Balhoff
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27517, United States
| | - Yaphet Kebede
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27517, United States
| | - Patrick Wang
- CoVar Applied Technologies, Durham, North Carolina 27701, United States
| | - Kenneth Morton
- CoVar Applied Technologies, Durham, North Carolina 27701, United States
| | - Karamarie Fecho
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27517, United States
| | - Alexander Tropsha
- School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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377
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Bean DM, Teo J, Wu H, Oliveira R, Patel R, Bendayan R, Shah AM, Dobson RJB, Scott PA. Semantic computational analysis of anticoagulation use in atrial fibrillation from real world data. PLoS One 2019; 14:e0225625. [PMID: 31765395 PMCID: PMC6876873 DOI: 10.1371/journal.pone.0225625] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/09/2019] [Indexed: 12/03/2022] Open
Abstract
Atrial fibrillation (AF) is the most common arrhythmia and significantly increases stroke risk. This risk is effectively managed by oral anticoagulation. Recent studies using national registry data indicate increased use of anticoagulation resulting from changes in guidelines and the availability of newer drugs. The aim of this study is to develop and validate an open source risk scoring pipeline for free-text electronic health record data using natural language processing. AF patients discharged from 1st January 2011 to 1st October 2017 were identified from discharge summaries (N = 10,030, 64.6% male, average age 75.3 ± 12.3 years). A natural language processing pipeline was developed to identify risk factors in clinical text and calculate risk for ischaemic stroke (CHA2DS2-VASc) and bleeding (HAS-BLED). Scores were validated vs two independent experts for 40 patients. Automatic risk scores were in strong agreement with the two independent experts for CHA2DS2-VASc (average kappa 0.78 vs experts, compared to 0.85 between experts). Agreement was lower for HAS-BLED (average kappa 0.54 vs experts, compared to 0.74 between experts). In high-risk patients (CHA2DS2-VASc ≥2) OAC use has increased significantly over the last 7 years, driven by the availability of DOACs and the transitioning of patients from AP medication alone to OAC. Factors independently associated with OAC use included components of the CHA2DS2-VASc and HAS-BLED scores as well as discharging specialty and frailty. OAC use was highest in patients discharged under cardiology (69%). Electronic health record text can be used for automatic calculation of clinical risk scores at scale. Open source tools are available today for this task but require further validation. Analysis of routinely collected EHR data can replicate findings from large-scale curated registries.
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Affiliation(s)
- Daniel M. Bean
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, England, United Kingdom
- Health Data Research UK London, University College London, London, England, United Kingdom
| | - James Teo
- Department of Stroke and Neurology, King’s College Hospital NHS Foundation Trust, London, England, United Kingdom
| | - Honghan Wu
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Scotland, United Kingdom
- School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing, China
- Health Data Research UK Scotland, Edinburgh, Scotland, United Kingdom
| | - Ricardo Oliveira
- Unidade de Doenças Imunomediadas Sistémicas (UDIMS), S. Medicina IV, Hospital Prof. Doutor Fernando Fonseca, Amadora, Portugal
| | - Raj Patel
- Department of Haematology, King’s College Hospital NHS Foundation Trust, London, England, United Kingdom
| | - Rebecca Bendayan
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, England, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, England, United Kingdom
| | - Ajay M. Shah
- British Heart Foundation Centre, King’s College London, London, England, United Kingdom
- Department of Cardiology, King’s College Hospital NHS Foundation Trust, London, England, United Kingdom
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, England, United Kingdom
- Health Data Research UK London, University College London, London, England, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, England, United Kingdom
- Institute of Health Informatics, University College London, London, England, United Kingdom
| | - Paul A. Scott
- British Heart Foundation Centre, King’s College London, London, England, United Kingdom
- Department of Cardiology, King’s College Hospital NHS Foundation Trust, London, England, United Kingdom
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378
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The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research. Genes (Basel) 2019; 10:genes10120960. [PMID: 31766582 PMCID: PMC6947307 DOI: 10.3390/genes10120960] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/31/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
Hearing impairment (HI) is a common sensory disorder that is defined as the partial or complete inability to detect sound in one or both ears. This diverse pathology is associated with a myriad of phenotypic expressions and can be non-syndromic or syndromic. HI can be caused by various genetic, environmental, and/or unknown factors. Some ontologies capture some HI forms, phenotypes, and syndromes, but there is no comprehensive knowledge portal which includes aspects specific to the HI disease state. This hampers inter-study comparability, integration, and interoperability within and across disciplines. This work describes the HI Ontology (HIO) that was developed based on the Sickle Cell Disease Ontology (SCDO) model. This is a collaboratively developed resource built around the ‘Hearing Impairment’ concept by a group of experts in different aspects of HI and ontologies. HIO is the first comprehensive, standardized, hierarchical, and logical representation of existing HI knowledge. HIO allows researchers and clinicians alike to readily access standardized HI-related knowledge in a single location and promotes collaborations and HI information sharing, including epidemiological, socio-environmental, biomedical, genetic, and phenotypic information. Furthermore, this ontology illustrates the adaptability of the SCDO framework for use in developing a disease-specific ontology.
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379
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Dias R, Torkamani A. Artificial intelligence in clinical and genomic diagnostics. Genome Med 2019; 11:70. [PMID: 31744524 PMCID: PMC6865045 DOI: 10.1186/s13073-019-0689-8] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
Artificial intelligence (AI) is the development of computer systems that are able to perform tasks that normally require human intelligence. Advances in AI software and hardware, especially deep learning algorithms and the graphics processing units (GPUs) that power their training, have led to a recent and rapidly increasing interest in medical AI applications. In clinical diagnostics, AI-based computer vision approaches are poised to revolutionize image-based diagnostics, while other AI subtypes have begun to show similar promise in various diagnostic modalities. In some areas, such as clinical genomics, a specific type of AI algorithm known as deep learning is used to process large and complex genomic datasets. In this review, we first summarize the main classes of problems that AI systems are well suited to solve and describe the clinical diagnostic tasks that benefit from these solutions. Next, we focus on emerging methods for specific tasks in clinical genomics, including variant calling, genome annotation and variant classification, and phenotype-to-genotype correspondence. Finally, we end with a discussion on the future potential of AI in individualized medicine applications, especially for risk prediction in common complex diseases, and the challenges, limitations, and biases that must be carefully addressed for the successful deployment of AI in medical applications, particularly those utilizing human genetics and genomics data.
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Affiliation(s)
- Raquel Dias
- The Scripps Translational Science Institute, The Scripps Research Institute, 3344 North Torrey Pines Court Suite 300, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 3344 North Torrey Pines Court Suite 300, La Jolla, CA, 92037, USA
| | - Ali Torkamani
- The Scripps Translational Science Institute, The Scripps Research Institute, 3344 North Torrey Pines Court Suite 300, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 3344 North Torrey Pines Court Suite 300, La Jolla, CA, 92037, USA.
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380
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Zolotareva O, Saik OV, Königs C, Bragina EY, Goncharova IA, Freidin MB, Dosenko VE, Ivanisenko VA, Hofestädt R. Comorbidity of asthma and hypertension may be mediated by shared genetic dysregulation and drug side effects. Sci Rep 2019; 9:16302. [PMID: 31705029 PMCID: PMC6841742 DOI: 10.1038/s41598-019-52762-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
Abstract
Asthma and hypertension are complex diseases coinciding more frequently than expected by chance. Unraveling the mechanisms of comorbidity of asthma and hypertension is necessary for choosing the most appropriate treatment plan for patients with this comorbidity. Since both diseases have a strong genetic component in this article we aimed to find and study genes simultaneously associated with asthma and hypertension. We identified 330 shared genes and found that they form six modules on the interaction network. A strong overlap between genes associated with asthma and hypertension was found on the level of eQTL regulated genes and between targets of drugs relevant for asthma and hypertension. This suggests that the phenomenon of comorbidity of asthma and hypertension may be explained by altered genetic regulation or result from drug side effects. In this work we also demonstrate that not only drug indications but also contraindications provide an important source of molecular evidence helpful to uncover disease mechanisms. These findings give a clue to the possible mechanisms of comorbidity and highlight the direction for future research.
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Affiliation(s)
- Olga Zolotareva
- Bielefeld University, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld, Germany.
| | - Olga V Saik
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Cassandra Königs
- Bielefeld University, Bioinformatics and Medical Informatics Department, Bielefeld, Germany
| | - Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | - Maxim B Freidin
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Ralf Hofestädt
- Bielefeld University, Bioinformatics and Medical Informatics Department, Bielefeld, Germany
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381
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Davidović R, Perovic V, Gemovic B, Veljkovic N. DiNGO: standalone application for Gene Ontology and Human Phenotype Ontology term enrichment analysis. Bioinformatics 2019; 36:btz836. [PMID: 31702762 DOI: 10.1093/bioinformatics/btz836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/21/2019] [Accepted: 11/05/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Although various tools for Gene Ontology (GO) term enrichment analysis are available, there is still room for improvement. Hence, we present DiNGO, a standalone application based on an open source code from BiNGO, a widely-used application to assess the overrepresentation of GO categories. Besides facilitating GO term enrichment analyses, DiNGO has been developed to allow for convenient Human Phenotype Ontology (HPO) term overrepresentation investigation. This is an important contribution considering the increasing interest in HPO in scientific research and its potential in clinical settings. DiNGO supports gene/protein identifier conversion and an automatic updating of GO and HPO annotation resources. Finally, DiNGO can rapidly process a large amount of data due to its multithread design. AVAILABILITY AND IMPLEMENTATION DiNGO is implemented in the JAVA language, and its source code, example datasets and instructions are available on GitHub: https://github.com/radoslav180/DiNGO. A pre-compiled jar file is available at: https://www.vin.bg.ac.rs/180/tools/DiNGO.php. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Radoslav Davidović
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Mike Petrovica-Alasa 12-14, Belgrade, Serbia
| | - Vladimir Perovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Mike Petrovica-Alasa 12-14, Belgrade, Serbia
| | - Branislava Gemovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Mike Petrovica-Alasa 12-14, Belgrade, Serbia
| | - Nevena Veljkovic
- Laboratory for Bioinformatics and Computational Chemistry, Institute of Nuclear Sciences Vinca, University of Belgrade, Mike Petrovica-Alasa 12-14, Belgrade, Serbia
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382
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Lindstrand A, Eisfeldt J, Pettersson M, Carvalho CMB, Kvarnung M, Grigelioniene G, Anderlid BM, Bjerin O, Gustavsson P, Hammarsjö A, Georgii-Hemming P, Iwarsson E, Johansson-Soller M, Lagerstedt-Robinson K, Lieden A, Magnusson M, Martin M, Malmgren H, Nordenskjöld M, Norling A, Sahlin E, Stranneheim H, Tham E, Wincent J, Ygberg S, Wedell A, Wirta V, Nordgren A, Lundin J, Nilsson D. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. Genome Med 2019; 11:68. [PMID: 31694722 PMCID: PMC6836550 DOI: 10.1186/s13073-019-0675-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022] Open
Abstract
Background Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test. Methods We analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n = 68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n = 156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure. Results First, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850 kb (min 500 bp, max 155 Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (> 10 kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data. Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively. Conclusion The overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.
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Affiliation(s)
- Anna Lindstrand
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. .,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Jesper Eisfeldt
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Maria Pettersson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Malin Kvarnung
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giedre Grigelioniene
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olof Bjerin
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Erik Iwarsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Johansson-Soller
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agne Lieden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Måns Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Helena Malmgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ameli Norling
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Josephine Wincent
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sofia Ygberg
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Lundin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Nilsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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383
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Ossio R, Garcia-Salinas OI, Anaya-Mancilla DS, Garcia-Sotelo JS, Aguilar LA, Adams DJ, Robles-Espinoza CD. VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects. Bioinformatics 2019; 35:4803-4805. [PMID: 31161195 PMCID: PMC6853650 DOI: 10.1093/bioinformatics/btz458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 11/14/2022] Open
Abstract
Motivation Identifying disease-causing variants from exome sequencing projects remains a challenging task that often requires bioinformatics expertise. Here we describe a user-friendly graphical application that allows medical professionals and bench biologists to prioritize and visualize genetic variants from human exome sequencing data. Results We have implemented VCF/Plotein, a graphical, fully interactive web application able to display exome sequencing data in VCF format. Gene and variant information is extracted from Ensembl. Cross-referencing with external databases and application-based gene and variant filtering have also been implemented. All data processing is done locally by the user’s CPU to ensure the security of patient data. Availability and implementation Freely available on the web at https://vcfplotein.liigh.unam.mx. Website implemented in JavaScript using the Vue.js framework, with all major browsers supported. Source code freely available for download at https://github.com/raulossio/VCF-plotein. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Raul Ossio
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - O Isaac Garcia-Salinas
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - Diego Said Anaya-Mancilla
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - Jair S Garcia-Sotelo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - Luis A Aguilar
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro 76230, Mexico.,Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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384
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Pope MK, Ratajska A, Johnsen H, Rypdal KB, Sejersted Y, Paus B. Diagnostics of Hereditary Connective Tissue Disorders by Genetic Next-Generation Sequencing. Genet Test Mol Biomarkers 2019; 23:783-790. [DOI: 10.1089/gtmb.2019.0064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
| | | | - Hilde Johnsen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Yngve Sejersted
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Benedicte Paus
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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385
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Jan M, Gobet N, Diessler S, Franken P, Xenarios I. A multi-omics digital research object for the genetics of sleep regulation. Sci Data 2019; 6:258. [PMID: 31672980 PMCID: PMC6823400 DOI: 10.1038/s41597-019-0171-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
With the aim to uncover the molecular pathways underlying the regulation of sleep, we recently assembled an extensive and comprehensive systems genetics dataset interrogating a genetic reference population of mice at the levels of the genome, the brain and liver transcriptomes, the plasma metabolome, and the sleep-wake phenome. To facilitate a meaningful and efficient re-use of this public resource by others we designed, describe in detail, and made available a Digital Research Object (DRO), embedding data, documentation, and analytics. We present and discuss both the advantages and limitations of our multi-modal resource and analytic pipeline. The reproducibility of the results was tested by a bioinformatician not implicated in the original project and the robustness of results was assessed by re-annotating genetic and transcriptome data from the mm9 to the mm10 mouse genome assembly.
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Affiliation(s)
- Maxime Jan
- Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Nastassia Gobet
- Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Vital-IT, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Shanaz Diessler
- Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Paul Franken
- Centre for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Ioannis Xenarios
- Ludwig Cancer Research/CHUV-UNIL, Lausanne, Switzerland.
- Health 2030 Genome Center, Geneva, Switzerland.
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386
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Shohat S, Shifman S. Genes essential for embryonic stem cells are associated with neurodevelopmental disorders. Genome Res 2019; 29:1910-1918. [PMID: 31649057 PMCID: PMC6836742 DOI: 10.1101/gr.250019.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/01/2019] [Indexed: 12/18/2022]
Abstract
Mouse embryonic stem cells (mESCs) are key components in generating mouse models for human diseases and performing basic research on pluripotency, yet the number of genes essential for mESCs is still unknown. We performed a genome-wide screen for essential genes in mESCs and compared it to screens in human cells. We found that essential genes are enriched for basic cellular functions, are highly expressed in mESCs, and tend to lack paralog genes. We discovered that genes that are essential specifically in mESCs play a role in pathways associated with their pluripotent state. We show that 29.5% of human genes intolerant to loss-of-function mutations are essential in mouse or human ESCs, and that the human phenotypes most significantly associated with genes essential for ESCs are neurodevelopmental. Our results provide insights into essential genes in the mouse, the pathways which govern pluripotency, and suggest that many genes associated with neurodevelopmental disorders are essential at very early embryonic stages.
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Affiliation(s)
- Shahar Shohat
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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387
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Liu C, Ta CN, Rogers JR, Li Z, Lee J, Butler AM, Shang N, Kury FSP, Wang L, Shen F, Liu H, Ena L, Friedman C, Weng C. Ensembles of natural language processing systems for portable phenotyping solutions. J Biomed Inform 2019; 100:103318. [PMID: 31655273 DOI: 10.1016/j.jbi.2019.103318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/15/2019] [Accepted: 10/21/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND Manually curating standardized phenotypic concepts such as Human Phenotype Ontology (HPO) terms from narrative text in electronic health records (EHRs) is time consuming and error prone. Natural language processing (NLP) techniques can facilitate automated phenotype extraction and thus improve the efficiency of curating clinical phenotypes from clinical texts. While individual NLP systems can perform well for a single cohort, an ensemble-based method might shed light on increasing the portability of NLP pipelines across different cohorts. METHODS We compared four NLP systems, MetaMapLite, MedLEE, ClinPhen and cTAKES, and four ensemble techniques, including intersection, union, majority-voting and machine learning, for extracting generic phenotypic concepts. We addressed two important research questions regarding automated phenotype recognition. First, we evaluated the performance of different approaches in identifying generic phenotypic concepts. Second, we compared the performance of different methods to identify patient-specific phenotypic concepts. To better quantify the effects caused by concept granularity differences on performance, we developed a novel evaluation metric that considered concept hierarchies and frequencies. Each of the approaches was evaluated on a gold standard set of clinical documents annotated by clinical experts. One dataset containing 1,609 concepts derived from 50 clinical notes from two different institutions was used in both evaluations, and an additional dataset of 608 concepts derived from 50 case report abstracts obtained from PubMed was used for evaluation of identifying generic phenotypic concepts only. RESULTS For generic phenotypic concept recognition, the top three performers in the NYP/CUIMC dataset are union ensemble (F1, 0.634), training-based ensemble (F1, 0.632), and majority vote-based ensemble (F1, 0.622). In the Mayo dataset, the top three are majority vote-based ensemble (F1, 0.642), cTAKES (F1, 0.615), and MedLEE (F1, 0.559). In the PubMed dataset, the top three are majority vote-based ensemble (F1, 0.719), training-based (F1, 0.696) and MetaMapLite (F1, 0.694). For identifying patient specific phenotypes, the top three performers in the NYP/CUIMC dataset are majority vote-based ensemble (F1, 0.610), MedLEE (F1, 0.609), and training-based ensemble (F1, 0.585). In the Mayo dataset, the top three are majority vote-based ensemble (F1, 0.604), cTAKES (F1, 0.531) and MedLEE (F1, 0.527). CONCLUSIONS Our study demonstrates that ensembles of natural language processing can improve both generic phenotypic concept recognition and patient specific phenotypic concept identification over individual systems. Among the individual NLP systems, each individual system performed best when they were applied in the dataset that they were primary designed for. However, combining multiple NLP systems to create an ensemble can generally improve the performance. Specifically, the ensemble can increase the results reproducibility across different cohorts and tasks, and thus provide a more portable phenotyping solution compared to individual NLP systems.
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Affiliation(s)
- Cong Liu
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Casey N Ta
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - James R Rogers
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Ziran Li
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Junghwan Lee
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Alex M Butler
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Ning Shang
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | | | - Liwei Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55901, USA
| | - Feichen Shen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55901, USA
| | - Hongfang Liu
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55901, USA
| | - Lyudmila Ena
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Carol Friedman
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
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388
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Salnikova LE, Chernyshova EV, Anastasevich LA, Larin SS. Gene- and Disease-Based Expansion of the Knowledge on Inborn Errors of Immunity. Front Immunol 2019; 10:2475. [PMID: 31695696 PMCID: PMC6816315 DOI: 10.3389/fimmu.2019.02475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 12/31/2022] Open
Abstract
The recent report of the International Union of Immunological Societies (IUIS) has provided the categorized list of 354 inborn errors of immunity. We performed a systematic analysis of genes and diseases from the IUIS report with the use of the OMIM, ORPHANET, and HPO resources. To measure phenotypic similarity we applied the Jaccard/Tanimoto (J/T) coefficient for HPO terms and top-level categories. Low J/T coefficients for HPO terms for OMIM or ORPHANET disease pairs associated with the same genes indicated high pleiotropy of these genes. Gene ORGANizer enrichment analysis demonstrated that gene sets related to HPO top-level categories were most often enriched in immune, lymphatic, and corresponding body systems (for example, genes from the category "Cardiovascular" were enriched in cardiovascular system). We presented available data on frequent and very frequent clinical signs and symptoms in inborn errors of immunity. With the use of DisGeNET, we generated the list of 25 IUIS/OMIM diseases with two or more relatively high score gene-disease associations, found for unrelated genes and/or for clusters of genes coding for interacting proteins. Our study showed the enrichment of gene sets related to several IUIS categories with neoplastic and autoimmune diseases from the GWAS Catalog and reported individual genes with phenotypic overlap between inborn errors of immunity and GWAS diseases/traits. We concluded that genetic background may play a role in phenotypic diversity of inborn errors of immunity.
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Affiliation(s)
- Lyubov E Salnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Ekaterina V Chernyshova
- The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Lyudmila A Anastasevich
- The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Sergey S Larin
- The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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389
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Holt JM, Wilk B, Birch CL, Brown DM, Gajapathy M, Moss AC, Sosonkina N, Wilk MA, Anderson JA, Harris JM, Kelly JM, Shaterferdosian F, Uno-Antonison AE, Weborg A, Worthey EA. VarSight: prioritizing clinically reported variants with binary classification algorithms. BMC Bioinformatics 2019; 20:496. [PMID: 31615419 PMCID: PMC6792253 DOI: 10.1186/s12859-019-3026-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient's phenotypes. Typically, this is done through annotation, filtering, and then prioritization of variants for manual curation. However, prioritization of variants in rare disease patients remains a challenging task due to the high degree of variability in phenotype presentation and molecular source of disease. Thus, methods that can identify and/or prioritize variants to be clinically reported in the presence of such variability are of critical importance. METHODS We tested the application of classification algorithms that ingest variant annotations along with phenotype information for predicting whether a variant will ultimately be clinically reported and returned to a patient. To test the classifiers, we performed a retrospective study on variants that were clinically reported to 237 patients in the Undiagnosed Diseases Network. RESULTS We treated the classifiers as variant prioritization systems and compared them to four variant prioritization algorithms and two single-measure controls. We showed that the trained classifiers outperformed all other tested methods with the best classifiers ranking 72% of all reported variants and 94% of reported pathogenic variants in the top 20. CONCLUSIONS We demonstrated how freely available binary classification algorithms can be used to prioritize variants even in the presence of real-world variability. Furthermore, these classifiers outperformed all other tested methods, suggesting that they may be well suited for working with real rare disease patient datasets.
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Affiliation(s)
- James M. Holt
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Brandon Wilk
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Camille L. Birch
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Donna M. Brown
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Manavalan Gajapathy
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Alexander C. Moss
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Nadiya Sosonkina
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
- University of Alabama at Birmingham, Department of Genetics, 720 20th Street South, Birmingham, 35294 USA
| | - Melissa A. Wilk
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Julie A. Anderson
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Jeremy M. Harris
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Jacob M. Kelly
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Fariba Shaterferdosian
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Angelina E. Uno-Antonison
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Arthur Weborg
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
| | - Elizabeth A. Worthey
- HudsonAlpha Institute for Biotechnology, Software Development and Informatics, 601 Genome Way, Huntsville, 35806 USA
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390
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Rachwani Anil R, Rocha-de-Lossada C, Ayala CH, Contreras ME. A new mutation in the PAX2 gene in a Papillorenal Syndrome patient. Am J Ophthalmol Case Rep 2019; 16:100563. [PMID: 31692565 PMCID: PMC6806373 DOI: 10.1016/j.ajoc.2019.100563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 09/29/2019] [Accepted: 10/07/2019] [Indexed: 11/18/2022] Open
Abstract
Purpose To present a new mutation in a patient with Papillorenal Syndrome (PAPRS). Observations PAPRS is an autosomal dominant disease that involves ocular and renal abnormalities. We present a patient with PAPRS with a genetically diagnosed PAX2 and new pathogenic mutation. A complete ophthalmological, neurological, nephrological and Ears-Nose-Throat (ENT) examination were undertaken. The patient suffered from Focal Segmental Glomerulosclerosis (FSGS) and some typical ophthalmological signs of PAPRS, including optic nerve coloboma and optic disc pit (ODP) maculopathy associated with an abnormal retinal vessel distribution and numerous cilioretinal arteries in the right eye. The left eye showed similar vessel abnormalities although the optic disc had a normal morphology. Conclusions A new mutation in the PAX2 gene was identified in a patient with ocular and renal abnormalities.
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Affiliation(s)
- Rahul Rachwani Anil
- Corresponding author. Plaza del Hospital Civil s/n, Ophthalmology Department, 29009, Málaga, Spain.
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391
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Saraf A, Book WM, Nelson TJ, Xu C. Hypoplastic left heart syndrome: From bedside to bench and back. J Mol Cell Cardiol 2019; 135:109-118. [PMID: 31419439 PMCID: PMC10831616 DOI: 10.1016/j.yjmcc.2019.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 02/09/2023]
Abstract
Hypoplastic Left Heart Syndrome (HLHS) is a complex Congenital Heart Disease (CHD) that was almost universally fatal until the advent of the Norwood operation in 1981. Children with HLHS who largely succumbed to the disease within the first year of life, are now surviving to adulthood. However, this survival is associated with multiple comorbidities and HLHS infants have a higher mortality rate as compared to other non-HLHS single ventricle patients. In this review we (a) discuss current clinical challenges associated in the care of HLHS patients, (b) explore the use of systems biology in understanding the molecular framework of this disease, (c) evaluate induced pluripotent stem cells as a translational model to understand molecular mechanisms and manipulate them to improve outcomes, and (d) investigate cell therapy, gene therapy, and tissue engineering as a potential tool to regenerate hypoplastic cardiac structures and improve outcomes.
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Affiliation(s)
- Anita Saraf
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Wendy M Book
- Division of Cardiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Timothy J Nelson
- Division of General Internal Medicine, Center for Regenerative Medicine, Pediatric Cardiothoracic Surgery, Division of Cardiovascular Diseases, Transplant Center, Division of Biomedical Statistics and Informatics, Division of Pediatric Cardiology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Chunhui Xu
- Division of Pediatric Cardiology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
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392
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Chagoyen M, Ranea JAG, Pazos F. Applications of molecular networks in biomedicine. Biol Methods Protoc 2019; 4:bpz012. [PMID: 32395629 PMCID: PMC7200821 DOI: 10.1093/biomethods/bpz012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/20/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Due to the large interdependence between the molecular components of living systems, many phenomena, including those related to pathologies, cannot be explained in terms of a single gene or a small number of genes. Molecular networks, representing different types of relationships between molecular entities, embody these large sets of interdependences in a framework that allow their mining from a systemic point of view to obtain information. These networks, often generated from high-throughput omics datasets, are used to study the complex phenomena of human pathologies from a systemic point of view. Complementing the reductionist approach of molecular biology, based on the detailed study of a small number of genes, systemic approaches to human diseases consider that these are better reflected in large and intricate networks of relationships between genes. These networks, and not the single genes, provide both better markers for diagnosing diseases and targets for treating them. Network approaches are being used to gain insight into the molecular basis of complex diseases and interpret the large datasets associated with them, such as genomic variants. Network formalism is also suitable for integrating large, heterogeneous and multilevel datasets associated with diseases from the molecular level to organismal and epidemiological scales. Many of these approaches are available to nonexpert users through standard software packages.
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Affiliation(s)
- Monica Chagoyen
- Computational Systems Biology Group, Systems Biology Program, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Juan A G Ranea
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Florencio Pazos
- Computational Systems Biology Group, Systems Biology Program, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
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393
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Ebiki M, Okazaki T, Kai M, Adachi K, Nanba E. Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders. Yonago Acta Med 2019; 62:244-252. [PMID: 31582890 DOI: 10.33160/yam.2019.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/17/2019] [Indexed: 12/24/2022]
Abstract
Background During the investigation of causative variants of Mendelian disorders using next-generation sequencing, the enormous number of possible candidates makes the detection process complex, and the use of multidimensional methods is required. Although the utility of several variant prioritization tools has been reported, their effectiveness in Japanese patients remains largely unknown. Methods We selected 5 free variant prioritization tools (PhenIX, hiPHIVE, Phen-Gen, eXtasy-order statistics, and eXtasy-combined max) and assessed their effectiveness in Japanese patient populations. To compare these tools, we conducted 2 studies: one based on simulated data of 100 diseases and another based on the exome data of 20 in-house patients with Mendelian disorders. To this end we selected 100 pathogenic variants from the "Database of Pathogenic Variants (DPV)" and created 100 variant call format (VCF) files that each had pathogenic variants based on reference human genome data from the 1000 Genomes Project. The later "in-house" study used exome data from 20 Japanese patients with Mendelian disorders. In both studies, we utilized 1-5 terms of "Human Phenotype Ontology" as clinical information. Results In our analysis based on simulated disease data, the detection rate of the top 10 causative variants was 91% for hiPHIVE, and 88% for PhenIX, based on 100 sets of simulated disease VCF data. Also, both software packages detected 82% of the top 1 causative variants. When we used data from our in-house patients instead, we found that these two programs (PhenIX and hiPHIVE) produced higher detection rates than the other three systems in our study. The detection rate of the top 1 causative variant was 71.4% for PhenIX, 65.0% for hiPHIVE. Conclusion The rates of detecting causative variants in two Exomizer software packages, hiPHIVE and PhenIX, were higher than for the other three software systems we analyzed, with respect to Japanese patients.
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Affiliation(s)
- Mitsutaka Ebiki
- The Development of Innovative Future Medical Treatment, Graduate School of Medical Sciences, Tottori University, Yonago 683-8504, Japan.,KUSUNOKI SCALE INC., Yonago 683-0832, Japan
| | - Tetsuya Okazaki
- Division of Child Neurology, Department of Brain and Neurosciences, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan.,Division of Clinical Genetics, Tottori University Hospital, Yonago 683-8504, Japan, ‖Technical Department, Tottori University, Yonago 683-8503, Japan
| | - Masachika Kai
- Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University, Yonago 683-8503, Japan
| | - Kaori Adachi
- Research Strategy Division, Organization for Research Initiative and Promotion, Tottori University, Yonago 683-8503, Japan
| | - Eiji Nanba
- Division of Clinical Genetics, Tottori University Hospital, Yonago 683-8504, Japan, ‖Technical Department, Tottori University, Yonago 683-8503, Japan.,Research Strategy Division, Organization for Research Initiative and Promotion, Tottori University, Yonago 683-8503, Japan
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394
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Köhler S, Øien NC, Buske OJ, Groza T, Jacobsen JOB, McNamara C, Vasilevsky N, Carmody LC, Gourdine JP, Gargano M, McMurry J, Danis D, Mungall CJ, Smedley D, Haendel M, Robinson PN. Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. CURRENT PROTOCOLS IN HUMAN GENETICS 2019; 103:e92. [PMID: 31479590 PMCID: PMC6814016 DOI: 10.1002/cphg.92] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The Human Phenotype Ontology (HPO) is a standardized set of phenotypic terms that are organized in a hierarchical fashion. It is a widely used resource for capturing human disease phenotypes for computational analysis to support differential diagnostics. The HPO is frequently used to create a set of terms that accurately describe the observed clinical abnormalities of an individual being evaluated for suspected rare genetic disease. This profile is compared with computational disease profiles in the HPO database with the aim of identifying genetic diseases with comparable phenotypic profiles. The computational analysis can be coupled with the analysis of whole-exome or whole-genome sequencing data through applications such as Exomiser. This article explains how to choose an optimal set of HPO terms for these cases and enter them with software, such as PhenoTips and PatientArchive, and demonstrates how to use Phenomizer and Exomiser to generate a computational differential diagnosis. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Sebastian Köhler
- Charité Centrum für Therapieforschung, Charité-Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
- Einstein Center Digital Future, Berlin 10117, Germany
- Monarch Initiative, monarchinitiative.org
| | | | | | | | - Julius OB Jacobsen
- Monarch Initiative, monarchinitiative.org
- Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Nicole Vasilevsky
- Monarch Initiative, monarchinitiative.org
- Oregon Health & Science University, Portland, OR 97217, USA
| | - Leigh C Carmody
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - JP Gourdine
- Monarch Initiative, monarchinitiative.org
- Oregon Health & Science University, Portland, OR 97217, USA
| | - Michael Gargano
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Julie McMurry
- Monarch Initiative, monarchinitiative.org
- Oregon State University, Corvallis, OR, USA
| | - Daniel Danis
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Christopher J Mungall
- Monarch Initiative, monarchinitiative.org
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Damian Smedley
- Monarch Initiative, monarchinitiative.org
- Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Melissa Haendel
- Monarch Initiative, monarchinitiative.org
- Oregon Health & Science University, Portland, OR 97217, USA
- Oregon State University, Corvallis, OR, USA
| | - Peter N Robinson
- Monarch Initiative, monarchinitiative.org
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT, USA
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395
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Braun JM, Kalloo G, Kingsley SL, Li N. Using phenome-wide association studies to examine the effect of environmental exposures on human health. ENVIRONMENT INTERNATIONAL 2019; 130:104877. [PMID: 31200158 PMCID: PMC6682449 DOI: 10.1016/j.envint.2019.05.071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/10/2019] [Accepted: 05/27/2019] [Indexed: 05/04/2023]
Abstract
The field of environmental epidemiology has been using "-omics" technologies, including the exposome, metabolome, and methylome, to understand the potential effects and biological pathways of a number of environmental pollutants. However, the majority of studies have focused on a single disease or phenotype, and have not systematically considered patterns of multimorbidity and whether environmental pollutants have pleiotropic effects. These questions could be addressed by examining the relation between environmental exposures and the phenome - the patterns and profiles of human health that individuals experience from birth to death. By conducting Phenome Wide Association Studies (PheWAS), we can generate new hypotheses about new or poorly understood exposures, identify novel associations for established toxicants, and better understand biological pathways affected by environmental pollutants. In this article, we provide a conceptual framework for conducting PheWAS in environmental epidemiology and summarize some of the advantages and challenges to using the PheWAS to study environmental pollutant exposures. Ultimately, by adding the PheWAS to our "-omics" toolbox, we could substantially improve our understanding of the potential health effects of environmental pollutants.
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Affiliation(s)
- Joseph M Braun
- Department of Epidemiology, Brown University, Providence, RI, United States of America.
| | - Geetika Kalloo
- Department of Epidemiology, Brown University, Providence, RI, United States of America
| | - Samantha L Kingsley
- Department of Epidemiology, Brown University, Providence, RI, United States of America
| | - Nan Li
- Department of Epidemiology, Brown University, Providence, RI, United States of America
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396
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Gil-da-Silva-Lopes V, Fontes M, dos Santos A, Appenzeller S, Fett-Conte A, Francisquetti M, Monlleó I. Syndromic Oral Clefts: Challenges of Genetic Assessment in Brazil and Suggestions to Improve Health Policies. Public Health Genomics 2019; 22:69-76. [DOI: 10.1159/000501973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
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397
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Reuser AJJ, van der Ploeg AT, Chien YH, Llerena J, Abbott MA, Clemens PR, Kimonis VE, Leslie N, Maruti SS, Sanson BJ, Araujo R, Periquet M, Toscano A, Kishnani PS, On Behalf Of The Pompe Registry Sites. GAA variants and phenotypes among 1,079 patients with Pompe disease: Data from the Pompe Registry. Hum Mutat 2019; 40:2146-2164. [PMID: 31342611 PMCID: PMC6852536 DOI: 10.1002/humu.23878] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/11/2022]
Abstract
Identification of variants in the acid α‐glucosidase (GAA) gene in Pompe disease provides valuable insights and systematic overviews are needed. We report on the number, nature, frequency, and geographic distribution of GAA sequence variants listed in the Pompe Registry, a long‐term, observational program and the largest global repository of Pompe disease data. Variant information was reviewed and compared with publicly available GAA databases/resources. Among 1,079 eligible patients, 2,075 GAA variants (80 unique novel) were reported. Variants were listed by groups representing Pompe disease phenotypes. Patients were classified as Group A: Symptom onset ≤ 12 months of age with cardiomyopathy; Group B: Symptom onset ≤ 12 years of age (includes patients with symptom onset ≤ 12 months of age without cardiomyopathy); or Group C: Symptom onset > 12 years of age. Likely impact of novel variants was predicted using bioinformatics algorithms. Variants were classified by pathogenicity using ACMG guidelines. Data reported from the Pompe Registry provide new information about the distribution of GAA variants globally and across the clinical spectrum, add to the number and diversity of GAA variants registered in public databases through published data sharing, provide a first indication of the severity of novel variants, and assist in diagnostic practice and outcome prediction.
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Affiliation(s)
- Arnold J J Reuser
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ans T van der Ploeg
- Center for Lysosomal and Metabolic Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Juan Llerena
- Departamento de Genética Médica, Instituto Fernandes Figueira (FIOCRUZ), Rio de Janeiro RJ, Brazil
| | - Mary-Alice Abbott
- Department of Pediatrics, Baystate Medical Center, Springfield, Massachusetts
| | - Paula R Clemens
- Department of Neurology and Department of Veterans Affairs Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Virginia E Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, School of Medicine, University of California, Irvine, California
| | - Nancy Leslie
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | | | | | | | - Antonio Toscano
- Department of Clinical and Experimental Medicine, Reference Center for Rare Neuromuscular Disorders, University of Messina, Messina, Italy
| | - Priya S Kishnani
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina
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398
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Boyles R, Thessen A, Waldrop A, Haendel M. Ontology-based data integration for advancing toxicological knowledge. CURRENT OPINION IN TOXICOLOGY 2019. [DOI: 10.1016/j.cotox.2019.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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399
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Aguirre M, Rivas MA, Priest J. Phenome-wide Burden of Copy-Number Variation in the UK Biobank. Am J Hum Genet 2019; 105:373-383. [PMID: 31353025 PMCID: PMC6699064 DOI: 10.1016/j.ajhg.2019.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/28/2019] [Indexed: 10/26/2022] Open
Abstract
Copy-number variations (CNVs) represent a significant proportion of the genetic differences between individuals and many CNVs associate causally with syndromic disease and clinical outcomes. Here, we characterize the landscape of copy-number variation and their phenome-wide effects in a sample of 472,228 array-genotyped individuals from the UK Biobank. In addition to population-level selection effects against genic loci conferring high mortality, we describe genetic burden from potentially pathogenic and previously uncharacterized CNV loci across more than 3,000 quantitative and dichotomous traits, with separate analyses for common and rare classes of variation. Specifically, we highlight the effects of CNVs at two well-known syndromic loci 16p11.2 and 22q11.2, previously uncharacterized variation at 9p23, and several genic associations in the context of acute coronary artery disease and high body mass index. Our data constitute a deeply contextualized portrait of population-wide burden of copy-number variation, as well as a series of dosage-mediated genic associations across the medical phenome.
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Affiliation(s)
- Matthew Aguirre
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - James Priest
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94035, USA.
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400
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Paganini C, Costantini R, Superti-Furga A, Rossi A. Bone and connective tissue disorders caused by defects in glycosaminoglycan biosynthesis: a panoramic view. FEBS J 2019; 286:3008-3032. [PMID: 31286677 DOI: 10.1111/febs.14984] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/22/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023]
Abstract
Glycosaminoglycans (GAGs) are a heterogeneous family of linear polysaccharides that constitute the carbohydrate moiety covalently attached to the protein core of proteoglycans, macromolecules present on the cell surface and in the extracellular matrix. Several genetic disorders of bone and connective tissue are caused by mutations in genes encoding for glycosyltransferases, sulfotransferases and transporters that are responsible for the synthesis of sulfated GAGs. Phenotypically, these disorders all reflect alterations in crucial biological functions of GAGs in the development, growth and homoeostasis of cartilage and bone. To date, up to 27 different skeletal phenotypes have been linked to mutations in 23 genes encoding for proteins involved in GAG biosynthesis. This review focuses on recent genetic, molecular and biochemical studies of bone and connective tissue disorders caused by GAG synthesis defects. These insights and future research in the field will provide a deeper understanding of the molecular pathogenesis of these disorders and will pave the way for developing common therapeutic strategies that might be targeted to a range of individual phenotypes.
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Affiliation(s)
- Chiara Paganini
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Italy
| | - Rossella Costantini
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Italy
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Antonio Rossi
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Italy
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