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Renaux A, Terwagne C, Cochez M, Tiddi I, Nowé A, Lenaerts T. A knowledge graph approach to predict and interpret disease-causing gene interactions. BMC Bioinformatics 2023; 24:324. [PMID: 37644440 PMCID: PMC10463539 DOI: 10.1186/s12859-023-05451-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Understanding the impact of gene interactions on disease phenotypes is increasingly recognised as a crucial aspect of genetic disease research. This trend is reflected by the growing amount of clinical research on oligogenic diseases, where disease manifestations are influenced by combinations of variants on a few specific genes. Although statistical machine-learning methods have been developed to identify relevant genetic variant or gene combinations associated with oligogenic diseases, they rely on abstract features and black-box models, posing challenges to interpretability for medical experts and impeding their ability to comprehend and validate predictions. In this work, we present a novel, interpretable predictive approach based on a knowledge graph that not only provides accurate predictions of disease-causing gene interactions but also offers explanations for these results. RESULTS We introduce BOCK, a knowledge graph constructed to explore disease-causing genetic interactions, integrating curated information on oligogenic diseases from clinical cases with relevant biomedical networks and ontologies. Using this graph, we developed a novel predictive framework based on heterogenous paths connecting gene pairs. This method trains an interpretable decision set model that not only accurately predicts pathogenic gene interactions, but also unveils the patterns associated with these diseases. A unique aspect of our approach is its ability to offer, along with each positive prediction, explanations in the form of subgraphs, revealing the specific entities and relationships that led to each pathogenic prediction. CONCLUSION Our method, built with interpretability in mind, leverages heterogenous path information in knowledge graphs to predict pathogenic gene interactions and generate meaningful explanations. This not only broadens our understanding of the molecular mechanisms underlying oligogenic diseases, but also presents a novel application of knowledge graphs in creating more transparent and insightful predictors for genetic research.
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Affiliation(s)
- Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Chloé Terwagne
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Michael Cochez
- Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Discovery Lab, Elsevier, Amsterdam, The Netherlands
| | - Ilaria Tiddi
- Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles - Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence lab, Vrije Universiteit Brussel, Brussels, Belgium
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2
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The simplest explanation does not have to be preferred: co-occurrence of pathogenic variants in cancer-predisposing genes. Eur J Hum Genet 2022; 30:260-261. [PMID: 34983941 PMCID: PMC8904836 DOI: 10.1038/s41431-021-01031-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022] Open
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3
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Mukherjee S, Cogan JD, Newman JH, Phillips JA, Hamid R, Meiler J, Capra JA. Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. Am J Hum Genet 2021; 108:1946-1963. [PMID: 34529933 PMCID: PMC8546038 DOI: 10.1016/j.ajhg.2021.08.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Abstract
Rare diseases affect millions of people worldwide, and discovering their genetic causes is challenging. More than half of the individuals analyzed by the Undiagnosed Diseases Network (UDN) remain undiagnosed. The central hypothesis of this work is that many of these rare genetic disorders are caused by multiple variants in more than one gene. However, given the large number of variants in each individual genome, experimentally evaluating combinations of variants for potential to cause disease is currently infeasible. To address this challenge, we developed the digenic predictor (DiGePred), a random forest classifier for identifying candidate digenic disease gene pairs by features derived from biological networks, genomics, evolutionary history, and functional annotations. We trained the DiGePred classifier by using DIDA, the largest available database of known digenic-disease-causing gene pairs, and several sets of non-digenic gene pairs, including variant pairs derived from unaffected relatives of UDN individuals. DiGePred achieved high precision and recall in cross-validation and on a held-out test set (PR area under the curve > 77%), and we further demonstrate its utility by using digenic pairs from the recent literature. In contrast to other approaches, DiGePred also appropriately controls the number of false positives when applied in realistic clinical settings. Finally, to enable the rapid screening of variant gene pairs for digenic disease potential, we freely provide the predictions of DiGePred on all human gene pairs. Our work enables the discovery of genetic causes for rare non-monogenic diseases by providing a means to rapidly evaluate variant gene pairs for the potential to cause digenic disease.
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Affiliation(s)
- Souhrid Mukherjee
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Joy D Cogan
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John H Newman
- Pulmonary Hypertension Center, Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John A Phillips
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Rizwan Hamid
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Department of Pharmacology, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Institute for Drug Discovery, Leipzig University Medical School, Leipzig 04103, Germany; Department of Chemistry, Leipzig University, Leipzig 04109, Germany; Department of Computer Science, Leipzig University, Leipzig 04109, Germany.
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA.
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4
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Najafi A, Caspar SM, Meienberg J, Rohrbach M, Steinmann B, Matyas G. Variant filtering, digenic variants, and other challenges in clinical sequencing: a lesson from fibrillinopathies. Clin Genet 2020; 97:235-245. [PMID: 31506931 PMCID: PMC7004123 DOI: 10.1111/cge.13640] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/04/2019] [Accepted: 09/07/2019] [Indexed: 12/23/2022]
Abstract
Genome-scale high-throughput sequencing enables the detection of unprecedented numbers of sequence variants. Variant filtering and interpretation are facilitated by mutation databases, in silico tools, and population-based reference datasets such as ExAC/gnomAD, while variants are classified using the ACMG/AMP guidelines. These methods, however, pose clinically relevant challenges. We queried the gnomAD dataset for (likely) pathogenic variants in genes causing autosomal-dominant disorders. Furthermore, focusing on the fibrillinopathies Marfan syndrome (MFS) and congenital contractural arachnodactyly (CCA), we screened 500 genomes of our patients for co-occurring variants in FBN1 and FBN2. In gnomAD, we detected 2653 (likely) pathogenic variants in 253 genes associated with autosomal-dominant disorders, enabling the estimation of variant-filtering thresholds and disease predisposition/prevalence rates. In our database, we discovered two families with hitherto unreported co-occurrence of FBN1/FBN2 variants causing phenotypes with mixed or modified MFS/CCA clinical features. We show that (likely) pathogenic gnomAD variants may be more frequent than expected and are challenging to classify according to the ACMG/AMP guidelines as well as that fibrillinopathies are likely underdiagnosed and may co-occur. Consequently, selection of appropriate frequency cutoffs, recognition of digenic variants, and variant classification represent considerable challenges in variant interpretation. Neglecting these challenges may lead to incomplete or missed diagnoses.
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Affiliation(s)
- Arash Najafi
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
- Cantonal Hospital WinterthurInstitute of Radiology and Nuclear MedicineWinterthurSwitzerland
| | - Sylvan M. Caspar
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
| | - Janine Meienberg
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
| | - Marianne Rohrbach
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital Zurich Eleonore FoundationZurichSwitzerland
| | - Beat Steinmann
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital Zurich Eleonore FoundationZurichSwitzerland
| | - Gabor Matyas
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
- Zurich Center for Integrative Human PhysiologyUniversity of ZurichZurichSwitzerland
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5
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Duerinckx S, Jacquemin V, Drunat S, Vial Y, Passemard S, Perazzolo C, Massart A, Soblet J, Racapé J, Desmyter L, Badoer C, Papadimitriou S, Le Borgne YA, Lefort A, Libert F, De Maertelaer V, Rooman M, Costagliola S, Verloes A, Lenaerts T, Pirson I, Abramowicz M. Digenic inheritance of human primary microcephaly delineates centrosomal and non-centrosomal pathways. Hum Mutat 2019; 41:512-524. [PMID: 31696992 PMCID: PMC7496698 DOI: 10.1002/humu.23948] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 12/30/2022]
Abstract
Primary microcephaly (PM) is characterized by a small head since birth and is vastly heterogeneous both genetically and phenotypically. While most cases are monogenic, genetic interactions between Aspm and Wdr62 have recently been described in a mouse model of PM. Here, we used two complementary, holistic in vivo approaches: high throughput DNA sequencing of multiple PM genes in human patients with PM, and genome‐edited zebrafish modeling for the digenic inheritance of PM. Exomes of patients with PM showed a significant burden of variants in 75 PM genes, that persisted after removing monogenic causes of PM (e.g., biallelic pathogenic variants in CEP152). This observation was replicated in an independent cohort of patients with PM, where a PM gene panel showed in addition that the burden was carried by six centrosomal genes. Allelic frequencies were consistent with digenic inheritance. In zebrafish, non‐centrosomal gene casc5 −/− produced a severe PM phenotype, that was not modified by centrosomal genes aspm or wdr62 invalidation. A digenic, quadriallelic PM phenotype was produced by aspm and wdr62. Our observations provide strong evidence for digenic inheritance of human PM, involving centrosomal genes. Absence of genetic interaction between casc5 and aspm or wdr62 further delineates centrosomal and non‐centrosomal pathways in PM.
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Affiliation(s)
- Sarah Duerinckx
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
| | - Valérie Jacquemin
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Séverine Drunat
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Yoann Vial
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Sandrine Passemard
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Camille Perazzolo
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Annick Massart
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Julie Soblet
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium.,Department of Genetics, ULB Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, ULB Center of Human Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Judith Racapé
- Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Laurence Desmyter
- Department of Genetics, ULB Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Cindy Badoer
- Department of Genetics, ULB Center of Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium.,Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yann-Aël Le Borgne
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Anne Lefort
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Frédérick Libert
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Viviane De Maertelaer
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Sabine Costagliola
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Alain Verloes
- Department of Genetics, Robert Debré University Hospital, APHP, Paris, France.,INSERM UMR 1141, Université de Paris Diderot, Paris, France
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium.,Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Isabelle Pirson
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Marc Abramowicz
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium.,Present Address: Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
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6
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Yilmaz E, Mihci E, Nur B, Alper ÖM, Taçoy Ş. Recent Advances in Craniosynostosis. Pediatr Neurol 2019; 99:7-15. [PMID: 31421914 DOI: 10.1016/j.pediatrneurol.2019.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 12/25/2018] [Accepted: 01/24/2019] [Indexed: 12/27/2022]
Abstract
Craniosynostosis is a pathologic craniofacial disorder and is defined as the premature fusion of one or more cranial (calvarial) sutures. Cranial sutures are fibrous joints consisting of nonossified mesenchymal cells that play an important role in the development of healthy craniofacial skeletons. Early fusion of these sutures results in incomplete brain development that may lead to complications of several severe medical conditions including seizures, brain damage, mental delay, complex deformities, strabismus, and visual and breathing problems. As a congenital disease, craniosynostosis has a heterogeneous origin that can be affected by genetic and epigenetic alterations, teratogens, and environmental factors and make the syndrome highly complex. To date, approximately 200 syndromes have been linked to craniosynostosis. In addition to being part of a syndrome, craniosynostosis can be nonsyndromic, formed without any additional anomalies. More than 50 nuclear genes that relate to craniosynostosis have been identified. Besides genetic factors, epigenetic factors like microRNAs and mechanical forces also play important roles in suture fusion. As craniosynostosis is a multifactorial disorder, evaluating the craniosynostosis syndrome requires and depends on all the information obtained from clinical findings, genetic analysis, epigenetic or environmental factors, or gene modulators. In this review, we will focus on embryologic and genetic studies, as well as epigenetic and environmental studies. We will discuss published studies and correlate the findings with unknown aspects of craniofacial disorders.
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Affiliation(s)
- Elanur Yilmaz
- Department of Medical Biology and Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Banu Nur
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
| | - Özgül M Alper
- Department of Medical Biology and Genetics, Akdeniz University Medical School, Antalya, Turkey.
| | - Şükran Taçoy
- Department of Pediatric Genetics, Akdeniz University Medical School, Antalya, Turkey
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7
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Abstract
The practice of genomic medicine stands to revolutionize our approach to medical care, and to realize this goal will require discovery of the relationship between rare variation at each of the ~ 20,000 protein-coding genes and their consequent impact on individual health and expression of Mendelian disease. The step-wise evolution of broad-based, genome-wide cytogenetic and molecular genomic testing approaches (karyotyping, chromosomal microarray [CMA], exome sequencing [ES]) has driven much of the rare disease discovery to this point, with genome sequencing representing the newest member of this team. Each step has brought increased sensitivity to interrogate individual genomic variation in an unbiased method that does not require clinical prediction of the locus or loci involved. Notably, each step has also brought unique limitations in variant detection, for example, the low sensitivity of ES for detection of triploidy, and of CMA for detection of copy neutral structural variants. The utility of genome sequencing (GS) as a clinical molecular diagnostic test, and the increased sensitivity afforded by addition of long-read sequencing or other -omics technologies such as RNAseq or metabolomics, are not yet fully explored, though recent work supports improved sensitivity of variant detection, at least in a subset of cases. The utility of GS will also rely upon further elucidation of the complexities of genetic and allelic heterogeneity, multilocus rare variation, and the impact of rare and common variation at a locus, as well as advances in functional annotation of identified variants. Much discovery remains to be done before the potential utility of GS is fully appreciated.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, T603, Houston, TX, 77030, USA.
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8
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Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 2019; 21:798-812. [PMID: 30655598 PMCID: PMC6691975 DOI: 10.1038/s41436-018-0408-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Kumar
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corinne Boehm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Shrikant Mane
- Yale Center for Genome Analysis, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Richard P Lifton
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
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9
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Andolfo I, De Rosa G, Errichiello E, Manna F, Rosato BE, Gambale A, Vetro A, Calcaterra V, Pelizzo G, De Franceschi L, Zuffardi O, Russo R, Iolascon A. PIEZO1 Hypomorphic Variants in Congenital Lymphatic Dysplasia Cause Shape and Hydration Alterations of Red Blood Cells. Front Physiol 2019; 10:258. [PMID: 30930797 PMCID: PMC6428731 DOI: 10.3389/fphys.2019.00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/26/2019] [Indexed: 12/20/2022] Open
Abstract
PIEZO1 is a cation channel activated by mechanical force. It plays an important physiological role in several biological processes such as cardiovascular, renal, endothelial and hematopoietic systems. Two different diseases are associated with alteration in the DNA sequence of PIEZO1: (i) dehydrated hereditary stomatocytosis (DHS1, #194380), an autosomal dominant hemolytic anemia caused by gain-of-function mutations; (ii) lymphatic dysplasia with non-immune fetal hydrops (LMPH3, #616843), an autosomal recessive condition caused by biallelic loss-of-function mutations. We analyzed a 14-year-old boy affected by severe lymphatic dysplasia already present prenatally, with peripheral edema, hydrocele, and chylothoraces. By whole exome sequencing, we identified compound heterozygosity for PIEZO1, with one splicing and one deletion mutation, the latter causing the formation of a premature stop codon that leads to mRNA decay. The functional analysis of the erythrocytes of the patient highlighted altered hydration with the intracellular loss of the potassium content and structural abnormalities with anisopoikolocytosis and presence of both spherocytes and stomatocytes. This novel erythrocyte trait, sharing features with both hereditary spherocytosis and overhydrated hereditary stomatocytosis, complements the clinical features associated with loss-of-function mutations of PIEZO1 in the context of the generalized lymphatic dysplasia of LMPH3 type.
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Affiliation(s)
- Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - Gianluca De Rosa
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE, Biotecnologie Avanzate, Naples, Italy
| | | | - Francesco Manna
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - Barbara Eleni Rosato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - Antonella Gambale
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - Annalisa Vetro
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, A. Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Valeria Calcaterra
- Pediatric Unit, Department of Maternal and Children's Health, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Gloria Pelizzo
- Department of Pediatric Surgery, Children's Hospital "G. Di Cristina", ARNAS Civico-Di Cristina-Benfretelli, Palermo, Italy
| | | | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE, Biotecnologie Avanzate, Naples, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE, Biotecnologie Avanzate, Naples, Italy
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10
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Hsu JSJ, So M, Tang CSM, Karim A, Porsch RM, Wong C, Yu M, Yeung F, Xia H, Zhang R, Cherny SS, Chung PHY, Wong KKY, Sham PC, Ngo ND, Li M, Tam PKH, Lui VCH, Garcia-Barcelo MM. De novo mutations in Caudal Type Homeo Box transcription Factor 2 (CDX2) in patients with persistent cloaca. Hum Mol Genet 2019; 27:351-358. [PMID: 29177441 DOI: 10.1093/hmg/ddx406] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/27/2017] [Indexed: 12/24/2022] Open
Abstract
The cloaca is an embryonic cavity that is divided into the urogenital sinus and rectum upon differentiation of the cloacal epithelium triggered by tissue-specific transcription factors including CDX2. Defective differentiation leads to persistent cloaca in humans (PC), a phenotype recapitulated in Cdx2 mutant mice. PC is linked to hypo/hyper-vitaminosis A. Although no gene has ever been identified, there is a strong evidence for a genetic contribution to PC. We applied whole-exome sequencing and copy-number-variants analyses to 21 PC patients and their unaffected parents. The damaging p.Cys132* and p.Arg237His de novo CDX2 variants were identified in two patients. These variants altered the expression of CYP26A1, a direct CDX2 target encoding the major retinoic acid (RA)-degrading enzyme. Other RA genes, including the RA-receptor alpha, were also mutated. Genes governing the development of cloaca-derived structures were recurrently mutated and over-represented in the basement-membrane components set (q-value < 1.65 × 10-6). Joint analysis of the patients' profile highlighted the extracellular matrix-receptor interaction pathway (MsigDBID: M7098, FDR: q-value < 7.16 × 10-9). This is the first evidence that PC is genetic, with genes involved in the RA metabolism at the lead. Given the CDX2 de novo variants and the role of RA, our observations could potentiate preventive measures. For the first time, a gene recapitulating PC in mouse models is found mutated in humans.
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Affiliation(s)
- Jacob S J Hsu
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Manting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anwarul Karim
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Robert M Porsch
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Carol Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Michelle Yu
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Fanny Yeung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Huimin Xia
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, Guandong, China
| | - Ruizhong Zhang
- Department of Pediatric Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, Guandong, China
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Patrick H Y Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth K Y Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Ngoc Diem Ngo
- Department of Human Genetics, National Hospital of Pediatrics, Hà N?i, Vietnam
| | - Miaoxin Li
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul K H Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vincent C H Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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11
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The classification, genetic diagnosis and modelling of monogenic autoinflammatory disorders. Clin Sci (Lond) 2018; 132:1901-1924. [PMID: 30185613 PMCID: PMC6123071 DOI: 10.1042/cs20171498] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 07/30/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
Abstract
Monogenic autoinflammatory disorders are an increasingly heterogeneous group of conditions characterised by innate immune dysregulation. Improved genetic sequencing in recent years has led not only to the discovery of a plethora of conditions considered to be 'autoinflammatory', but also the broadening of the clinical and immunological phenotypic spectra seen in these disorders. This review outlines the classification strategies that have been employed for monogenic autoinflammatory disorders to date, including the primary innate immune pathway or the dominant cytokine implicated in disease pathogenesis, and highlights some of the advantages of these models. Furthermore, the use of the term 'autoinflammatory' is discussed in relation to disorders that cross the innate and adaptive immune divide. The utilisation of next-generation sequencing (NGS) in this population is examined, as are potential in vivo and in vitro methods of modelling to determine pathogenicity of novel genetic findings. Finally, areas where our understanding can be improved are highlighted, such as phenotypic variability and genotype-phenotype correlations, with the aim of identifying areas of future research.
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12
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Akamine S, Sagata N, Sakai Y, Kato TA, Nakahara T, Matsushita Y, Togao O, Hiwatashi A, Sanefuji M, Ishizaki Y, Torisu H, Saitsu H, Matsumoto N, Hara T, Sawa A, Kano S, Furue M, Kanba S, Shaw CA, Ohga S. Early-onset epileptic encephalopathy and severe developmental delay in an association with de novo double mutations in NF1 and MAGEL2. Epilepsia Open 2018; 3:81-85. [PMID: 29588991 PMCID: PMC5839317 DOI: 10.1002/epi4.12085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2017] [Indexed: 01/01/2023] Open
Abstract
Advance in the exome-wide sequencing analysis contributes to identifying hundreds of genes that are associated with early-onset epileptic encephalopathy and neurodevelopmental disorders. On the basis of massive sequencing data, functional interactions among different genes are suggested to explain the common molecular pathway underlying the pathogenic process of these disorders. However, the relevance of such interactions with the phenotypic severity or variety in an affected individual remains elusive. In this report, we present a 45-year-old woman with neurofibromatosis type 1 (NF1), infantile-onset epileptic encephalopathy, and severe developmental delay. Whole-exome sequencing identified de novo pathogenic mutations in NF1 and the Schaaf-Yang syndrome-associated gene, MAGEL2. Literature-curated interaction data predicted that NF1 and MAGEL2 proteins were closely connected in this network via their common interacting proteins. Direct conversion of fibroblasts into neurons in vitro showed that neuronal cells from 9 patients with NF1 expressed significantly lower levels of MAGEL2 (54%, p = 0.0047) than those from healthy individuals. These data provide the first evidence that pathogenic mutations of NF1 deregulate the expression of other neurodevelopmental disease-associated genes. De novo mutations in multiple genes may lead to severe developmental phenotypes through their cumulative effects or synergistic interactions.
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Affiliation(s)
- Satoshi Akamine
- Department of Pediatrics Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Noriaki Sagata
- Department of Neuropsychiatry Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Yasunari Sakai
- Department of Pediatrics Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry Graduate School of Medical Sciences Kyushu University Fukuoka Japan.,Innovation Center for Medical Redox Navigation Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Takeshi Nakahara
- Department of Dermatology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Yuki Matsushita
- Department of Pediatrics Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Osamu Togao
- Department of Radiology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Akio Hiwatashi
- Department of Radiology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Masafumi Sanefuji
- Department of Pediatrics Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Yoshito Ishizaki
- Department of Pediatrics Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Hiroyuki Torisu
- Department of Pediatrics Graduate School of Medical Sciences Kyushu University Fukuoka Japan.,Section of Pediatrics Department of Medicine Fukuoka Dental College Fukuoka Japan
| | - Hirotomo Saitsu
- Department of Human Genetics Yokohama City University Graduate School of Medicine Yokohama Japan.,Department of Biochemistry Hamamatsu University School of Medicine Hamamatsu Japan
| | - Naomichi Matsumoto
- Department of Human Genetics Yokohama City University Graduate School of Medicine Yokohama Japan
| | | | - Akira Sawa
- Departments of Psychiatry Mental Health, Neuroscience, and Biomedical Engineering Johns Hopkins University School of Medicine and Bloomberg School of Public Health Baltimore Maryland U.S.A
| | - Shinichi Kano
- Department of Psychiatry and Behavioral Sciences Johns Hopkins University School of Medicine and Bloomberg School of Public Health Baltimore Maryland U.S.A
| | - Masutaka Furue
- Department of Dermatology Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Shigenobu Kanba
- Department of Neuropsychiatry Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Chad A Shaw
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas U.S.A
| | - Shouichi Ohga
- Department of Pediatrics Graduate School of Medical Sciences Kyushu University Fukuoka Japan
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13
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Deltas C. Digenic inheritance and genetic modifiers. Clin Genet 2018; 93:429-438. [PMID: 28977688 DOI: 10.1111/cge.13150] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 12/28/2022]
Abstract
Digenic inheritance (DI) concerns pathologies with the simplest form of multigenic etiology, implicating more than 1 gene (and perhaps the environment). True DI is when biallelic or even triallelic mutations in 2 distinct genes, in cis or in trans, are necessary and sufficient to cause pathology with a defined diagnosis. In true DI, a heterozygous mutation in each of 2 genes alone is not associated with a recognizable phenotype. Well-documented diseases with true DI are so far rare and follow non-Mendelian inheritance. DI is also encountered when by serendipity, pathogenic mutations responsible for 2 distinct disease entities are co-inherited, leading to a mixed phenotype. Also, we can consider many true monogenic Mendelian conditions, which show impressively broad spectrum of phenotypes due to pseudo-DI, as a result of co-inheriting genetic modifiers (GMs). I am herewith reviewing examples of GM and embark on presenting some recent notable examples of true DI, with wider discussion of the literature. Undeniably, the advent of high throughput sequencing is bound to unravel more patients suffering with true DI conditions and elucidate many important GM, thus impacting precision medicine.
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Affiliation(s)
- C Deltas
- College of Medicine, Qatar University, Doha, Qatar.,Department of Biological Sciences, Molecular Medicine Research Center, University of Cyprus, Nicosia, Cyprus
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14
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Andolfo I, Russo R, Gambale A, Iolascon A. Hereditary stomatocytosis: An underdiagnosed condition. Am J Hematol 2018; 93:107-121. [PMID: 28971506 DOI: 10.1002/ajh.24929] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/26/2017] [Accepted: 09/27/2017] [Indexed: 12/11/2022]
Abstract
Hereditary stomatocytoses are a wide class of hemolytic anemias characterized by alterations of ionic flux with increased cation permeability that results in inappropriate shrinkage or swelling of the erythrocytes, and water lost or gained osmotically. The last few years have been crucial for new acquisitions in this field in terms of identifying new causative genes and of studying their pathogenetic mechanisms. This review summarizes the main features of erythrocyte membrane transport diseases, dividing them into forms with either isolated erythroid phenotype (nonsyndromic) or extra-hematological manifestations (syndromic), and focusing particularly on the most recent advances regarding dehydrated forms of hereditary stomatocytosis and familial pseudohyperkalemia.
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Affiliation(s)
- Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II; Napoli Italy
- CEINGE Biotecnologie Avanzate; Napoli Italy
| | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II; Napoli Italy
- CEINGE Biotecnologie Avanzate; Napoli Italy
| | - Antonella Gambale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II; Napoli Italy
- CEINGE Biotecnologie Avanzate; Napoli Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II; Napoli Italy
- CEINGE Biotecnologie Avanzate; Napoli Italy
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15
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Andolfo I, Manna F, De Rosa G, Rosato BE, Gambale A, Tomaiuolo G, Carciati A, Marra R, De Franceschi L, Iolascon A, Russo R. PIEZO1-R1864H rare variant accounts for a genetic phenotype-modifier role in dehydrated hereditary stomatocytosis. Haematologica 2017; 103:e94-e97. [PMID: 29191841 DOI: 10.3324/haematol.2017.180687] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples .,CEINGE, Biotecnologie Avanzate, Naples
| | - Francesco Manna
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples.,CEINGE, Biotecnologie Avanzate, Naples
| | - Gianluca De Rosa
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples.,CEINGE, Biotecnologie Avanzate, Naples
| | - Barbara Eleni Rosato
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples.,CEINGE, Biotecnologie Avanzate, Naples
| | - Antonella Gambale
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples.,CEINGE, Biotecnologie Avanzate, Naples
| | - Giovanna Tomaiuolo
- CEINGE, Biotecnologie Avanzate, Naples.,Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, "Federico II" University of Naples, Naples
| | - Antonio Carciati
- CEINGE, Biotecnologie Avanzate, Naples.,Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, "Federico II" University of Naples, Naples
| | - Roberta Marra
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples.,CEINGE, Biotecnologie Avanzate, Naples
| | | | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples.,CEINGE, Biotecnologie Avanzate, Naples
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples.,CEINGE, Biotecnologie Avanzate, Naples
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16
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Duerinckx S, Abramowicz M. The genetics of congenitally small brains. Semin Cell Dev Biol 2017; 76:76-85. [PMID: 28912110 DOI: 10.1016/j.semcdb.2017.09.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 12/14/2022]
Abstract
Primary microcephaly (PM) refers to a congenitally small brain, resulting from insufficient prenatal production of neurons, and serves as a model disease for brain volumic development. Known PM genes delineate several cellular pathways, among which the centriole duplication pathway, which provide interesting clues about the cellular mechanisms involved. The general interest of the genetic dissection of PM is illustrated by the convergence of Zika virus infection and PM gene mutations on congenital microcephaly, with CENPJ/CPAP emerging as a key target. Physical (protein-protein) and genetic (digenic inheritance) interactions of Wdr62 and Aspm have been demonstrated in mice, and should now be sought in humans using high throughput parallel sequencing of multiple PM genes in PM patients and control subjects, in order to categorize mutually interacting genes, hence delineating functional pathways in vivo in humans.
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Affiliation(s)
- Sarah Duerinckx
- IRIBHM, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Marc Abramowicz
- IRIBHM, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium; Department of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
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17
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Gazzo A, Raimondi D, Daneels D, Moreau Y, Smits G, Van Dooren S, Lenaerts T. Understanding mutational effects in digenic diseases. Nucleic Acids Res 2017; 45:e140. [PMID: 28911095 PMCID: PMC5587785 DOI: 10.1093/nar/gkx557] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 01/13/2023] Open
Abstract
To further our understanding of the complexity and genetic heterogeneity of rare diseases, it has become essential to shed light on how combinations of variants in different genes are responsible for a disease phenotype. With the appearance of a resource on digenic diseases, it has become possible to evaluate how digenic combinations differ in terms of the phenotypes they produce. All instances in this resource were assigned to two classes of digenic effects, annotated as true digenic and composite classes. Whereas in the true digenic class variants in both genes are required for developing the disease, in the composite class, a variant in one gene is sufficient to produce the phenotype, but an additional variant in a second gene impacts the disease phenotype or alters the age of onset. We show that a combination of variant, gene and higher-level features can differentiate between these two classes with high accuracy. Moreover, we show via the analysis of three digenic disorders that a digenic effect decision profile, extracted from the predictive model, motivates why an instance was assigned to either of the two classes. Together, our results show that digenic disease data generates novel insights, providing a glimpse into the oligogenic realm.
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Affiliation(s)
- Andrea Gazzo
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium
- MLG, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Daniele Raimondi
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium
- MLG, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dorien Daneels
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB, Laarbeeklaan 101, 1090 Brussel
| | - Yves Moreau
- ESAT-STADIUS, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Guillaume Smits
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium
- Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
- Center for Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium
| | - Sonia Van Dooren
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
- Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB, Laarbeeklaan 101, 1090 Brussel
| | - Tom Lenaerts
- Interuniversity Institute for Bioinformatics in Brussels, ULB-VUB, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium
- MLG, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium
- AI lab, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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18
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A commentary on ANKRD11 variants cause variable clinical features associated with KBG syndrome and Coffin-Siris-like syndrome. J Hum Genet 2017; 62:739-740. [PMID: 28566769 PMCID: PMC5537411 DOI: 10.1038/jhg.2017.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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19
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Kaur Y, de Souza RJ, Gibson WT, Meyre D. A systematic review of genetic syndromes with obesity. Obes Rev 2017; 18:603-634. [PMID: 28346723 DOI: 10.1111/obr.12531] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/29/2022]
Abstract
Syndromic monogenic obesity typically follows Mendelian patterns of inheritance and involves the co-presentation of other characteristics, such as mental retardation, dysmorphic features and organ-specific abnormalities. Previous reviews on obesity have reported 20 to 30 syndromes but no systematic review has yet been conducted on syndromic obesity. We searched seven databases using terms such as 'obesity', 'syndrome' and 'gene' to conduct a systematic review of literature on syndromic obesity. Our literature search identified 13,719 references. After abstract and full-text review, 119 relevant papers were eligible, and 42 papers were identified through additional searches. Our analysis of these 161 papers found that 79 obesity syndromes have been reported in literature. Of the 79 syndromes, 19 have been fully genetically elucidated, 11 have been partially elucidated, 27 have been mapped to a chromosomal region and for the remaining 22, neither the gene(s) nor the chromosomal location(s) have yet been identified. Interestingly, 54.4% of the syndromes have not been assigned a name, whereas 13.9% have more than one name. We report on organizational inconsistencies (e.g. naming discrepancies and syndrome classification) and provide suggestions for improvements. Overall, this review illustrates the need for increased clinical and genetic research on syndromes with obesity.
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Affiliation(s)
- Y Kaur
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - R J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - W T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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20
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Russo R, Andolfo I, Gambale A, De Rosa G, Manna F, Arillo A, Wandroo F, Bisconte MG, Iolascon A. GATA1 erythroid-specific regulation of SEC23B expression and its implication in the pathogenesis of congenital dyserythropoietic anemia type II. Haematologica 2017; 102:e371-e374. [PMID: 28550189 DOI: 10.3324/haematol.2016.162966] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy .,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Antonella Gambale
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Gianluca De Rosa
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Francesco Manna
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
| | | | - Farooq Wandroo
- Department of Haematology Sandwell and West Birmingham Hospital, NHS trust West Midlands UK
| | | | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Italy.,CEINGE Biotecnologie Avanzate, Napoli, Italy
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21
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Lattanzi W, Barba M, Di Pietro L, Boyadjiev SA. Genetic advances in craniosynostosis. Am J Med Genet A 2017; 173:1406-1429. [PMID: 28160402 DOI: 10.1002/ajmg.a.38159] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/30/2016] [Accepted: 01/06/2017] [Indexed: 12/22/2022]
Abstract
Craniosynostosis, the premature ossification of one or more skull sutures, is a clinically and genetically heterogeneous congenital anomaly affecting approximately one in 2,500 live births. In most cases, it occurs as an isolated congenital anomaly, that is, nonsyndromic craniosynostosis (NCS), the genetic, and environmental causes of which remain largely unknown. Recent data suggest that, at least some of the midline NCS cases may be explained by two loci inheritance. In approximately 25-30% of patients, craniosynostosis presents as a feature of a genetic syndrome due to chromosomal defects or mutations in genes within interconnected signaling pathways. The aim of this review is to provide a detailed and comprehensive update on the genetic and environmental factors associated with NCS, integrating the scientific findings achieved during the last decade. Focus on the neurodevelopmental, imaging, and treatment aspects of NCS is also provided.
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Affiliation(s)
- Wanda Lattanzi
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy.,Latium Musculoskeletal Tıssue Bank, Rome, Italy
| | - Marta Barba
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lorena Di Pietro
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Simeon A Boyadjiev
- Division of Genomic Medicine, Department of Pediatrics, Davis Medical Center, University of California, Sacramento, California
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22
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Wong JKL, Campbell D, Ngo ND, Yeung F, Cheng G, Tang CSM, Chung PHY, Tran NS, So MT, Cherny SS, Sham PC, Tam PK, Garcia-Barcelo MM. Genetic study of congenital bile-duct dilatation identifies de novo and inherited variants in functionally related genes. BMC Med Genomics 2016; 9:75. [PMID: 27955658 PMCID: PMC5154011 DOI: 10.1186/s12920-016-0236-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/07/2016] [Indexed: 12/18/2022] Open
Abstract
Background Congenital dilatation of the bile-duct (CDD) is a rare, mostly sporadic, disorder that results in bile retention with severe associated complications. CDD affects mainly Asians. To our knowledge, no genetic study has ever been conducted. Methods We aim to identify genetic risk factors by a “trio-based” exome-sequencing approach, whereby 31 CDD probands and their unaffected parents were exome-sequenced. Seven-hundred controls from the local population were used to detect gene-sets significantly enriched with rare variants in CDD patients. Results Twenty-one predicted damaging de novo variants (DNVs; 4 protein truncating and 17 missense) were identified in several evolutionarily constrained genes (p < 0.01). Six genes carrying DNVs were associated with human developmental disorders involving epithelial, connective or bone morphologies (PXDN, RTEL1, ANKRD11, MAP2K1, CYLD, ACAN) and four linked with cholangio- and hepatocellular carcinomas (PIK3CA, TLN1 CYLD, MAP2K1). Importantly, CDD patients have an excess of DNVs in cancer-related genes (p < 0.025). Thirteen genes were recurrently mutated at different sites, forming compound heterozygotes or functionally related complexes within patients. Conclusions Our data supports a strong genetic basis for CDD and show that CDD is not only genetically heterogeneous but also non-monogenic, requiring mutations in more than one genes for the disease to develop. The data is consistent with the rarity and sporadic presentation of CDD. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0236-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John K L Wong
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China
| | - Desmond Campbell
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China
| | | | - Fanny Yeung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Patrick H Y Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China.,Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 1F Room 5D HKJCBIR, 5 Sassoon Road, Hong Kong, SAR, China.,Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Paul K Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barcelo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China. .,Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
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23
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Timberlake AT, Choi J, Zaidi S, Lu Q, Nelson-Williams C, Brooks ED, Bilguvar K, Tikhonova I, Mane S, Yang JF, Sawh-Martinez R, Persing S, Zellner EG, Loring E, Chuang C, Galm A, Hashim PW, Steinbacher DM, DiLuna ML, Duncan CC, Pelphrey KA, Zhao H, Persing JA, Lifton RP. Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and common BMP2 alleles. eLife 2016; 5. [PMID: 27606499 PMCID: PMC5045293 DOI: 10.7554/elife.20125] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022] Open
Abstract
Premature fusion of the cranial sutures (craniosynostosis), affecting 1 in 2000 newborns, is treated surgically in infancy to prevent adverse neurologic outcomes. To identify mutations contributing to common non-syndromic midline (sagittal and metopic) craniosynostosis, we performed exome sequencing of 132 parent-offspring trios and 59 additional probands. Thirteen probands (7%) had damaging de novo or rare transmitted mutations in SMAD6, an inhibitor of BMP – induced osteoblast differentiation (p<10−20). SMAD6 mutations nonetheless showed striking incomplete penetrance (<60%). Genotypes of a common variant near BMP2 that is strongly associated with midline craniosynostosis explained nearly all the phenotypic variation in these kindreds, with highly significant evidence of genetic interaction between these loci via both association and analysis of linkage. This epistatic interaction of rare and common variants defines the most frequent cause of midline craniosynostosis and has implications for the genetic basis of other diseases. DOI:http://dx.doi.org/10.7554/eLife.20125.001 The bones in the front, back and sides of the human skull are not fused to one another at birth in order to allow the brain to double in size during the first year of life and continue growing into adulthood. However, one in 2,000 infants is born with a condition called craniosynostosis in which some of these bones have already fused. This fusion prevents the skull from growing properly, and can lead to the brain becoming compressed. As such, surgeons routinely undo the fusion in these infants to allow the brain and skull to grow normally. Eighty-five percent of craniosynostosis cases occur in infants with no other abnormalities, (called non-syndromic cases) and most have no other affected family member. It has therefore been unclear whether these infants have craniosynostosis due to a genetic or non-genetic cause. If the cause is genetic, it is also not clear whether a mutation in a single gene, the combined effects of many genes, or something in between is responsible. Now, by focusing on a group of 191 infants with premature fusion of bones joined at the midline of the skull, Timberlake et al. asked if any of the approximately 20,000 genes in the human genome were altered more frequently in these infants than would be expected by chance. This search revealed that rare mutations that disable one copy of a gene called SMAD6 in combination with a common DNA variant near another gene called BMP2 account for about 7% of infants with midline forms of craniosynostosis. These genes are both known to regulate how bones form, which explains how the mutation of these genes could lead to craniosynostosis. In all cases, the parents of these children were unaffected. This was typically because one parent had only the SMAD6 mutation while the other had only the common BMP2 variant; the transmission of both to their offspring resulted in craniosynostosis. The finding that a rare mutation’s effect is strongly modified by a common variant from another site in the genome is unprecedented. These findings will allow doctors to counsel families about the risk of having additional children with craniosynostosis. Timberlake et al. next plan to study more patients with craniosynostosis to identify additional genes that contribute to this disease. They will also look at other diseases to see whether the combination of rare mutation and common DNA variant could be behind other unexplained disorders. DOI:http://dx.doi.org/10.7554/eLife.20125.002
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Affiliation(s)
- Andrew T Timberlake
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States.,Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Jungmin Choi
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Samir Zaidi
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Qiongshi Lu
- Department of Biostatistics, Yale University School of Medicine, New Haven, United States
| | - Carol Nelson-Williams
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Eric D Brooks
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Kaya Bilguvar
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Yale Center for Genome Analysis, New Haven, United States
| | | | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Yale Center for Genome Analysis, New Haven, United States
| | - Jenny F Yang
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Rajendra Sawh-Martinez
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Sarah Persing
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Elizabeth G Zellner
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Erin Loring
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States.,Yale Center for Genome Analysis, New Haven, United States
| | - Carolyn Chuang
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Amy Galm
- Craniosynostosis and Positional Plagiocephaly Support, New York, United States
| | - Peter W Hashim
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Derek M Steinbacher
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Michael L DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, United States
| | - Charles C Duncan
- Department of Neurosurgery, Yale University School of Medicine, New Haven, United States
| | - Kevin A Pelphrey
- Child Study Center, Yale University School of Medicine, New Haven, United States
| | - Hongyu Zhao
- Department of Biostatistics, Yale University School of Medicine, New Haven, United States
| | - John A Persing
- Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, United States
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States.,Yale Center for Genome Analysis, New Haven, United States.,The Rockefeller University, New York, United States
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24
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Lupski JR. Clinical genomics: from a truly personal genome viewpoint. Hum Genet 2016; 135:591-601. [PMID: 27221143 DOI: 10.1007/s00439-016-1682-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/11/2016] [Indexed: 12/23/2022]
Abstract
The path to Clinical Genomics is punctuated by our understanding of what types of DNA structural and sequence variation contribute to disease, the many technical challenges to detect such variation genome-wide, and the initial struggles to interpret personal genome variation in the context of disease. This review describes one perspective of the development of clinical genomics; whereas the experimental challenges, and hurdles to overcoming them, might be deemed readily apparent, the non-technical issues for clinical implementation may be less obvious. Some of these latter challenges, including: (1) informed consent, (2) privacy, (3) what constitutes potentially pathogenic variation contributing to disease, (4) disease penetrance in populations, and (5) the genetic architecture of disease, and the struggles sometimes faced for solutions, are highlighted using illustrative examples.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 604B, One Baylor Plaza, Houston, TX, 77030, USA. .,Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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25
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Schüle R, Wiethoff S, Martus P, Karle KN, Otto S, Klebe S, Klimpe S, Gallenmüller C, Kurzwelly D, Henkel D, Rimmele F, Stolze H, Kohl Z, Kassubek J, Klockgether T, Vielhaber S, Kamm C, Klopstock T, Bauer P, Züchner S, Liepelt-Scarfone I, Schöls L. Hereditary spastic paraplegia: Clinicogenetic lessons from 608 patients. Ann Neurol 2016; 79:646-58. [DOI: 10.1002/ana.24611] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/14/2022]
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26
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Gazzo AM, Daneels D, Cilia E, Bonduelle M, Abramowicz M, Van Dooren S, Smits G, Lenaerts T. DIDA: A curated and annotated digenic diseases database. Nucleic Acids Res 2015; 44:D900-7. [PMID: 26481352 PMCID: PMC4702791 DOI: 10.1093/nar/gkv1068] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/05/2015] [Indexed: 02/07/2023] Open
Abstract
DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database is accessible via http://dida.ibsquare.be and currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided. Creating this new repository was essential as current databases do not allow one to retrieve detailed records regarding digenic combinations. Genes, variants, diseases and digenic combinations in DIDA are annotated with manually curated information and information mined from other online resources. Next to providing a unique resource for the development of new analysis methods, DIDA gives clinical and molecular geneticists a tool to find the most comprehensive information on the digenic nature of their diseases of interest.
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Affiliation(s)
- Andrea M Gazzo
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium MLG, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Dorien Daneels
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Elisa Cilia
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium MLG, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium
| | - Maryse Bonduelle
- Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Marc Abramowicz
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium
| | - Sonia Van Dooren
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, UZ Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium Center for Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Avenue JJ Crocq 15, 1020 Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Boulevard du Triomphe CP 263, 1050 Brussels, Belgium MLG, Département d'Informatique, Université Libre de Bruxelles, Boulevard du Triomphe, CP 212, 1050 Brussels, Belgium AI lab, Vakgroep Computerwetenschappen, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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27
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Kannengiesser C, Borie R, Ménard C, Réocreux M, Nitschké P, Gazal S, Mal H, Taillé C, Cadranel J, Nunes H, Valeyre D, Cordier JF, Callebaut I, Boileau C, Cottin V, Grandchamp B, Revy P, Crestani B. Heterozygous RTEL1 mutations are associated with familial pulmonary fibrosis. Eur Respir J 2015; 46:474-85. [PMID: 26022962 DOI: 10.1183/09031936.00040115] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 04/11/2015] [Indexed: 11/05/2022]
Abstract
Pulmonary fibrosis is a fatal disease with progressive loss of respiratory function. Defective telomere maintenance leading to telomere shortening is a cause of pulmonary fibrosis, as mutations in the telomerase component genes TERT (reverse transcriptase) and TERC (RNA component) are found in 15% of familial pulmonary fibrosis (FPF) cases. However, so far, about 85% of FPF remain genetically uncharacterised.Here, in order to identify new genetic causes of FPF, we performed whole-exome sequencing, with a candidate-gene approach, of 47 affected subjects from 35 families with FPF without TERT and TERC mutations.We identified heterozygous mutations in regulator of telomere elongation helicase 1 (RTEL1) in four families. RTEL1 is a DNA helicase with roles in DNA replication, genome stability, DNA repair and telomere maintenance. The heterozygous RTEL1 mutations segregated as an autosomal dominant trait in FPF, and were predicted by structural analyses to severely affect the function and/or stability of RTEL1. In agreement with this, RTEL1-mutated patients exhibited short telomeres in comparison with age-matched controls.Our results provide evidence that heterozygous RTEL1 mutations are responsible for FPF and, thereby, extend the clinical spectrum of RTEL1 deficiency. Thus, RTEL1 enlarges the number of telomere-associated genes implicated in FPF.
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Affiliation(s)
- Caroline Kannengiesser
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France These authors contributed equally to this work
| | - Raphael Borie
- APHP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE Centre de compétence des maladies pulmonaires rares, Paris, France These authors contributed equally to this work
| | | | | | - Patrick Nitschké
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France Imagine Institute, Paris, France
| | - Steven Gazal
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France Inserm, IAME, UMR 1137, Paris, France Plateforme de Génétique constitutionnelle-Nord (PfGC-Nord), Paris, France
| | - Hervé Mal
- APHP Service de Pneumologie B, Hôpital Bichat, Paris, France
| | - Camille Taillé
- APHP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE Centre de compétence des maladies pulmonaires rares, Paris, France
| | - Jacques Cadranel
- APHP, Service de Pneumologie, Centre de compétence des maladies pulmonaires rares, Hôpital Tenon, Paris, France Université paris 6, Paris, France
| | - Hilario Nunes
- APHP, Service de Pneumologie, Hôpital Avicenne, Centre de Compétence des Maladies Pulmonaires Rares, Bobigny, France Université Paris 13, Paris, France
| | - Dominique Valeyre
- APHP, Service de Pneumologie, Hôpital Avicenne, Centre de Compétence des Maladies Pulmonaires Rares, Bobigny, France Université Paris 13, Paris, France
| | - Jean François Cordier
- Université Claude Bernard Lyon 1, Lyon, France Service de Pneumologie, Centre national de référence des maladies pulmonaires rares, Hôpital Louis Pradel, Lyon, France
| | - Isabelle Callebaut
- IMPMC, Sorbonne Universités - UPMC Univ Paris 06, UMR CNRS 7590, Museum National d'Histoire Naturelle, IRD UMR 206, IUC, Paris, France
| | - Catherine Boileau
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Vincent Cottin
- Université Claude Bernard Lyon 1, Lyon, France Service de Pneumologie, Centre national de référence des maladies pulmonaires rares, Hôpital Louis Pradel, Lyon, France
| | - Bernard Grandchamp
- APHP Service de Génétique, Hôpital Bichat, Paris, France Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Patrick Revy
- Imagine Institute, Paris, France Laboratory of Genome Dynamics in the Immune System, INSERM UMR1163, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Paris, France
| | - Bruno Crestani
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France APHP, Hôpital Bichat, Service de Pneumologie A, DHU FIRE Centre de compétence des maladies pulmonaires rares, Paris, France
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28
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Excess of rare, inherited truncating mutations in autism. Nat Genet 2015; 47:582-8. [PMID: 25961944 PMCID: PMC4449286 DOI: 10.1038/ng.3303] [Citation(s) in RCA: 404] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/20/2015] [Indexed: 12/15/2022]
Abstract
To assess the relative impact of inherited and de novo variants on autism risk, we generated a comprehensive set of exonic single nucleotide variants (SNVs) and copy number variants (CNVs) from 2,377 autism families. We find that private, inherited truncating SNVs in conserved genes are enriched in probands (odds ratio=1.14, p=0.0002) compared to unaffected siblings, an effect with significant maternal transmission bias to sons. We also observe a bias for inherited CNVs, specifically for small (<100 kbp), maternally inherited events (p=0.01) that are enriched in CHD8 target genes (p=7.4×10−3). Using a logistic regression model, we show that private truncating SNVs and rare, inherited CNVs are statistically independent autism risk factors, with odds ratios of 1.11 (p=0.0002) and 1.23 (p=0.01), respectively. This analysis identifies a second class of candidate genes (e.g., RIMS1, CUL7, and LZTR1) where transmitted mutations may create a sensitized background but are unlikely to be completely penetrant.
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29
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Somatic mosaicism: implications for disease and transmission genetics. Trends Genet 2015; 31:382-92. [PMID: 25910407 DOI: 10.1016/j.tig.2015.03.013] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/21/2022]
Abstract
Nearly all of the genetic material among cells within an organism is identical. However, single-nucleotide variants (SNVs), small insertions/deletions (indels), copy-number variants (CNVs), and other structural variants (SVs) continually accumulate as cells divide during development. This process results in an organism composed of countless cells, each with its own unique personal genome. Thus, every human is undoubtedly mosaic. Mosaic mutations can go unnoticed, underlie genetic disease or normal human variation, and may be transmitted to the next generation as constitutional variants. We review the influence of the developmental timing of mutations, the mechanisms by which they arise, methods for detecting mosaic variants, and the risk of passing these mutations on to the next generation.
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Mutarelli M, Marwah V, Rispoli R, Carrella D, Dharmalingam G, Oliva G, di Bernardo D. A community-based resource for automatic exome variant-calling and annotation in Mendelian disorders. BMC Genomics 2014; 15 Suppl 3:S5. [PMID: 25078076 PMCID: PMC4083405 DOI: 10.1186/1471-2164-15-s3-s5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Mendelian disorders are mostly caused by single mutations in the DNA sequence of a gene, leading to a phenotype with pathologic consequences. Whole Exome Sequencing of patients can be a cost-effective alternative to standard genetic screenings to find causative mutations of genetic diseases, especially when the number of cases is limited. Analyzing exome sequencing data requires specific expertise, high computational resources and a reference variant database to identify pathogenic variants. Results We developed a database of variations collected from patients with Mendelian disorders, which is automatically populated thanks to an associated exome-sequencing pipeline. The pipeline is able to automatically identify, annotate and store insertions, deletions and mutations in the database. The resource is freely available online http://exome.tigem.it. The exome sequencing pipeline automates the analysis workflow (quality control and read trimming, mapping on reference genome, post-alignment processing, variation calling and annotation) using state-of-the-art software tools. The exome-sequencing pipeline has been designed to run on a computing cluster in order to analyse several samples simultaneously. The detected variants are annotated by the pipeline not only with the standard variant annotations (e.g. allele frequency in the general population, the predicted effect on gene product activity, etc.) but, more importantly, with allele frequencies across samples progressively collected in the database itself, stratified by Mendelian disorder. Conclusions We aim at providing a resource for the genetic disease community to automatically analyse whole exome-sequencing samples with a standard and uniform analysis pipeline, thus collecting variant allele frequencies by disorder. This resource may become a valuable tool to help dissecting the genotype underlying the disease phenotype through an improved selection of putative patient-specific causative or phenotype-associated variations.
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Manwar Hussain MR, Khan A, Ali Mohamoud HS. From genes to health - challenges and opportunities. Front Pediatr 2014; 2:12. [PMID: 24624370 PMCID: PMC3939617 DOI: 10.3389/fped.2014.00012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 02/10/2014] [Indexed: 11/13/2022] Open
Abstract
In genome science, the advancement in high-throughput sequencing technologies and bioinformatics analysis is facilitating the better understanding of Mendelian and complex trait inheritance. Charting the genetic basis of complex diseases - including pediatric cancer, and interpreting huge amount of next-generation sequencing data are among the major technical challenges to be overcome in order to understand the molecular basis of various diseases and genetic disorders. In this review, we provide insights into some major challenges currently hindering a better understanding of Mendelian and complex trait inheritance, and thus impeding medical benefits to patients.
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Affiliation(s)
- Muhammad Ramzan Manwar Hussain
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Diseases (PACER-HD), Department of Genetic Medicine, King Abdulaziz University , Jeddah , Saudi Arabia
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University , Mardan , Pakistan
| | - Hussein Sheikh Ali Mohamoud
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Diseases (PACER-HD), Department of Genetic Medicine, King Abdulaziz University , Jeddah , Saudi Arabia
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Marx SJ. Multiplicity of hormone-secreting tumors: common themes about cause, expression, and management. J Clin Endocrinol Metab 2013; 98:3139-48. [PMID: 23771922 PMCID: PMC3733851 DOI: 10.1210/jc.2013-1511] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
CONTEXT Multiplicity of hormone-secreting tumors occurs in a substantial portion of hormone-excess states. Multiplicity increases the difficulty of management and drives the selection of special strategies. EVIDENCE ACQUISITION This is a synthesis from publications about tumor development and expression, and also about types of clinical strategy for hormone-secreting tumors. EVIDENCE SYNTHESIS Comparisons were made between patient groups with solitary tumors vs those with multiple tumors. Major themes with clinical relevance emerged. Usually, tumor multiplicity develops from a genetic susceptibility in all cells of a tissue. This applies to hormone-secreting tumors that begin as either polyclonal (such as in the parathyroids of familial hypocalciuric hypercalcemia) or monoclonal tumors (such as in the parathyroids of multiple endocrine neoplasia type 1 [MEN1]). High penetrance of a hereditary tumor frequently results in bilaterality and in several other types of multiplicity. Managements are better for the hormone excess than for the associated cancers. Management strategies can be categorized broadly as ablation that is total, subtotal, or zero. Examples are discussed for each category, and 1 example of each category is named here: 1) total ablation of the entire tissue with effort to replace ablated functions (for example, in C-cell neoplasia of multiple endocrine neoplasia type 2); 2) subtotal ablation with increased likelihood of persistent disease or recurrent disease (for example, in the parathyroid tumors of MEN1); or 3) no ablation of tissue with or without the use of pharmacotherapy (for example, with blockers for secretion of stomach acid in gastrinomas of MEN1). CONCLUSIONS Tumor multiplicity usually arises from defects in all cells of the precursor tissue. Even the optimized managements involve compromises. Still, an understanding of pathophysiology and of therapeutic options should guide optimized management.
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Affiliation(s)
- Stephen J Marx
- Genetics and Endocrinology Section, Metabolic Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Abstract
The field of aortopathy, in common with other genomic disorders, is undergoing a revolution. This is largely driven by the implementation of newer forms of genetic sequencing (massively parallel or next-generation sequencing). Advantages conferred by this technology include reduced costs, reduced sequencing time and the ability to simultaneously test multiple genes. This has a significant advantage in the identification of genes disrupted in heritable aortopathies. These advances are enabling scientists and clinicians to identify key molecular pathways; translating fundamental genetic findings into a better understanding of disease mechanisms is ultimately leading to effective treatments. In outlining contemporary knowledge of genetic biomarkers in aortopathy we seek to demonstrate that the era of genomically orientated decision-making is here.
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Affiliation(s)
- Gillian Rea
- NIHR Biomedical Research Unit in Cardiovascular Disease, Royal Brompton & Harefield NHS Foundation Trust & Imperial College London, BRU Cardiovascular Genetics Office, Royal Brompton Hospital, Sydney Street, London, SW3 6NP, UK
- Northern Ireland Regional Genetics Service, Level A, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Fiona J Stewart
- Northern Ireland Regional Genetics Service, Level A, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
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Quinonez SC, Park JM, Rabah R, Owens KM, Yashar BM, Glover TW, Keegan CE. 9p partial monosomy and disorders of sex development: Review and postulation of a pathogenetic mechanism. Am J Med Genet A 2013; 161A:1882-96. [DOI: 10.1002/ajmg.a.36018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/27/2013] [Indexed: 12/12/2022]
Affiliation(s)
- Shane C. Quinonez
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - John M. Park
- Department of Urology; University of Michigan; Ann Arbor; Michigan
| | - Raja Rabah
- Department of Pathology; University of Michigan; Ann Arbor; Michigan
| | - Kailey M. Owens
- Department of Pediatrics, Division of Genetics; University of Michigan; Ann Arbor; Michigan
| | - Beverly M. Yashar
- Department of Human Genetics; University of Michigan; Ann Arbor; Michigan
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Esposito T, Sampaolo S, Limongelli G, Varone A, Formicola D, Diodato D, Farina O, Napolitano F, Pacileo G, Gianfrancesco F, Di Iorio G. Digenic mutational inheritance of the integrin alpha 7 and the myosin heavy chain 7B genes causes congenital myopathy with left ventricular non-compact cardiomyopathy. Orphanet J Rare Dis 2013; 8:91. [PMID: 23800289 PMCID: PMC3695851 DOI: 10.1186/1750-1172-8-91] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/12/2013] [Indexed: 12/19/2022] Open
Abstract
Background We report an Italian family in which the proband showed a severe phenotype characterized by the association of congenital fiber type disproportion (CFTD) with a left ventricular non-compaction cardiomyopathy (LVNC). This study was focused on the identification of the responsible gene/s. Methods and results Using the whole-exome sequencing approach, we identified the proband homozygous missense mutations in two genes, the myosin heavy chain 7B (MYH7B) and the integrin alpha 7 (ITGA7). Both genes are expressed in heart and muscle tissues, and both mutations were predicted to be deleterious and were not found in the healthy population. The R890C mutation in the MYH7B gene segregated with the LVNC phenotype in the examined family. It was also found in one unrelated patient affected by LVNC, confirming a causative role in cardiomyopathy. The E882K mutation in the ITGA7 gene, a key component of the basal lamina of muscle fibers, was found only in the proband, suggesting a role in CFTD. Conclusions This study identifies two novel disease genes. Mutation in MYH7B causes a classical LVNC phenotype, whereas mutation in ITGA7 causes CFTD. Both phenotypes represent alterations of skeletal and cardiac muscle maturation and are usually not severe. The severe phenotype of the proband is most likely due to a synergic effect of these two mutations. This study provides new insights into the genetics underlying Mendelian traits and demonstrates a role for digenic inheritance in complex phenotypes.
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Affiliation(s)
- Teresa Esposito
- Institute of Genetics and Biophysics, National Research Council of Italy, Naples, Italy.
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Boone PM, Campbell IM, Baggett BC, Soens ZT, Rao MM, Hixson PM, Patel A, Bi W, Cheung SW, Lalani SR, Beaudet AL, Stankiewicz P, Shaw CA, Lupski JR. Deletions of recessive disease genes: CNV contribution to carrier states and disease-causing alleles. Genome Res 2013; 23:1383-94. [PMID: 23685542 PMCID: PMC3759716 DOI: 10.1101/gr.156075.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Over 1200 recessive disease genes have been described in humans. The prevalence, allelic architecture, and per-genome load of pathogenic alleles in these genes remain to be fully elucidated, as does the contribution of DNA copy-number variants (CNVs) to carrier status and recessive disease. We mined CNV data from 21,470 individuals obtained by array-comparative genomic hybridization in a clinical diagnostic setting to identify deletions encompassing or disrupting recessive disease genes. We identified 3212 heterozygous potential carrier deletions affecting 419 unique recessive disease genes. Deletion frequency of these genes ranged from one occurrence to 1.5%. When compared with recessive disease genes never deleted in our cohort, the 419 recessive disease genes affected by at least one carrier deletion were longer and located farther from known dominant disease genes, suggesting that the formation and/or prevalence of carrier CNVs may be affected by both local and adjacent genomic features and by selection. Some subjects had multiple carrier CNVs (307 subjects) and/or carrier deletions encompassing more than one recessive disease gene (206 deletions). Heterozygous deletions spanning multiple recessive disease genes may confer carrier status for multiple single-gene disorders, for complex syndromes resulting from the combination of two or more recessive conditions, or may potentially cause clinical phenotypes due to a multiply heterozygous state. In addition to carrier mutations, we identified homozygous and hemizygous deletions potentially causative for recessive disease. We provide further evidence that CNVs contribute to the allelic architecture of both carrier and recessive disease-causing mutations. Thus, a complete recessive carrier screening method or diagnostic test should detect CNV alleles.
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Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Wirth B, Garbes L, Riessland M. How genetic modifiers influence the phenotype of spinal muscular atrophy and suggest future therapeutic approaches. Curr Opin Genet Dev 2013; 23:330-8. [PMID: 23602330 DOI: 10.1016/j.gde.2013.03.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/26/2013] [Accepted: 03/18/2013] [Indexed: 01/06/2023]
Abstract
Both complex disorders and monogenetic diseases are often modulated in their phenotype by further genetic, epigenetic or extrinsic factors. This gives rise to extensive phenotypic variability and potentially protection from disease manifestations, known as incomplete penetrance. Approaches including whole transcriptome, exome, genome, methylome or proteome analyses of highly discordant phenotypes in a few individuals harboring mutations at the same locus can help to identify these modifiers. This review describes the complexity of modifying factors of one of the most frequent autosomal recessively inherited disorders in humans, spinal muscular atrophy (SMA). We will outline how this knowledge contributes to understanding of the regulatory networks and molecular pathology of SMA and how this knowledge will influence future approaches to therapies.
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Affiliation(s)
- Brunhilde Wirth
- Institute of Human Genetics, Institute for Genetics, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
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Albers CA, Newbury-Ecob R, Ouwehand WH, Ghevaert C. New insights into the genetic basis of TAR (thrombocytopenia-absent radii) syndrome. Curr Opin Genet Dev 2013; 23:316-23. [PMID: 23602329 DOI: 10.1016/j.gde.2013.02.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/15/2013] [Accepted: 02/25/2013] [Indexed: 12/31/2022]
Abstract
Thrombocytopenia with absent radii (TAR) syndrome is a rare disorder combining specific skeletal abnormalities with a reduced platelet count. Rare proximal microdeletions of 1q21.1 are found in the majority of patients but are also found in unaffected parents. Recently it was shown that TAR syndrome is caused by the compound inheritance of a low-frequency noncoding SNP and a rare null allele in RBM8A, a gene encoding the exon-junction complex subunit member Y14 located in the deleted region. This finding provides new insight into the complex inheritance pattern and new clues to the molecular mechanisms underlying TAR syndrome. We discuss TAR syndrome in the context of abnormal phenotypes associated with proximal and distal 1q21.1 microdeletion and microduplications with incomplete penetrance and variable expressivity.
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Andersson L. Molecular consequences of animal breeding. Curr Opin Genet Dev 2013; 23:295-301. [PMID: 23601626 DOI: 10.1016/j.gde.2013.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/11/2013] [Accepted: 02/25/2013] [Indexed: 01/02/2023]
Abstract
The phenotypic diversity in domestic animals provides a unique opportunity to study genotype-phenotype relationships. The identification of causal mutations provides an insight into what types of mutations have contributed to phenotypic evolution in domestic animals. Whole genome sequencing has revealed that fixation of null alleles that inactivate genes, which are essential under natural conditions but disadvantageous on the farm, has not been a common mechanism for genetic adaptation in domestic animals. Numerous examples have been revealed where structural changes cause specific phenotypic effects by altering transcriptional regulation. An emerging feature is also the evolution of alleles by the accumulation of several consecutive mutations which affect gene function.
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Affiliation(s)
- Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-75123 Uppsala, Sweden.
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Auffray C, Caulfield T, Khoury MJ, Lupski JR, Schwab M, Veenstra T. 2012 highlights in translational 'omics. Genome Med 2013; 5:10. [PMID: 23369291 PMCID: PMC3707050 DOI: 10.1186/gm414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Charles Auffray
- CNRS Institute of Biological Sciences, European Institute for Systems Biology & Medicine, Claude Bernard University, Université de Lyon, France
| | - Timothy Caulfield
- Faculty of Law and School of Public Health, 461 Law Centre, University of Alberta, Edmonton, T6G 2H5, Canada
| | - Muin J Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, MS E61, Atlanta, GA 30333, USA
| | - James R Lupski
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbach Str. 112, 70367 Stuttgart, Germany
- Department of Clinical Pharmacology, Institute of Experimental and Clinical Pharmacology and Toxicology, University Hospital, 72076 Tübingen, Germany
| | - Timothy Veenstra
- Laboratory of Proteomics and Analytical Technologies, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
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