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Baker RI, Choi P, Curry N, Gebhart J, Gomez K, Henskens Y, Heubel-Moenen F, James P, Kadir RA, Kouides P, Lavin M, Lordkipanidze M, Lowe G, Mumford A, Mutch N, Nagler M, Othman M, Pabinger I, Sidonio R, Thomas W, O'Donnell JS. Standardization of definition and management for bleeding disorder of unknown cause: communication from the SSC of the ISTH. J Thromb Haemost 2024:S1538-7836(24)00163-6. [PMID: 38518896 DOI: 10.1016/j.jtha.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/08/2024] [Accepted: 03/08/2024] [Indexed: 03/24/2024]
Abstract
In many patients referred with significant bleeding phenotype, laboratory testing fails to define any hemostatic abnormalities. Clinical practice with respect to diagnosis and management of this patient cohort poses significant clinical challenges. We recommend that bleeding history in these patients should be objectively assessed using the International Society on Thrombosis and Haemostasis (ISTH) bleeding assessment tool. Patients with increased bleeding assessment tool scores should progress to hemostasis laboratory testing. To diagnose bleeding disorder of unknown cause (BDUC), normal complete blood count, prothrombin time, activated partial thromboplastin time, thrombin time, von Willebrand factor antigen, von Willebrand factor function, coagulation factors VIII, IX, and XI, and platelet light transmission aggregometry should be the minimum laboratory assessment. In some laboratories, additional specialized hemostasis testing may be performed to identify other rare causes of bleeding. We recommend that patients with a significant bleeding phenotype but normal laboratory investigations should be registered with a diagnosis of BDUC in preference to other terminology. Global hemostatic tests and markers of fibrinolysis demonstrate variable abnormalities, and their clinical significance remains uncertain. Targeted genomic sequencing examining candidate hemostatic genes has a low diagnostic yield. Underlying BDUC should be considered in patients with heavy menstrual bleeding since delays in diagnosis often extend to many years and negatively impact quality of life. Treatment options for BDUC patients include tranexamic acid, desmopressin, and platelet transfusions.
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Affiliation(s)
- Ross I Baker
- Western Australia Centre for Thrombosis and Haemostasis, Murdoch University, Perth, Australia; Perth Blood Institute, Clinical Research Unit, Perth, Australia; Hollywood Hospital Haemophilia Centre, Haematology Academic Unit, Perth, Australia; Irish-Australian Blood Collaborative Network, Royal College of Surgeons in Ireland, Ireland; Perth Blood Institute, Perth, Australia.
| | - Philip Choi
- Haematology Department, The Canberra Hospital, Canberra, Australia; Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Nicola Curry
- Department of Clinical Haematology, Haemophilia & Thrombosis Centre, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom; Radcliffe Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Johanna Gebhart
- Department of Medicine, Division of Hematology and Hemostaseology, Medical University Vienna, Vienna, Austria
| | - Keith Gomez
- Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London National Health Service Foundation Trust, London, United Kingdom
| | - Yvonne Henskens
- Central Diagnostic Laboratory, Maastricht University Medical Centre, Maastricht, The Netherlands; Department of Biochemistry, Institute for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Floor Heubel-Moenen
- Department of Hematology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Paula James
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Rezan Abdul Kadir
- Department of Obstetrics and Gynaecology, Katharine Dormandy Haemophilia and Thrombosis Centre, The Royal Free National Health Service Hospital, London, United Kingdom; Institute for Women's Health, University College, London, United Kingdom
| | - Peter Kouides
- Mary M. Gooley Hemophilia Center, Rochester, New York, USA
| | - Michelle Lavin
- Irish-Australian Blood Collaborative Network, Royal College of Surgeons in Ireland, Ireland; Perth Blood Institute, Perth, Australia; National Coagulation Centre, St. James's Hospital, Dublin, Ireland; Irish Centre for Vascular Biology, School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Marie Lordkipanidze
- Research Center, Montreal Heart Institute, Montreal, Quebec, Canada; Faculty of Pharmacy, Université de Montréal, Montreal, Quebec, Canada
| | - Gillian Lowe
- West Midlands Adult Comprehensive Care Haemophilia Centre, University Hospitals Birmingham National Health Service Foundation Trust, Birmingham, United Kingdom
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Nicola Mutch
- Aberdeen Cardiovascular and Diabetes Centre, Institute of Medical Sciences, School of Medicine, United Kingdom; Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Michael Nagler
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland; Department of Clinical Chemistry, Inselspital University Hospital Bern, Bern, Switzerland
| | - Maha Othman
- Department of Biomedical and Molecular Sciences, School of Medicine, Queen's University, Kingston, Ontario, Canada; School of Baccalaureate Nursing, St Lawrence College, Kingston, Ontario, Canada; Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Ingrid Pabinger
- Department of Medicine, Division of Hematology and Hemostaseology, Medical University Vienna, Vienna, Austria
| | - Robert Sidonio
- Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Will Thomas
- Department of Haematology, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, United Kingdom
| | - James S O'Donnell
- Irish-Australian Blood Collaborative Network, Royal College of Surgeons in Ireland, Ireland; Perth Blood Institute, Perth, Australia; National Coagulation Centre, St. James's Hospital, Dublin, Ireland; Irish Centre for Vascular Biology, School of Pharmacy & Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
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2
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Cuppens T, Kaur M, Kumar AA, Shatto J, Ng ACH, Leclercq M, Reformat MZ, Droit A, Dunham I, Bolduc FV. Developing a cluster-based approach for deciphering complexity in individuals with neurodevelopmental differences. Front Pediatr 2023; 11:1171920. [PMID: 37790694 PMCID: PMC10543689 DOI: 10.3389/fped.2023.1171920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/01/2023] [Indexed: 10/05/2023] Open
Abstract
Objective Individuals with neurodevelopmental disorders such as global developmental delay (GDD) present both genotypic and phenotypic heterogeneity. This diversity has hampered developing of targeted interventions given the relative rarity of each individual genetic etiology. Novel approaches to clinical trials where distinct, but related diseases can be treated by a common drug, known as basket trials, which have shown benefits in oncology but have yet to be used in GDD. Nonetheless, it remains unclear how individuals with GDD could be clustered. Here, we assess two different approaches: agglomerative and divisive clustering. Methods Using the largest cohort of individuals with GDD, which is the Deciphering Developmental Disorders (DDD), characterized using a systematic approach, we extracted genotypic and phenotypic information from 6,588 individuals with GDD. We then used a k-means clustering (divisive) and hierarchical agglomerative clustering (HAC) to identify subgroups of individuals. Next, we extracted gene network and molecular function information with regard to the clusters identified by each approach. Results HAC based on phenotypes identified in individuals with GDD revealed 16 clusters, each presenting with one dominant phenotype displayed by most individuals in the cluster, along with other minor phenotypes. Among the most common phenotypes reported were delayed speech, absent speech, and seizure. Interestingly, each phenotypic cluster molecularly included several (3-12) gene sub-networks of more closely related genes with diverse molecular function. k-means clustering also segregated individuals harboring those phenotypes, but the genetic pathways identified were different from the ones identified from HAC. Conclusion Our study illustrates how divisive (k-means) and agglomerative clustering can be used in order to group individuals with GDD for future basket trials. Moreover, the result of our analysis suggests that phenotypic clusters should be subdivided into molecular sub-networks for an increased likelihood of successful treatment. Finally, a combination of both agglomerative and divisive clustering may be required for developing of a comprehensive treatment.
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Affiliation(s)
- Tania Cuppens
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Manpreet Kaur
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Ajay A. Kumar
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julie Shatto
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Andy Cheuk-Him Ng
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
| | - Mickael Leclercq
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Marek Z. Reformat
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire de L'Université Laval, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom
| | - François V. Bolduc
- Department of Pediatric Neurology, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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3
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Gebetsberger J, Mott K, Bernar A, Klopocki E, Streif W, Schulze H. State-of-the-Art Targeted High-Throughput Sequencing for Detecting Inherited Platelet Disorders. Hamostaseologie 2023; 43:244-251. [PMID: 37611606 DOI: 10.1055/a-2099-3266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
Inherited platelet disorders (IPDs) are a heterogeneous group of rare entities caused by molecular divergence in genes relevant for platelet formation and function. A rational diagnostic approach is necessary to counsel and treat patients with IPDs. With the introduction of high-throughput sequencing at the beginning of this millennium, a more accurate diagnosis of IPDs has become available. We discuss advantages and limitations of genetic testing, technical issues, and ethical aspects. Additionally, we provide information on the clinical significance of different classes of variants and how they are correctly reported.
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Affiliation(s)
- Jennifer Gebetsberger
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Tirol, Austria
| | - Kristina Mott
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Aline Bernar
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Tirol, Austria
| | - Eva Klopocki
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Werner Streif
- Department of Pediatrics I, Medical University of Innsbruck, Innsbruck, Tirol, Austria
| | - Harald Schulze
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
- Center for Rare Blood Cell Disorders, Center for Rare Diseases, University Hospital Würzburg, Würzburg, Germany
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Liu X, Gao L, Peng Y, Fang Z, Wang J. PheSom: a term frequency-based method for measuring human phenotype similarity on the basis of MeSH vocabulary. Front Genet 2023; 14:1185790. [PMID: 37496714 PMCID: PMC10366691 DOI: 10.3389/fgene.2023.1185790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Background: Phenotype similarity calculation should be used to help improve drug repurposing. In this study, based on the MeSH terms describing the phenotypes deposited in OMIM, we proposed a method, namely, PheSom (Phenotype Similarity On MeSH), to measure the similarity between phenotypes. PheSom counted the number of overlapping MeSH terms between two phenotypes and then took the weight of every MeSH term within each phenotype into account according to the term frequency-inverse document frequency (FIDC). Phenotype-related genes were used for the evaluation of our method. Results: A 7,739 × 7,739 similarity score matrix was finally obtained and the number of phenotype pairs was dramatically decreased with the increase of similarity score. Besides, the overlapping rates of phenotype-related genes were remarkably increased with the increase of similarity score between phenotypes, which supports the reliability of our method. Conclusion: We anticipate our method can be applied to identifying novel therapeutic methods for complex diseases.
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Affiliation(s)
- Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Ling Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yonglin Peng
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhonghai Fang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering and Technology, Tianjin Medical University, Tianjin, China
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5
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Marconi C, Pecci A, Palombo F, Melazzini F, Bottega R, Nardi E, Bozzi V, Faleschini M, Barozzi S, Giangregorio T, Magini P, Balduini CL, Savoia A, Seri M, Noris P, Pippucci T. Exome sequencing in 116 patients with inherited thrombocytopenia that remained of unknown origin after systematic phenotype-driven diagnostic workup. Haematologica 2023; 108:1909-1919. [PMID: 36519321 PMCID: PMC10316235 DOI: 10.3324/haematol.2022.280993] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/29/2022] [Indexed: 11/01/2023] Open
Abstract
Inherited thrombocytopenias (IT) are genetic diseases characterized by low platelet count, sometimes associated with congenital defects or a predisposition to develop additional conditions. Next-generation sequencing has substantially improved our knowledge of IT, with more than 40 genes identified so far, but obtaining a molecular diagnosis remains a challenge especially for patients with non-syndromic forms, having no clinical or functional phenotypes that raise suspicion about specific genes. We performed exome sequencing (ES) in a cohort of 116 IT patients (89 families), still undiagnosed after a previously validated phenotype-driven diagnostic algorithm including a targeted analysis of suspected genes. ES achieved a diagnostic yield of 36%, with a gain of 16% over the diagnostic algorithm. This can be explained by genetic heterogeneity and unspecific genotype-phenotype relationships that make the simultaneous analysis of all the genes, enabled by ES, the most reasonable strategy. Furthermore, ES disentangled situations that had been puzzling because of atypical inheritance, sex-related effects or false negative laboratory results. Finally, ES-based copy number variant analysis disclosed an unexpectedly high prevalence of RUNX1 deletions, predisposing to hematologic malignancies. Our findings demonstrate that ES, including copy number variant analysis, can substantially contribute to the diagnosis of IT and can solve diagnostic problems that would otherwise remain a challenge.
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Affiliation(s)
- Caterina Marconi
- Department of Medical and Surgical Science, University of Bologna, Bologna
| | - Alessandro Pecci
- Department of Internal Medicine, University of Pavia, Pavia, Italy; Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Flavia Palombo
- Department of Medical and Surgical Science, University of Bologna, Bologna
| | - Federica Melazzini
- Department of Internal Medicine, University of Pavia, Pavia, Italy; Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Roberta Bottega
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste
| | - Elena Nardi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna
| | - Valeria Bozzi
- Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | | | - Serena Barozzi
- Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | | | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna
| | | | - Anna Savoia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy; Department of Medical Sciences, University of Trieste, Trieste
| | - Marco Seri
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; Medical Genetics Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna.
| | - Patrizia Noris
- Department of Internal Medicine, University of Pavia, Pavia, Italy; Medicina Generale 1, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Tommaso Pippucci
- Medical Genetics Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, Policlinico di Sant'Orsola, Bologna
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6
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Ver Donck F, Ramaekers K, Thys C, Van Laer C, Peerlinck K, Van Geet C, Eto K, Labarque V, Freson K. Ribosome dysfunction underlies SLFN14-related thrombocytopenia. Blood 2023; 141:2261-2274. [PMID: 36790527 PMCID: PMC10646786 DOI: 10.1182/blood.2022017712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/16/2023] Open
Abstract
Pathogenic missense variants in SLFN14, which encode an RNA endoribonuclease protein that regulates ribosomal RNA (rRNA) degradation, are known to cause inherited thrombocytopenia (TP) with impaired platelet aggregation and adenosine triphosphate secretion. Despite mild laboratory defects, the patients displayed an obvious bleeding phenotype. However, the function of SLFN14 in megakaryocyte (MK) and platelet biology remains unknown. This study aimed to model the disease in an immortalized MK cell line (imMKCL) and to characterize the platelet transcriptome in patients with the SLFN14 K219N variant. MK derived from heterozygous and homozygous SLFN14 K219N imMKCL and stem cells of blood from patients mainly presented with a defect in proplatelet formation and mitochondrial organization. SLFN14-defective platelets and mature MK showed signs of rRNA degradation; however, this was absent in undifferentiated imMKCL cells and granulocytes. Total platelet RNA was sequenced in 2 patients and 19 healthy controls. Differential gene expression analysis yielded 2999 and 2888 significantly (|log2 fold change| >1, false discovery rate <0.05) up- and downregulated genes, respectively. Remarkably, these downregulated genes were not enriched in any biological pathway, whereas upregulated genes were enriched in pathways involved in (mitochondrial) translation and transcription, with a significant upregulation of 134 ribosomal protein genes (RPGs). The upregulation of mitochondrial RPGs through increased mammalian target of rapamycin complex 1 (mTORC1) signaling in SLFN14 K219N MK seems to be a compensatory response to rRNA degradation. mTORC1 inhibition with rapamycin resulted in further enhanced rRNA degradation in SLFN14 K219N MK. Taken together, our study indicates dysregulation of mTORC1 coordinated ribosomal biogenesis is the disease mechanism for SLFN14-related TP.
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Affiliation(s)
- Fabienne Ver Donck
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Kato Ramaekers
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Chantal Thys
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Christine Van Laer
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
- Clinical Department of Laboratory Medicine, Leuven University Hospitals, Leuven, Belgium
| | - Kathelijne Peerlinck
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
- Vascular Medicine and Hemostasis, Leuven University Hospitals, Leuven, Belgium
| | - Chris Van Geet
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
- Paediatric Hemato-Oncology, Leuven University Hospitals, Leuven, Belgium
| | - Koji Eto
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Regenerative Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Veerle Labarque
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
- Paediatric Hemato-Oncology, Leuven University Hospitals, Leuven, Belgium
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
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7
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Greene D, Pirri D, Frudd K, Sackey E, Al-Owain M, Giese APJ, Ramzan K, Riaz S, Yamanaka I, Boeckx N, Thys C, Gelb BD, Brennan P, Hartill V, Harvengt J, Kosho T, Mansour S, Masuno M, Ohata T, Stewart H, Taibah K, Turner CLS, Imtiaz F, Riazuddin S, Morisaki T, Ostergaard P, Loeys BL, Morisaki H, Ahmed ZM, Birdsey GM, Freson K, Mumford A, Turro E. Genetic association analysis of 77,539 genomes reveals rare disease etiologies. Nat Med 2023; 29:679-688. [PMID: 36928819 PMCID: PMC10033407 DOI: 10.1038/s41591-023-02211-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/06/2023] [Indexed: 03/18/2023]
Abstract
The genetic etiologies of more than half of rare diseases remain unknown. Standardized genome sequencing and phenotyping of large patient cohorts provide an opportunity for discovering the unknown etiologies, but this depends on efficient and powerful analytical methods. We built a compact database, the 'Rareservoir', containing the rare variant genotypes and phenotypes of 77,539 participants sequenced by the 100,000 Genomes Project. We then used the Bayesian genetic association method BeviMed to infer associations between genes and each of 269 rare disease classes assigned by clinicians to the participants. We identified 241 known and 19 previously unidentified associations. We validated associations with ERG, PMEPA1 and GPR156 by searching for pedigrees in other cohorts and using bioinformatic and experimental approaches. We provide evidence that (1) loss-of-function variants in the Erythroblast Transformation Specific (ETS)-family transcription factor encoding gene ERG lead to primary lymphoedema, (2) truncating variants in the last exon of transforming growth factor-β regulator PMEPA1 result in Loeys-Dietz syndrome and (3) loss-of-function variants in GPR156 give rise to recessive congenital hearing impairment. The Rareservoir provides a lightweight, flexible and portable system for synthesizing the genetic and phenotypic data required to study rare disease cohorts with tens of thousands of participants.
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Affiliation(s)
- Daniel Greene
- Department of Medicine, University of Cambridge, Cambridge, UK
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Pirri
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Karen Frudd
- National Heart and Lung Institute, Imperial College London, London, UK
- University College London Institute of Ophthalmology, University College London, London, UK
| | - Ege Sackey
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
| | - Mohammed Al-Owain
- Department of Medical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Arnaud P J Giese
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Khushnooda Ramzan
- Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Sehar Riaz
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Itaru Yamanaka
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Nele Boeckx
- Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
| | - Chantal Thys
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul Brennan
- Northern Genetics Service, Newcastle upon Tyne Hospitals National Health Service Trust International Centre for Life, Newcastle upon Tyne, UK
| | - Verity Hartill
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds Teaching Hospitals National Health Service Trust, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Julie Harvengt
- Centre for Medical Genetics, Centre Hospitalier Universitaire de Liège, Liège, Belgium
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Nagano, Japan
- Center for Medical Genetics, Shinshu University Hospital, Nagano, Japan
| | - Sahar Mansour
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
- South West Thames Regional Genetics Service, St. George's University Hospitals National Health Service Foundation Trust, London, UK
| | - Mitsuo Masuno
- Department of Medical Genetics, Kawasaki Medical School Hospital, Okayama, Japan
| | | | - Helen Stewart
- Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Khalid Taibah
- Ear Nose and Throat Medical Centre, Riyadh, Saudi Arabia
| | - Claire L S Turner
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - Faiqa Imtiaz
- Department of Clinical Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Takayuki Morisaki
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
- Division of Molecular Pathology and Department of Internal Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Pia Ostergaard
- Molecular and Clinical Sciences Institute, St. George's University of London, London, UK
| | - Bart L Loeys
- Center for Medical Genetics, Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hiroko Morisaki
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center, Osaka, Japan
- Department of Medical Genetics, Sakakibara Heart Institute, Tokyo, Japan
| | - Zubair M Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, Baltimore, MD, USA
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Graeme M Birdsey
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- South West National Health Service Genomic Medicine Service Alliance, Bristol, UK
| | - Ernest Turro
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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8
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Shu B, Shen H, Shao X, Luo F, Li T, Zhou Z. Human phenotype ontology annotation and cluster analysis for pulmonary atresia to unravel clinical outcomes. Front Cardiovasc Med 2022; 9:898289. [PMID: 35966552 PMCID: PMC9372274 DOI: 10.3389/fcvm.2022.898289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
Background Pulmonary atresia (PA) is a heterogeneous congenital heart defect and ventricular septal defect (VSD) is the most vital factor for the conventional classification of PA patients. The simple dichotomy could not fully describe the cardiac morphologies and pathophysiology in such a complex disease. We utilized the Human Phenotype Ontology (HPO) database to explore the phenotypic patterns of PA and the phenotypic influence on prognosis. Methods We recruited 786 patients with diagnoses of PA between 2008 and 2016 at Fuwai Hospital. According to cardiovascular phenotypes of patients, we retrieved 52 HPO terms for further analyses. The patients were classified into three clusters based on unsupervised hierarchical clustering. We used Kaplan–Meier curves to estimate survival, the log-rank test to compare survival between clusters, and univariate and multivariate Cox proportional hazards regression modeling to investigate potential risk factors. Results According to HPO term distribution, we observed significant differences of morphological abnormalities in 3 clusters. We defined cluster 1 as being associated with Tetralogy of Fallot (TOF), VSD, right ventricular hypertrophy (RVH), and aortopulmonary collateral arteries (ACA). ACA was not included in the cluster classification because it was not an HPO term. Cluster 2 was associated with hypoplastic right heart (HRH), atrial septal defect (ASD) and tricuspid disease as the main morphological abnormalities. Cluster 3 presented higher frequency of single ventricle (SV), dextrocardia, and common atrium (CA). The mortality rate in cluster 1 was significantly lower than the rates in cluster 2 and 3 (p = 0.04). Multivariable analysis revealed that abnormal atrioventricular connection (AAC, p = 0.011) and persistent left superior vena cava (LSVC, p = 0.003) were associated with an increased risk of mortality. Conclusions Our study reported a large cohort with clinical phenotypic, surgical strategy and long time follow-up. In addition, we provided a precise classification and successfully risk stratification for patients with PA.
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9
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Network-Based Methods for Approaching Human Pathologies from a Phenotypic Point of View. Genes (Basel) 2022; 13:genes13061081. [PMID: 35741843 PMCID: PMC9222217 DOI: 10.3390/genes13061081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 01/27/2023] Open
Abstract
Network and systemic approaches to studying human pathologies are helping us to gain insight into the molecular mechanisms of and potential therapeutic interventions for human diseases, especially for complex diseases where large numbers of genes are involved. The complex human pathological landscape is traditionally partitioned into discrete “diseases”; however, that partition is sometimes problematic, as diseases are highly heterogeneous and can differ greatly from one patient to another. Moreover, for many pathological states, the set of symptoms (phenotypes) manifested by the patient is not enough to diagnose a particular disease. On the contrary, phenotypes, by definition, are directly observable and can be closer to the molecular basis of the pathology. These clinical phenotypes are also important for personalised medicine, as they can help stratify patients and design personalised interventions. For these reasons, network and systemic approaches to pathologies are gradually incorporating phenotypic information. This review covers the current landscape of phenotype-centred network approaches to study different aspects of human diseases.
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10
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Gomez K. Advances in the diagnosis of heritable platelet disorders. Blood Rev 2022; 56:100972. [PMID: 35595614 DOI: 10.1016/j.blre.2022.100972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
The last decade has seen large increases in the number of patients registered with heritable platelet disorders in national databases of bleeding disorders. Although individually rare, collectively they are a relatively common cause of heritable bleeding. This revolution has come about through the application of high-throughput sequencing strategies and efforts to standardize diagnostic testing. There is renewed interest in established parameters such as platelet volume and utilising simple tools such as blood smears. The diagnostic yield from peripheral blood smears can be improved with new microscopy techniques that could potentially assist in determining which patients need to be referred to tertiary centres for specialist testing. A better understanding of the other clinical features that can accompany abnormalities of platelet number or function, can lead to better clinical management and prevention of serious complications. There are challenges for clinicians who need to be aware of these developments, understand the limitations of new diagnostic techniques and keep abreast of strategies for incorporation into clinical practice. This review discusses some of these approaches, the limitations that clinicians need to be aware of and techniques that may enter clinical use in the future.
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Affiliation(s)
- Keith Gomez
- Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK.
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11
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Wang YC, Wu Y, Choi J, Allington G, Zhao S, Khanfar M, Yang K, Fu PY, Wrubel M, Yu X, Mekbib KY, Ocken J, Smith H, Shohfi J, Kahle KT, Lu Q, Jin SC. Computational Genomics in the Era of Precision Medicine: Applications to Variant Analysis and Gene Therapy. J Pers Med 2022; 12:175. [PMID: 35207663 PMCID: PMC8878256 DOI: 10.3390/jpm12020175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid methodological advances in statistical and computational genomics have enabled researchers to better identify and interpret both rare and common variants responsible for complex human diseases. As we continue to see an expansion of these advances in the field, it is now imperative for researchers to understand the resources and methodologies available for various data types and study designs. In this review, we provide an overview of recent methods for identifying rare and common variants and understanding their roles in disease etiology. Additionally, we discuss the strategy, challenge, and promise of gene therapy. As computational and statistical approaches continue to improve, we will have an opportunity to translate human genetic findings into personalized health care.
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Affiliation(s)
- Yung-Chun Wang
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Yuchang Wu
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Julie Choi
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Garrett Allington
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA; (H.S.); (K.T.K.)
| | - Shujuan Zhao
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Mariam Khanfar
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Kuangying Yang
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Po-Ying Fu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Max Wrubel
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
| | - Xiaobing Yu
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
- Department of Computer Science & Engineering, Washington University, St. Louis, MO 63130, USA
| | - Kedous Y. Mekbib
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - Jack Ocken
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - Hannah Smith
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA; (H.S.); (K.T.K.)
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - John Shohfi
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA; (K.Y.M.); (J.O.); (J.S.)
| | - Kristopher T. Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA; (H.S.); (K.T.K.)
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Qiongshi Lu
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Sheng Chih Jin
- Department of Genetics, School of Medicine, Washington University, St. Louis, MO 63110, USA; (Y.-C.W.); (J.C.); (S.Z.); (M.K.); (K.Y.); (P.-Y.F.); (M.W.); (X.Y.)
- Department of Pediatrics, School of Medicine, Washington University, St. Louis, MO 63110, USA
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12
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He Q, Shen H, Shao X, Chen W, Wu Y, Liu R, Li S, Zhou Z. Cardiovascular Phenotypes Profiling for L-Transposition of the Great Arteries and Prognosis Analysis. Front Cardiovasc Med 2022; 8:781041. [PMID: 35127856 PMCID: PMC8814104 DOI: 10.3389/fcvm.2021.781041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/23/2021] [Indexed: 11/24/2022] Open
Abstract
Objectives Congenitally corrected transposition of the great arteries (ccTGA) is a rare and complex congenital heart disease with the characteristics of double discordance. Enormous co-existed anomalies are the culprit of prognosis evaluation and clinical decision. We aim at delineating a novel ccTGA clustering modality under human phenotype ontology (HPO) instruction and elucidating the relationship between phenotypes and prognosis in patients with ccTGA. Methods A retrospective review of 270 patients diagnosed with ccTGA in Fuwai hospital from 2009 to 2020 and cross-sectional follow-up were performed. HPO-instructed clustering method was administered in ccTGA risk stratification. Kaplan-Meier survival, Landmark analysis, and cox regression analysis were used to investigate the difference of outcomes among clusters. Results The median follow-up time was 4.29 (2.07–7.37) years. A total of three distinct phenotypic clusters were obtained after HPO-instructed clustering with 21 in cluster 1, 136 in cluster 2, and 113 in cluster 3. Landmark analysis revealed significantly worse mid-term outcomes in all-cause mortality (p = 0.021) and composite endpoints (p = 0.004) of cluster 3 in comparison with cluster 1 and cluster 2. Multivariate analysis indicated that pulmonary arterial hypertension (PAH), atrioventricular septal defect (AVSD), and arrhythmia were risk factors for composite endpoints. Moreover, the surgical treatment was significantly different among the three groups (p < 0.001) and surgical strategies had different effects on the prognosis of the different phenotypic clusters. Conclusions Human phenotype ontology-instructed clustering can be a potentially powerful tool for phenotypic risk stratification in patients with complex congenital heart diseases, which may improve prognosis prediction and clinical decision.
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Affiliation(s)
- Qiyu He
- Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huayan Shen
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyang Shao
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen Chen
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafeng Wu
- Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing, China
| | - Rui Liu
- Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shoujun Li
- Pediatric Cardiac Center, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Shoujun Li
| | - Zhou Zhou
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Zhou Zhou
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13
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Shen H, He Q, Shao X, Li S, Zhou Z. Deep Phenotypic Analysis for Transposition of the Great Arteries and Prognosis Implication. J Am Heart Assoc 2022; 11:e023181. [PMID: 35001652 PMCID: PMC9238490 DOI: 10.1161/jaha.121.023181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background Transposition of the great arteries (TGA) consists of about 3% of all congenital heart diseases and 20% of cyanotic congenital heart diseases. It is always accompanied by a series of other cardiac malformations that affect the surgical intervention strategy as well as prognosis. In this study, we comprehensively analyzed the phenotypes of the patients who had TGA with concordant atrioventricular and discordant ventriculoarterial connections and explored their association with prognosis. Methods and Results We retrospectively reviewed 666 patients with a diagnosis of TGA with concordant atrioventricular and discordant ventriculoarterial connections in Fuwai Hospital from 1997 to 2019. Under the guidance of the Human Phenotype Ontology database, patients were classified into 3 clusters. The Kaplan‐Meier method was used to analyze the prognosis, and the Cox proportional regression model was used to investigate the risk factors. In this 666‐patient TGA cohort, the overall 5‐year survival rate was 94.70% (92.95%–96.49%). Three clusters with distinct phenotypes were obtained by the Human Phenotype Ontology database. Kaplan‐Meier analysis revealed a significant difference in freedom from reintervention among 3 clusters (P<0.001). To eliminate the effect of surgeries, we analyzed patients who only received an arterial switch operation and still found a significant difference in reintervention (P=0.019). Conclusions We delineated a big cardiovascular phenotypic profile of an unprecedentedly large TGA cohort and successfully risk stratified them to reveal prognostic significance. Also, we reported the outcomes of a large TGA population in China.
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Affiliation(s)
- Huayan Shen
- Department of Laboratory Medicine State Key Laboratory of Cardiovascular Disease Fuwai HospitalNational Center for Cardiovascular DiseasesChinese Academy of Medical SciencesPeking Union Medical College Beijing China
| | - Qiyu He
- Pediatric Cardiac Surgery Center Fuwai HospitalNational Center for Cardiovascular DiseasesChinese Academy of Medical SciencesPeking Union Medical College Beijing China
| | - Xinyang Shao
- Department of Laboratory Medicine State Key Laboratory of Cardiovascular Disease Fuwai HospitalNational Center for Cardiovascular DiseasesChinese Academy of Medical SciencesPeking Union Medical College Beijing China
| | - Shoujun Li
- Pediatric Cardiac Surgery Center Fuwai HospitalNational Center for Cardiovascular DiseasesChinese Academy of Medical SciencesPeking Union Medical College Beijing China
| | - Zhou Zhou
- Department of Laboratory Medicine State Key Laboratory of Cardiovascular Disease Fuwai HospitalNational Center for Cardiovascular DiseasesChinese Academy of Medical SciencesPeking Union Medical College Beijing China
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14
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Haimel M, Pazmandi J, Heredia RJ, Dmytrus J, Bal SK, Zoghi S, van Daele P, Briggs TA, Wouters C, Bader-Meunier B, Aeschlimann FA, Caorsi R, Eleftheriou D, Hoppenreijs E, Salzer E, Bakhtiar S, Derfalvi B, Saettini F, Kusters MAA, Elfeky R, Trück J, Rivière JG, van der Burg M, Gattorno M, Seidel MG, Burns S, Warnatz K, Hauck F, Brogan P, Gilmour KC, Schuetz C, Simon A, Bock C, Hambleton S, de Vries E, Robinson PN, van Gijn M, Boztug K. Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity. J Allergy Clin Immunol 2022; 149:369-378. [PMID: 33991581 PMCID: PMC9346194 DOI: 10.1016/j.jaci.2021.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Accurate, detailed, and standardized phenotypic descriptions are essential to support diagnostic interpretation of genetic variants and to discover new diseases. The Human Phenotype Ontology (HPO), extensively used in rare disease research, provides a rich collection of vocabulary with standardized phenotypic descriptions in a hierarchical structure. However, to date, the use of HPO has not yet been widely implemented in the field of inborn errors of immunity (IEIs), mainly due to a lack of comprehensive IEI-related terms. OBJECTIVES We sought to systematically review available terms in HPO for the depiction of IEIs, to expand HPO, yielding more comprehensive sets of terms, and to reannotate IEIs with HPO terms to provide accurate, standardized phenotypic descriptions. METHODS We initiated a collaboration involving expert clinicians, geneticists, researchers working on IEIs, and bioinformaticians. Multiple branches of the HPO tree were restructured and extended on the basis of expert review. Our ontology-guided machine learning coupled with a 2-tier expert review was applied to reannotate defined subgroups of IEIs. RESULTS We revised and expanded 4 main branches of the HPO tree. Here, we reannotated 73 diseases from 4 International Union of Immunological Societies-defined IEI disease subgroups with HPO terms. We achieved a 4.7-fold increase in the number of phenotypic terms per disease. Given the new HPO annotations, we demonstrated improved ability to computationally match selected IEI cases to their known diagnosis, and improved phenotype-driven disease classification. CONCLUSIONS Our targeted expansion and reannotation presents enhanced precision of disease annotation, will enable superior HPO-based IEI characterization, and hence benefit both IEI diagnostic and research activities.
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Affiliation(s)
- Matthias Haimel
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Raúl Jiménez Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jasmin Dmytrus
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sevgi Köstel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Paul van Daele
- Department of Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tracy A Briggs
- NW Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Carine Wouters
- Department of Microbiology and Immunology, Immunobiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Pediatric Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Brigitte Bader-Meunier
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Florence A Aeschlimann
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Roberta Caorsi
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Despina Eleftheriou
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Esther Hoppenreijs
- Department of Paediatric Rheumatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Elisabeth Salzer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Shahrzad Bakhtiar
- Department for Children and Adolescents, Division for Stem Cell Transplantation, Immunology and Intensive Care Unit, Goethe University, Frankfurt, Germany
| | - Beata Derfalvi
- Department of Pediatrics, Division of Immunology, Dalhousie University/IWK Health Centre Halifax, Halifax, Nova Scotia, Canada
| | - Francesco Saettini
- Pediatric Hematology Department, Fondazione MBBM, University of Milano Bicocca, via Pergolesi 33, Monza, Italy
| | - Maaike A A Kusters
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Reem Elfeky
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jacques G Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Mirjam van der Burg
- Department of Immunology, University Medical Center Rotterdam, Rotterdam, The Netherlands; Laboratory for Pediatric Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Markus G Seidel
- Research Unit for Pediatric Hematology and Immunology, Division of Pediatric Hemato-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Graz, Austria
| | - Siobhan Burns
- Department of Immunology, UCL Institute of Immunity & Transplantation, Department of Immunology, Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | - Klaus Warnatz
- Division of Immunodeficiency, Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Munich Centre for Rare Diseases (M-ZSE(LMU)), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul Brogan
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Kimberly C Gilmour
- Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Catharina Schuetz
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Anna Simon
- Radboudumc Expertise Centre for Immunodeficiency and Autoinflammation (REIA), Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christoph Bock
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Sophie Hambleton
- Immunity and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Esther de Vries
- Tranzo, Tilburg University, Tilburg, The Netherlands; Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | | | - Marielle van Gijn
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.
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15
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Slater K, Williams JA, Karwath A, Fanning H, Ball S, Schofield PN, Hoehndorf R, Gkoutos GV. Multi-faceted semantic clustering with text-derived phenotypes. Comput Biol Med 2021; 138:104904. [PMID: 34600327 PMCID: PMC8573608 DOI: 10.1016/j.compbiomed.2021.104904] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 02/03/2023]
Abstract
Identification of ontology concepts in clinical narrative text enables the creation of phenotype profiles that can be associated with clinical entities, such as patients or drugs. Constructing patient phenotype profiles using formal ontologies enables their analysis via semantic similarity, in turn enabling the use of background knowledge in clustering or classification analyses. However, traditional semantic similarity approaches collapse complex relationships between patient phenotypes into a unitary similarity scores for each pair of patients. Moreover, single scores may be based only on matching terms with the greatest information content (IC), ignoring other dimensions of patient similarity. This process necessarily leads to a loss of information in the resulting representation of patient similarity, and is especially apparent when using very large text-derived and highly multi-morbid phenotype profiles. Moreover, it renders finding a biological explanation for similarity very difficult; the black box problem. In this article, we explore the generation of multiple semantic similarity scores for patients based on different facets of their phenotypic manifestation, which we define through different sub-graphs in the Human Phenotype Ontology. We further present a new methodology for deriving sets of qualitative class descriptions for groups of entities described by ontology terms. Leveraging this strategy to obtain meaningful explanations for our semantic clusters alongside other evaluation techniques, we show that semantic clustering with ontology-derived facets enables the representation, and thus identification of, clinically relevant phenotype relationships not easily recoverable using overall clustering alone. In this way, we demonstrate the potential of faceted semantic clustering for gaining a deeper and more nuanced understanding of text-derived patient phenotypes.
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Affiliation(s)
- Karin Slater
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, UK; Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, UK; MRC Health Data Research UK (HDR UK) Midlands, UK; University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, UK.
| | - John A Williams
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, UK; Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, UK; University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, UK
| | - Andreas Karwath
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, UK; Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, UK; MRC Health Data Research UK (HDR UK) Midlands, UK; University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, UK
| | - Hilary Fanning
- Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, UK; University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, UK
| | - Simon Ball
- Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, UK; University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, UK
| | - Paul N Schofield
- Dept of Physiology, Development, and Neuroscience, University of Cambridge, UK
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia
| | - Georgios V Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, UK; Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, UK; NIHR Experimental Cancer Medicine Centre, UK; NIHR Surgical Reconstruction and Microbiology Research Centre, UK; NIHR Biomedical Research Centre, UK; MRC Health Data Research UK (HDR UK) Midlands, UK; University Hospitals Birmingham NHS Foundation Trust, Edgbaston, Birmingham, UK
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16
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Collins J, Astle WJ, Megy K, Mumford AD, Vuckovic D. Advances in understanding the pathogenesis of hereditary macrothrombocytopenia. Br J Haematol 2021; 195:25-45. [PMID: 33783834 DOI: 10.1111/bjh.17409] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 12/14/2022]
Abstract
Low platelet count, or thrombocytopenia, is a common haematological abnormality, with a wide differential diagnosis, which may represent a clinically significant underlying pathology. Macrothrombocytopenia, the presence of large platelets in combination with thrombocytopenia, can be acquired or hereditary and indicative of a complex disorder. In this review, we discuss the interpretation of platelet count and volume measured by automated haematology analysers and highlight some important technical considerations relevant to the analysis of blood samples with macrothrombocytopenia. We review how large cohorts, such as the UK Biobank and INTERVAL studies, have enabled an accurate description of the distribution and co-variation of platelet parameters in adult populations. We discuss how genome-wide association studies have identified hundreds of genetic associations with platelet count and mean platelet volume, which in aggregate can explain large fractions of phenotypic variance, consistent with a complex genetic architecture and polygenic inheritance. Finally, we describe the large genetic diagnostic and discovery programmes, which, simultaneously to genome-wide association studies, have expanded the repertoire of genes and variants associated with extreme platelet phenotypes. These have advanced our understanding of the pathogenesis of hereditary macrothrombocytopenia and support a future clinical diagnostic strategy that utilises genotype alongside clinical and laboratory phenotype data.
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Affiliation(s)
- Janine Collins
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, Barts Health NHS Trust, London, UK
| | - William J Astle
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge, UK
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK
| | - Andrew D Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Dragana Vuckovic
- Department of Biostatistics and Epidemiology, Faculty of Medicine, Imperial College London, London, UK
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK
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17
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Monoallelic loss-of-function THPO variants cause heritable thrombocytopenia. Blood Adv 2021; 4:920-924. [PMID: 32150607 DOI: 10.1182/bloodadvances.2019001293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 12/23/2019] [Indexed: 12/26/2022] Open
Abstract
Key Points
We report rare monoallelic variants of THPO that alter intracellular trafficking and diminish thrombopoietin secretion. Affected cases have autosomal-dominant thrombocytopenia but no other hematological features.
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18
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Chan MV, Hayman MA, Sivapalaratnam S, Crescente M, Allan HE, Edin ML, Zeldin DC, Milne GL, Stephens J, Greene D, Hanif M, O'Donnell VB, Dong L, Malkowski MG, Lentaigne C, Wedderburn K, Stubbs M, Downes K, Ouwehand WH, Turro E, BioResource N, Hart DP, Freson K, Laffan MA, Warner TD. Identification of a homozygous recessive variant in PTGS1 resulting in a congenital aspirin-like defect in platelet function. Haematologica 2021; 106:1423-1432. [PMID: 32299908 PMCID: PMC8094108 DOI: 10.3324/haematol.2019.235895] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Indexed: 12/15/2022] Open
Abstract
We have identified a rare missense variant on chromosome 9, position 125145990 (GRCh37), in exon 8 in PTGS1 (the gene encoding cyclo-oxygenase 1, COX-1, the target of anti-thrombotic aspirin therapy). We report that in the homozygous state within a large consanguineous family this variant is associated with a bleeding phenotype and alterations in platelet reactivity and eicosanoid production. Western blotting and confocal imaging demonstrated that COX-1 was absent in the platelets of three family members homozygous for the PTGS1 variant but present in their leukocytes. Platelet reactivity, as assessed by aggregometry, lumi-aggregometry and flow cytometry, was impaired in homozygous family members, as were platelet adhesion and spreading. The productions of COX-derived eicosanoids by stimulated platelets were greatly reduced but there were no changes in the levels of urinary metabolites of COX-derived eicosanoids. The proband exhibited additional defects in platelet aggregation and spreading which may explain why her bleeding phenotype was slightly more severe than those of other homozygous affected relatives. This is the first demonstration in humans of the specific loss of platelet COX-1 activity and provides insight into its consequences for platelet function and eicosanoid metabolism. Notably despite the absence of thromboxane A2 (TXA2) formation by platelets, urinary TXA2 metabolites were in the normal range indicating these cannot be assumed as markers of in vivo platelet function. Results from this study are important benchmarks for the effects of aspirin upon platelet COX-1, platelet function and eicosanoid production as they define selective platelet COX-1 ablation within humans.
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Affiliation(s)
| | | | | | | | | | - Matthew L Edin
- National Institutes of Health, National Institute of Environmental Health Sciences
| | - Darryl C Zeldin
- National Institutes of Health, National Institute of Environmental Health Sciences
| | | | | | | | | | | | | | | | | | | | - Matthew Stubbs
- Imperial College Healthcare National Health Service Trust
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19
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Xiang J, Zhang J, Zheng R, Li X, Li M. NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. Brief Bioinform 2021; 22:6236070. [PMID: 33866352 DOI: 10.1093/bib/bbab080] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 12/12/2022] Open
Abstract
The prediction of genes related to diseases is important to the study of the diseases due to high cost and time consumption of biological experiments. Network propagation is a popular strategy for disease-gene prediction. However, existing methods focus on the stable solution of dynamics while ignoring the useful information hidden in the dynamical process, and it is still a challenge to make use of multiple types of physical/functional relationships between proteins/genes to effectively predict disease-related genes. Therefore, we proposed a framework of network impulsive dynamics on multiplex biological network (NIDM) to predict disease-related genes, along with four variants of NIDM models and four kinds of impulsive dynamical signatures (IDSs). NIDM is to identify disease-related genes by mining the dynamical responses of nodes to impulsive signals being exerted at specific nodes. By a series of experimental evaluations in various types of biological networks, we confirmed the advantage of multiplex network and the important roles of functional associations in disease-gene prediction, demonstrated superior performance of NIDM compared with four types of network-based algorithms and then gave the effective recommendations of NIDM models and IDS signatures. To facilitate the prioritization and analysis of (candidate) genes associated to specific diseases, we developed a user-friendly web server, which provides three kinds of filtering patterns for genes, network visualization, enrichment analysis and a wealth of external links (http://bioinformatics.csu.edu.cn/DGP/NID.jsp). NIDM is a protocol for disease-gene prediction integrating different types of biological networks, which may become a very useful computational tool for the study of disease-related genes.
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Affiliation(s)
- Ju Xiang
- School of Computer Science and Engineering, Central South University, Human, China
| | - Jiashuai Zhang
- School of Computer Science and Engineering, Central South University, Human, China
| | - Ruiqing Zheng
- School of Computer Science and Engineering, Central South University, China
| | - Xingyi Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China
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20
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Rosenberg N, Dardik R, Hauschner H, Nakav S, Barel O, Luboshitz J, Yacobovich J, Tamary H, Kenet G. Mutations in RASGRP2 gene identified in patients misdiagnosed as Glanzmann thrombasthenia patients. Blood Cells Mol Dis 2021; 89:102560. [PMID: 33711653 DOI: 10.1016/j.bcmd.2021.102560] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Glanzmann thrombasthenia (GT) is a severe inherited platelet function disorder (IPFD), presenting with bleeding diathesis and impaired platelet aggregation, is caused by mutations in the genes ITGA2B or ITGB3. AIM We aimed to study the genetic cause of IPFD mimicking GT. METHODS During 2017-2019, 16 patients were referred to our tertiary center with bleeding symptoms, impaired platelet aggregation and normal platelet count and size. RESULTS Using flow cytometry, 13/16 patients were diagnosed with GT, yet three patients displayed normal surface expression of the integrins αIIbβ3 and αvβ3, as well as normal integrin αIIbβ3 activation following incubation with the activating monoclonal antibody anti-LIBS6, while platelet activation following ADP or epinephrine was impaired. Whole exome sequencing detected 2 variants in RASGRP2 gene in all 3 patients. DISCUSSION Both RASGRP2 mutations predicted frameshift, premature stop codon (p. I427Mfs*92 and p. R494Afs*54, respectively) and truncated calcium-sensing guanine nucleotide exchange factor [CalDAG-GEFI]- the major signaling molecule that regulates integrin-mediated aggregation and granule secretion, causing IPFD-18. CONCLUSION Patients who suffer from bleeding diathesis without immune dysregulation, may be mistakenly diagnosed as GT. Further studies are required to confirm the diagnosis of specific IPFD.
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Affiliation(s)
- Nurit Rosenberg
- The Israeli National Hemophilia Center and Thrombosis Institute, Sheba Medical Center, Tel Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Amalia Biron Research Institute of Thrombosis and Hemostasis, Sheba Medical Center, Tel Hashomer, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rima Dardik
- The Israeli National Hemophilia Center and Thrombosis Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Hagit Hauschner
- The Israeli National Hemophilia Center and Thrombosis Institute, Sheba Medical Center, Tel Hashomer, Israel; Amalia Biron Research Institute of Thrombosis and Hemostasis, Sheba Medical Center, Tel Hashomer, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sigal Nakav
- Coagulation and Hemostasis Laboratory, Hematology Laboratories, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Ortal Barel
- Bioinformatic Unit, Sheba Cancer Research Center, Tel-Hashomer, Israel
| | - Jacob Luboshitz
- The Israeli National Hemophilia Center and Thrombosis Institute, Sheba Medical Center, Tel Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Joanne Yacobovich
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Hematology, Schneider Children's Medical Center, Petach-Tikva; Israel
| | - Hannah Tamary
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Hematology, Schneider Children's Medical Center, Petach-Tikva; Israel
| | - Gili Kenet
- The Israeli National Hemophilia Center and Thrombosis Institute, Sheba Medical Center, Tel Hashomer, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Amalia Biron Research Institute of Thrombosis and Hemostasis, Sheba Medical Center, Tel Hashomer, and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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21
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Nurden P, Stritt S, Favier R, Nurden AT. Inherited platelet diseases with normal platelet count: phenotypes, genotypes and diagnostic strategy. Haematologica 2021; 106:337-350. [PMID: 33147934 PMCID: PMC7849565 DOI: 10.3324/haematol.2020.248153] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
Inherited platelet disorders resulting from platelet function defects and a normal platelet count cause a moderate or severe bleeding diathesis. Since the description of Glanzmann thrombasthenia resulting from defects of ITGA2B and ITGB3, new inherited platelet disorders have been discovered, facilitated by the use of high throughput sequencing and genomic analyses. Defects of RASGRP2 and FERMT3 responsible for severe bleeding syndromes and integrin activation have illustrated the critical role of signaling molecules. Important are mutations of P2RY12 encoding the major ADP receptor causal for an inherited platelet disorder with inheritance characteristics that depend on the variant identified. Interestingly, variants of GP6 encoding the major subunit of the collagen receptor GPVI/FcRassociate only with mild bleeding. The numbers of genes involved in dense granule defects including Hermansky-Pudlak and Chediak Higashi syndromes continue to progress and are updated. The ANO6 gene encoding a Ca2+-activated ion channel required for phospholipid scrambling is responsible for the rare Scott syndrome and decreased procoagulant activity. A novel EPHB2 defect in a familial bleeding syndrome demonstrates a role for this tyrosine kinase receptor independent of the classical model of its interaction with ephrins. Such advances highlight the large diversity of variants affecting platelet function but not their production, despite the difficulties in establishing a clear phenotype when few families are affected. They have provided insights into essential pathways of platelet function and have been at the origin of new and improved therapies for ischemic disease. Nevertheless, many patients remain without a diagnosis and requiring new strategies that are now discussed.
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Affiliation(s)
| | - Simon Stritt
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala
| | - Remi Favier
- French National Reference Center for Inherited Platelet Disorders, Armand Trousseau Hospital, Assistance Publique-Hôpitaux de Paris, Paris
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22
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Chan L, Vasilevsky N, Thessen A, McMurry J, Haendel M. The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. Database (Oxford) 2021; 2021:baab003. [PMID: 33494105 PMCID: PMC7833928 DOI: 10.1093/database/baab003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 12/14/2022]
Abstract
Informatics has become an essential component of research in the past few decades, capitalizing on the efficiency and power of computation to improve the knowledge gained from increasing quantities and types of data. While other fields of research such as genomics are well represented in informatics resources, nutrition remains underrepresented. Nutrition is one of the most integral components of human life, and it impacts individuals far beyond just nutrient provisions. For example, nutrition plays a role in cultural practices, interpersonal relationships and body image. Despite this, integrated computational investigations have been limited due to challenges within nutrition informatics (nutri-informatics) and nutrition data. The purpose of this review is to describe the landscape of nutri-informatics resources available for use in computational nutrition research and clinical utilization. In particular, we will focus on the application of biomedical ontologies and their potential to improve the standardization and interoperability of nutrition terminologies and relationships between nutrition and other biomedical disciplines such as disease and phenomics. Additionally, we will highlight challenges currently faced by the nutri-informatics community including experimental design, data aggregation and the roles scientific journals and primary nutrition researchers play in facilitating data reuse and successful computational research. Finally, we will conclude with a call to action to create and follow community standards regarding standardization of language, documentation specifications and requirements for data reuse. With the continued movement toward community standards of this kind, the entire nutrition research community can transition toward greater usage of Findability, Accessibility, Interoperability and Reusability principles and in turn more transparent science.
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Affiliation(s)
- Lauren Chan
- College of Public Health and Human Sciences, Oregon State University, 101 Milam Hall, Corvallis, OR 97331, USA
| | - Nicole Vasilevsky
- Oregon Clinical and Translational Research Institute, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd SN4N, Portland, OR 97239, USA
| | - Anne Thessen
- Environmental and Molecular Toxicology Department, Oregon State University, 1007 Ag & Life Sciences Building, Corvallis, OR 97331, USA
| | - Julie McMurry
- College of Public Health and Human Sciences, Oregon State University, 101 Milam Hall, Corvallis, OR 97331, USA
| | - Melissa Haendel
- Oregon Clinical and Translational Research Institute, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, 3181 SW Sam Jackson Park Rd SN4N, Portland, OR 97239, USA
- Environmental and Molecular Toxicology Department, Oregon State University, 1007 Ag & Life Sciences Building, Corvallis, OR 97331, USA
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23
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Buyse G, Di Michele M, Wijgaerts A, Louwette S, Wittevrongel C, Thys C, Downes K, Ceulemans B, Van Esch H, Van Geet C, Freson K. Unravelling the disease mechanism for TSPYL1 deficiency. Hum Mol Genet 2020; 29:3431-3442. [PMID: 33075815 DOI: 10.1093/hmg/ddaa233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
We describe a lethal combined nervous and reproductive systems disease in three affected siblings of a consanguineous family. The phenotype was characterized by visceroautonomic dysfunction (neonatal bradycardia/apnea, feeding problems, hyperactive startle reflex), severe postnatal progressive neurological abnormalities (including abnormal neonatal cry, hypotonia, epilepsy, polyneuropathy, cerebral gray matter atrophy), visual impairment, testicular dysgenesis in males and sudden death at infant age by brainstem-mediated cardiorespiratory arrest. Whole-exome sequencing revealed a novel homozygous frameshift variant p.Val242GlufsTer52 in the TSPY-like 1 gene (TSPYL1). The truncated TSPYL1 protein that lacks the nucleosome assembly protein domain was retained in the Golgi of fibroblasts from the three patients, whereas control fibroblasts express full-length TSPYL1 in the nucleus. Proteomic analysis of nuclear extracts from fibroblasts identified 24 upregulated and 20 downregulated proteins in the patients compared with 5 controls with 'regulation of cell cycle' as the highest scored biological pathway affected. TSPYL1-deficient cells had prolonged S and G2 phases with reduced cellular proliferation rates. Tspyl1 depletion in zebrafish mimicked the patients' phenotype with early lethality, defects in neurogenesis and cardiac dilation. In conclusion, this study reports the third pedigree with recessive TSPYL1 variants, confirming that TSPYL1 deficiency leads to a combined nervous and reproductive systems disease, and provides for the first time insights into the disease mechanism.
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Affiliation(s)
- Gunnar Buyse
- Department of Pediatric Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Michela Di Michele
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, Université de Montpellier, Ecole Nationale Supérieure de Chimie de Montpellier, 34090 Montpellier, France
| | - Anouck Wijgaerts
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven 3000, Belgium
| | - Sophie Louwette
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven 3000, Belgium
| | - Christine Wittevrongel
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven 3000, Belgium
| | - Chantal Thys
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven 3000, Belgium
| | - Kate Downes
- East Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Berten Ceulemans
- Department of Pediatric Neurology, University hospital, University of Antwerp, 2000 Antwerp, Belgium
| | - Hild Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium.,Laboratory for the Genetics of Cognition, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Chris Van Geet
- Department of Pediatric Neurology, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven 3000, Belgium
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24
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Lassmann T, Francis RW, Weeks A, Tang D, Jamieson SE, Broley S, Dawkins HJS, Dreyer L, Goldblatt J, Groza T, Kamien B, Kiraly-Borri C, McKenzie F, Murphy L, Pachter N, Pathak G, Poulton C, Samanek A, Skoss R, Slee J, Townshend S, Ward M, Baynam GS, Blackwell JM. A flexible computational pipeline for research analyses of unsolved clinical exome cases. NPJ Genom Med 2020; 5:54. [PMID: 33303739 PMCID: PMC7730424 DOI: 10.1038/s41525-020-00161-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/12/2020] [Indexed: 12/25/2022] Open
Abstract
Exome sequencing has enabled molecular diagnoses for rare disease patients but often with initial diagnostic rates of ~25-30%. Here we develop a robust computational pipeline to rank variants for reassessment of unsolved rare disease patients. A comprehensive web-based patient report is generated in which all deleterious variants can be filtered by gene, variant characteristics, OMIM disease and Phenolyzer scores, and all are annotated with an ACMG classification and links to ClinVar. The pipeline ranked 21/34 previously diagnosed variants as top, with 26 in total ranked ≤7th, 3 ranked ≥13th; 5 failed the pipeline filters. Pathogenic/likely pathogenic variants by ACMG criteria were identified for 22/145 unsolved cases, and a previously undefined candidate disease variant for 27/145. This open access pipeline supports the partnership between clinical and research laboratories to improve the diagnosis of unsolved exomes. It provides a flexible framework for iterative developments to further improve diagnosis.
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Affiliation(s)
- Timo Lassmann
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
| | - Richard W Francis
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Alexia Weeks
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Dave Tang
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Sarra E Jamieson
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Stephanie Broley
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Hugh J S Dawkins
- Office of Population Health Genomics, Public Health Division, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Lauren Dreyer
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Jack Goldblatt
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Tudor Groza
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Fiona McKenzie
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics, University of Western Australia, Perth, WA, Australia
| | | | - Nicholas Pachter
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Gargi Pathak
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Cathryn Poulton
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Amanda Samanek
- GaRDN Genetics and Rare Diseases Network, Booragoon, WA, Australia
| | - Rachel Skoss
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Jennie Slee
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Sharron Townshend
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Gareth S Baynam
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, WA, Australia
- Faculty of Health and Medical Sciences, Division of Pediatrics, University of Western Australia, Perth, WA, Australia
- Western Australian Register of Developmental Anomalies, Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Jenefer M Blackwell
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia.
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25
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Lambert MP. Improving interpretation of genetic testing for hereditary hemorrhagic, thrombotic, and platelet disorders. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2020; 2020:76-81. [PMID: 33275718 PMCID: PMC7727548 DOI: 10.1182/hematology.2020000091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The last 10 years have seen an explosion in the amount of data available through next-generation sequencing. These data are advancing quickly, and this pace makes it difficult for most practitioners to easily keep up with all of the new information. Complicating this understanding is sometimes conflicting information about variant pathogenicity or even about the role of some genes in the pathogenesis of disease. The more widespread clinical use of sequencing has expanded phenotypes, including the identification of mild phenotypes associated with previously serious disease, such as with some variants in RUNX1, MYH9, ITG2A, and others. Several organizations have taken up the task of cataloging and systematically evaluating genes and variants using a standardized approach and making the data publicly available so that others can benefit from their gene/variant curation. The efforts in testing for hereditary hemorrhagic, thrombotic, and platelet disorders have been led by the International Society on Thrombosis and Haemostasis Scientific Standardization Committee on Genomics in Thrombosis and Hemostasis, the American Society of Hematology, and the National Institutes of Health National Human Genome Research Institute Clinical Genome Resource. This article outlines current efforts to improve the interpretation of genetic testing and the role of standardizing and disseminating information. By assessing the strength of gene-disease associations, standardizing variant curation guidelines, sharing genomic data among expert members, and incorporating data from existing disease databases, the number of variants of uncertain significance will decrease, thereby improving the value of genetic testing as a diagnostic tool.
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Affiliation(s)
- Michele P Lambert
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA; and Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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26
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Negahdari S, Zamani M, Seifi T, Sedighzadeh S, Mazaheri N, Zeighami J, Sedaghat A, Saberi A, Hamid M, Keikhaei B, Radpour R, Shariati G, Galehdari H. Identification of Three Novel Mutations in the FANCA, FANCC, and ITGA2B Genes by Whole Exome Sequencing. Int J Prev Med 2020; 11:117. [PMID: 33088445 PMCID: PMC7554563 DOI: 10.4103/ijpvm.ijpvm_462_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/27/2020] [Indexed: 11/04/2022] Open
Abstract
Background Various blood diseases are caused by mutations in the FANCA, FANCC, and ITGA2B genes. Exome sequencing is a suitable method for identifying single-gene disease and genetic heterogeneity complaints. Methods Among families who were referred to Narges Genetic and PND Laboratory in 2015-2017, five families with a history of blood diseases were analyzed using the whole exome sequencing (WES) method. Results We detected two novel mutations (c.190-2A>G and c.2840C>G) in the FANCA gene, c. 1429dupA mutation in the FANCC gene, and c.1392A>G mutation in the ITGA2B gene. The prediction of variant pathogenicity has been done using bioinformatics tools such as Mutation taster PhD-SNP and polyphen2 and were confirmed by Sanger sequencing. Conclusions WES could be as a precise tool for identifying the pathologic variants in affected patient and heterozygous carriers among families. This highly successful technique will remain at the forefront of platelet and blood genomic research.
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Affiliation(s)
| | - Mina Zamani
- Narges Genetics Diagnostic Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Tahereh Seifi
- Narges Genetics Diagnostic Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sahar Sedighzadeh
- Narges Genetics Diagnostic Laboratory, Ahvaz, Iran.,Department of Genetics, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | | | - Alireza Sedaghat
- Narges Genetics Diagnostic Laboratory, Ahvaz, Iran.,Health Research Institute, Diabetes Research Center, Ahvaz Jundishapur Universityof medical Sciences, Ahvaz, Iran
| | - Alihossein Saberi
- Narges Genetics Diagnostic Laboratory, Ahvaz, Iran.,Department of Genetics, Ahvaz Jundishapur University of medical Sciences, Ahvaz, Iran
| | - Mohammad Hamid
- Narges Genetics Diagnostic Laboratory, Ahvaz, Iran.,Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Bijan Keikhaei
- Health Research Institute, Research Centre of Thalassemia and Hemoglobinopathies, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ramin Radpour
- Tumor Immunology, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland.,Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gholamreza Shariati
- Narges Genetics Diagnostic Laboratory, Ahvaz, Iran.,Department of Genetics, Ahvaz Jundishapur University of medical Sciences, Ahvaz, Iran
| | - Hamid Galehdari
- Health Research Institute, Research Centre of Thalassemia and Hemoglobinopathies, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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27
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Sims MC, Mayer L, Collins JH, Bariana TK, Megy K, Lavenu-Bombled C, Seyres D, Kollipara L, Burden FS, Greene D, Lee D, Rodriguez-Romera A, Alessi MC, Astle WJ, Bahou WF, Bury L, Chalmers E, Da Silva R, De Candia E, Deevi SVV, Farrow S, Gomez K, Grassi L, Greinacher A, Gresele P, Hart D, Hurtaud MF, Kelly AM, Kerr R, Le Quellec S, Leblanc T, Leinøe EB, Mapeta R, McKinney H, Michelson AD, Morais S, Nugent D, Papadia S, Park SJ, Pasi J, Podda GM, Poon MC, Reed R, Sekhar M, Shalev H, Sivapalaratnam S, Steinberg-Shemer O, Stephens JC, Tait RC, Turro E, Wu JKM, Zieger B, Kuijpers TW, Whetton AD, Sickmann A, Freson K, Downes K, Erber WN, Frontini M, Nurden P, Ouwehand WH, Favier R, Guerrero JA. Novel manifestations of immune dysregulation and granule defects in gray platelet syndrome. Blood 2020; 136:1956-1967. [PMID: 32693407 PMCID: PMC7582559 DOI: 10.1182/blood.2019004776] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Gray platelet syndrome (GPS) is a rare recessive disorder caused by biallelic variants in NBEAL2 and characterized by bleeding symptoms, the absence of platelet α-granules, splenomegaly, and bone marrow (BM) fibrosis. Due to the rarity of GPS, it has been difficult to fully understand the pathogenic processes that lead to these clinical sequelae. To discern the spectrum of pathologic features, we performed a detailed clinical genotypic and phenotypic study of 47 patients with GPS and identified 32 new etiologic variants in NBEAL2. The GPS patient cohort exhibited known phenotypes, including macrothrombocytopenia, BM fibrosis, megakaryocyte emperipolesis of neutrophils, splenomegaly, and elevated serum vitamin B12 levels. Novel clinical phenotypes were also observed, including reduced leukocyte counts and increased presence of autoimmune disease and positive autoantibodies. There were widespread differences in the transcriptome and proteome of GPS platelets, neutrophils, monocytes, and CD4 lymphocytes. Proteins less abundant in these cells were enriched for constituents of granules, supporting a role for Nbeal2 in the function of these organelles across a wide range of blood cells. Proteomic analysis of GPS plasma showed increased levels of proteins associated with inflammation and immune response. One-quarter of plasma proteins increased in GPS are known to be synthesized outside of hematopoietic cells, predominantly in the liver. In summary, our data show that, in addition to the well-described platelet defects in GPS, there are immune defects. The abnormal immune cells may be the drivers of systemic abnormalities such as autoimmune disease.
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Affiliation(s)
- Matthew C Sims
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Oxford Haemophilia and Thrombosis Centre, Oxford University Hospitals NHS Foundation Trust, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Louisa Mayer
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Janine H Collins
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
| | - Tadbir K Bariana
- Department of Haematology, University of Cambridge, and
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Karyn Megy
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Cecile Lavenu-Bombled
- Assistance Publique-Hôpitaux de Paris, Centre de Reference des Pathologies Plaquettaires, Hôpitaux Armand Trousseau, Bicêtre, Robert Debré, Paris, France
| | - Denis Seyres
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Frances S Burden
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Daniel Greene
- Department of Haematology, University of Cambridge, and
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Forvie Site, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Dave Lee
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Antonio Rodriguez-Romera
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Marie-Christine Alessi
- Centre for CardioVascular and Nutrition Research, INSERM 1263, INRAE 1260, Marseille, France
| | - William J Astle
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Forvie Site, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Wadie F Bahou
- Department of Medicine, Stony Brook University, Stony Brook, NY
| | - Loredana Bury
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | | | - Rachael Da Silva
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Erica De Candia
- Institute of Internal Medicine and Geriatrics, Catholic University School of Medicine, Rome, Italy
- Fondazione Policlinico Universitario Agostino Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Sri V V Deevi
- Department of Haematology, University of Cambridge, and
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Keith Gomez
- Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Luigi Grassi
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Andreas Greinacher
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Paolo Gresele
- Department of Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Dan Hart
- The Royal London Hospital Haemophilia Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Marie-Françoise Hurtaud
- Assistance Publique-Hôpitaux de Paris, Centre de Reference des Pathologies Plaquettaires, Hôpitaux Armand Trousseau, Bicêtre, Robert Debré, Paris, France
| | - Anne M Kelly
- Department of Haematology, University of Cambridge, and
| | - Ron Kerr
- Department of Haematology, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Sandra Le Quellec
- Service d'Hématologie Biologique, Hospices Civils de Lyon, Lyon, France
| | - Thierry Leblanc
- Assistance Publique-Hôpitaux de Paris, Centre de Reference des Pathologies Plaquettaires, Hôpitaux Armand Trousseau, Bicêtre, Robert Debré, Paris, France
| | - Eva B Leinøe
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
| | - Rutendo Mapeta
- Department of Haematology, University of Cambridge, and
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Harriet McKinney
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Alan D Michelson
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Sara Morais
- Serviço de Hematologia Clínica, Hospital de Santo António, Centro Hospitalar Universitário do Porto, Porto, Portugal
- Unidade Multidisciplinar de Investigação Biomédica, Instituto de Ciências Biomédicas, Universidade do Porto, Porto, Portugal
| | - Diane Nugent
- Center for Inherited Bleeding Disorders, Children's Hospital of Orange County, Orange, CA
| | - Sofia Papadia
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Soo J Park
- Division of Hematology and Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, CA
| | - John Pasi
- The Royal London Hospital Haemophilia Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Gian Marco Podda
- Unità di Medicina 2, ASST Santi Paolo e Carlo, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Man-Chiu Poon
- University of Calgary Cumming School of Medicine and Southern Alberta Rare Blood and Bleeding Disorders Comprehensive Care Program, Calgary, AB, Canada
| | - Rachel Reed
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Mallika Sekhar
- Department of Haematology, Royal Free London NHS Trust, London, United Kingdom
| | - Hanna Shalev
- Department of Pediatric Hematology/Oncology, Soroka Medical Center, Faculty of Medicine, Ben-Gurion University, Beer Sheva, Israel
| | - Suthesh Sivapalaratnam
- Department of Haematology, University of Cambridge, and
- Department of Haematology, Barts Health NHS Trust, London, United Kingdom
| | - Orna Steinberg-Shemer
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan C Stephens
- Department of Haematology, University of Cambridge, and
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Robert C Tait
- Department of Haematology, Royal Infirmary, Glasgow, United Kingdom
| | - Ernest Turro
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Forvie Site, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - John K M Wu
- Division of Hematology-Oncology, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Barbara Zieger
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center-Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Sanquin Research Institute, Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Anthony D Whetton
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e. V., Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, United Kingdom
- Medizinische Fakultät, Medizinisches Proteom Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Kate Downes
- Department of Haematology, University of Cambridge, and
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Wendy N Erber
- Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
- PathWest Laboratory Medicine, The University of Western Australia, Nedlands, Australia
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation, Cambridge Centre for Research Excellence, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Paquita Nurden
- Institut Hospitalo-Universitaire L'Institut de Rythmologie et Modélisation Cardiaque, Plateforme Technologique d'Innovation Biomédicale, Hôpital Xavier Arnozan, Pessac, France
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom; and
| | - Remi Favier
- Assistance Publique-Hôpitaux de Paris, Centre de Reference des Pathologies Plaquettaires, Hôpitaux Armand Trousseau, Bicêtre, Robert Debré, Paris, France
- INSERM Unité Mixte de Recherche 1170, Gustave Roussy Cancer Campus, Universite Paris-Saclay, Villejuif, France
| | - Jose A Guerrero
- Department of Haematology, University of Cambridge, and
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
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28
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Westbury SK, Whyte CS, Stephens J, Downes K, Turro E, Claesen K, Mertens JC, Hendriks D, Latif AL, Leishman EJ, Mutch NJ, Tait RC, Mumford AD. A new pedigree with thrombomodulin-associated coagulopathy in which delayed fibrinolysis is partially attenuated by co-inherited TAFI deficiency. J Thromb Haemost 2020; 18:2209-2214. [PMID: 32634856 DOI: 10.1111/jth.14990] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 01/27/2023]
Abstract
BACKGROUND Thrombomodulin-associated coagulopathy (TM-AC) is a rare bleeding disorder in which a single reported p.Cys537* variant in the thrombomodulin gene THBD causes high plasma thrombomodulin (TM) levels. High TM levels attenuate thrombin generation and delay fibrinolysis. OBJECTIVES To report the characteristics of pedigree with a novel THBD variant causing TM-AC, and co-inherited deficiency of thrombin-activatable fibrinolysis inhibitor (TAFI). PATIENTS/METHODS Identification of pathogenic variants in hemostasis genes by next-generation sequencing and case recall for deep phenotyping. RESULTS Pedigree members with a previously reported THBD variant predicting p.Pro496Argfs*10 and chain truncation in TM transmembrane domain had abnormal bleeding and greatly increased plasma TM levels. Affected cases had attenuated thrombin generation and delayed fibrinolysis similar to previous reported TM_AC cases with THBD p.Cys537*. Coincidentally, some pedigree members also harbored a stop-gain variant in CPB2 encoding TAFI. This reduced plasma TAFI levels but was asymptomatic. Pedigree members with TM-AC caused by the p.Pro496Argfs*10 THBD variant and also TAFI deficiency had a partially attenuated delay in fibrinolysis, but no change in the defective thrombin generation. CONCLUSIONS These data extend the reported genetic repertoire of TM-AC and establish a common molecular pathogenesis arising from high plasma levels of TM extra-cellular domain. The data further confirm that the delay in fibrinolysis associated with TM-AC is directly linked to increased TAFI activation. The combination of the rare variants in the pedigree members provides a unique genetic model to develop understanding of the thrombin-TM system and its regulation of TAFI.
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Affiliation(s)
- Sarah K Westbury
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Claire S Whyte
- Aberdeen Cardiovascular and Diabetes Centre, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | | | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge, UK
- East Midlands and East of England Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Karen Claesen
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | - Joachim C Mertens
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | - Dirk Hendriks
- Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium
| | | | - Emma J Leishman
- Department of Haematology, Glasgow Royal Infirmary, Glasgow, UK
| | - Nicola J Mutch
- Aberdeen Cardiovascular and Diabetes Centre, Institute of Medical Sciences, Foresterhill, University of Aberdeen, Aberdeen, UK
| | - R Campbell Tait
- Department of Haematology, Glasgow Royal Infirmary, Glasgow, UK
| | - Andrew D Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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29
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Guéguen P, Dupuis A, Py JY, Desprès A, Masson E, Le Marechal C, Cooper DN, Gachet C, Chen JM, Férec C. Pathogenic and likely pathogenic variants in at least five genes account for approximately 3% of mild isolated nonsyndromic thrombocytopenia. Transfusion 2020; 60:2419-2431. [PMID: 32757236 DOI: 10.1111/trf.15992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Thrombocytopenia has a variety of different etiologies, both acquired and hereditary. Inherited thrombocytopenia may be associated with other symptoms (syndromic forms) or may be strictly isolated. To date, only about half of all the familial forms of thrombocytopenia have been accounted for in terms of well-defined genetic abnormalities. However, data are limited on the nature and frequency of the underlying causative genetic variants in individuals with mild isolated nonsyndromic thrombocytopenia. STUDY DESIGN AND METHODS Thirteen known or candidate genes for isolated thrombocytopenia were included in a gene panel analysis in which targeted next-generation sequencing was performed on 448 French blood donors with mild isolated nonsyndromic thrombocytopenia. RESULTS A total of 68 rare variants, including missense, splice site, frameshift, nonsense, and in-frame variants (all heterozygous) were identified in 11 of the 13 genes screened. Twenty-nine percent (N = 20) of the variants detected were absent from both the French Exome Project and gnomAD exome databases. Using stringent criteria and an unbiased approach, we classified seven predicted loss-of-function variants (three in ITGA2B and four in TUBB1) and four missense variants (one in GP1BA, two in ITGB3 and one in ACTN1) as being pathogenic or likely pathogenic. Altogether, they were found in 13 members (approx. 3%) of our studied cohort. CONCLUSION We present the results of gene panel sequencing of known and candidate thrombocytopenia genes in mild isolated nonsyndromic thrombocytopenia. Pathogenic and likely pathogenic variants in five known thrombocytopenia genes were identified, accounting for approximately 3% of individuals with the condition.
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Affiliation(s)
- Paul Guéguen
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
| | - Arnaud Dupuis
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, Etablissement Français du Sang Grand Est, Unité Mixte de Recherche-S 1255, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Jean-Yves Py
- EFS Centre-Pays de la Loire, Site d'Orléans, Orléans, France
| | | | - Emmanuelle Masson
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
| | - Cédric Le Marechal
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Christian Gachet
- Université de Strasbourg, Institut National de la Santé et de la Recherche Médicale, Etablissement Français du Sang Grand Est, Unité Mixte de Recherche-S 1255, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | | | - Claude Férec
- CHRU Brest, Brest, France.,EFS, Univ Brest, Inserm, UMR 1078, GGB, Brest, France
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30
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Loyau Inserm S, Faille D, Gautier P, Nurden P, Jandrot-Perrus M, Ajzenberg N. Absence of bleeding upon dual antiplatelet therapy in a patient with a immune GPVI deficiency. Platelets 2020; 32:705-709. [PMID: 32627625 DOI: 10.1080/09537104.2020.1787974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acquired deficiencies in platelet glycoprotein VI are rare and have not been found associated with other defects. Here we report the case of a 64-year old male patient presenting an immune GPVI deficiency associated to a mutation in the alpha-actinin gene and who has been treated with dual anti platelet therapy without bleeding.Introduction: Glycoprotein (GP) VI, a pluripotent receptor interacting with collagen and fibrin(ogen) is responsible for thrombus formation, growth and stability (1-4). It is co-expressed with the Fc receptor γ (FcRγ) chain (5). GPVI is not critical for haemostasis since subjects with a GPVI deficiency usually present low or even no bleeding tendency (6, 7). Acquired GPVI deficiency due to antibody-induced GPVI depletion is the most frequent finding. At least 10 patients have been described with an acquired GPVI deficiency, most often associated to immune thrombocytopenia, moderate bleeding and impaired collagen-induced platelet aggregation (7). Several mechanisms leading to the GPVI deficiency are proposed including antibody-triggered GPVI internalization and/or shedding of the extracellular domain (8, 9). We report the case of a patient presenting an acquired GPVI deficiency different from those previously described: (i) he is male whereas all previous cases were female, (ii) he is heterozygous for a mutation in α (alpha)-actinin-1 gene and (iii) he was treated with dual antiplatelet therapy with no haemorrhagic manifestation.
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Affiliation(s)
| | - Dorothée Faille
- Inserm UMR_S1148, Université de Paris, Paris, France.,Laboratoire d'Hématologie, AP-HP, Hôpital Bichat, Paris, France
| | - Philippe Gautier
- Hemophilia Center, Laboratory of Hematology, University Hospital, Caen, France
| | - Paquita Nurden
- Institut Hospitalo-Universitaire LIRYC, Hôpital Xavier Arnozan, Pessac, France
| | | | - Nadine Ajzenberg
- Inserm UMR_S1148, Université de Paris, Paris, France.,Laboratoire d'Hématologie, AP-HP, Hôpital Bichat, Paris, France
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31
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Haijes HA, Jaeken J, van Hasselt PM. Hypothesis: determining phenotypic specificity facilitates understanding of pathophysiology in rare genetic disorders. J Inherit Metab Dis 2020; 43:701-711. [PMID: 31804708 PMCID: PMC7383723 DOI: 10.1002/jimd.12201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 12/17/2022]
Abstract
In the rapidly growing group of rare genetic disorders, data scarcity demands an intelligible use of available data, in order to improve understanding of underlying pathophysiology. We hypothesize, based on the principle that clinical similarities may be indicative of shared pathophysiology, that determining phenotypic specificity could provide unsuspected insights in pathophysiology of rare genetic disorders. We explored our hypothesis by studying subunit deficiencies of the conserved oligomeric Golgi (COG) complex, a subgroup of congenital disorders of glycosylation (CDG). In this systematic data assessment, all 45 reported patients with COG-CDG were included. The vocabulary of the Human Phenotype Ontology was used to annotate all phenotypic features and to assess occurrence in other genetic disorders. Gene occurrence ratios were calculated by dividing the frequency in the patient cohort over the number of associated genes, according to the Human Phenotype Ontology. Prioritisation based on phenotypic specificity was highly informative and captured phenotypic features commonly associated with glycosylation disorders. Moreover, it captured features not seen in any other glycosylation disorder, among which episodic fever, likely reflecting underappreciated other cellular functions of the COG complex. Interestingly, the COG complex was recently implicated in the autophagy pathway, as are more than half of the genes underlying disorders that present with episodic fever. This suggests that whereas many phenotypic features in these patients are caused by disrupted glycosylation, episodic fever might be caused by disrupted autophagy. Thus, we here demonstrate support for our hypothesis that determining phenotypic specificity could facilitate understanding of pathophysiology in rare genetic disorders.
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Affiliation(s)
- Hanneke A. Haijes
- Department of Biomedical Genetics, Section Metabolic DiagnosticsWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
- Department of Pediatrics, Subdivision Metabolic DiseasesWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
| | - Jaak Jaeken
- Department of PediatricsCentre for Metabolic Diseases, University Hospital GasthuisbergLeuvenBelgium
| | - Peter M. van Hasselt
- Department of Pediatrics, Subdivision Metabolic DiseasesWilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht UniversityUtrechtThe Netherlands
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32
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Nurden AT, Nurden P. Inherited thrombocytopenias: history, advances and perspectives. Haematologica 2020; 105:2004-2019. [PMID: 32527953 PMCID: PMC7395261 DOI: 10.3324/haematol.2019.233197] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/08/2020] [Indexed: 12/11/2022] Open
Abstract
Over the last 100 years the role of platelets in hemostatic events and their production by megakaryocytes have gradually been defined. Progressively, thrombocytopenia was recognized as a cause of bleeding, first through an acquired immune disorder; then, since 1948, when Bernard-Soulier syndrome was first described, inherited thrombocytopenia became a fascinating example of Mendelian disease. The platelet count is often severely decreased and platelet size variable; associated platelet function defects frequently aggravate bleeding. Macrothrombocytopenia with variable proportions of enlarged platelets is common. The number of circulating platelets will depend on platelet production, consumption and lifespan. The bulk of macrothrombocytopenias arise from defects in megakaryopoiesis with causal variants in transcription factor genes giving rise to altered stem cell differentiation and changes in early megakaryocyte development and maturation. Genes encoding surface receptors, cytoskeletal and signaling proteins also feature prominently and Sanger sequencing associated with careful phenotyping has allowed their early classification. It quickly became apparent that many inherited thrombocytopenias are syndromic while others are linked to an increased risk of hematologic malignancies. In the last decade, the application of next-generation sequencing, including whole exome sequencing, and the use of gene platforms for rapid testing have greatly accelerated the discovery of causal genes and extended the list of variants in more common disorders. Genes linked to an increased platelet turnover and apoptosis have also been identified. The current challenges are now to use next-generation sequencing in first-step screening and to define bleeding risk and treatment better.
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Affiliation(s)
- Alan T Nurden
- Institut Hospitalo-Universitaire LIRYC, Pessac, France
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Tang X, Chen W, Zeng Z, Ding K, Zhou Z. An ontology-based classification of Ebstein's anomaly and its implications in clinical adverse outcomes. Int J Cardiol 2020; 316:79-86. [PMID: 32348812 DOI: 10.1016/j.ijcard.2020.04.073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/17/2020] [Accepted: 04/24/2020] [Indexed: 01/21/2023]
Abstract
BACKGROUND Ebstein's anomaly (EA) is a rare congenital heart disease with significantly phenotypic heterogeneity, accompanied with multiple associated phenotypes. The classification of cases with EA based on a standardized vocabulary of phenotypic abnormalities from Human Phenotype Ontology (HPO) and its association with adverse clinical outcomes has yet to be investigated. METHODS We developed a deep phenotyping algorithm for Chinese electronic medical records (EMRs) from the Fuwai Hospital to ascertain EA cases. EA-associated phenotypes were standardized according to HPO annotation, and an unsupervised hierarchical cluster analysis was used to classify EA cases according to their phenotypic similarities. A survival analysis was conducted to study the association of the HPO-based cluster with survival or adverse clinical outcomes. RESULTS The ascertained EA cases were annotated to have a single or multiple HPO terms. Three distinct clusters with different combinations of HPO term in these cases were identified. The HPO-based classification of EA cases was not significantly associated with survival or adverse clinical outcomes at a mid-term follow-up. CONCLUSIONS Our study provided an important implication for studying the classification of congenital heart disease using HPO-based annotation. A long time follow-up will enable to confirm its association with adverse clinical outcomes.
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Affiliation(s)
- Xia Tang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, Henan Province 450003, China; NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, Henan Province 450003, China
| | - Wen Chen
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Ziyi Zeng
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Keyue Ding
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Henan Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, Henan Province 450003, China; NHC Key Laboratory of Birth Defect Prevention, Zhengzhou, Henan Province 450003, China.
| | - Zhou Zhou
- Department of Laboratory Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China.
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34
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Germline mutations in the transcription factor IKZF5 cause thrombocytopenia. Blood 2020; 134:2070-2081. [PMID: 31217188 DOI: 10.1182/blood.2019000782] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/10/2019] [Indexed: 01/09/2023] Open
Abstract
To identify novel causes of hereditary thrombocytopenia, we performed a genetic association analysis of whole-genome sequencing data from 13 037 individuals enrolled in the National Institute for Health Research (NIHR) BioResource, including 233 cases with isolated thrombocytopenia. We found an association between rare variants in the transcription factor-encoding gene IKZF5 and thrombocytopenia. We report 5 causal missense variants in or near IKZF5 zinc fingers, of which 2 occurred de novo and 3 co-segregated in 3 pedigrees. A canonical DNA-zinc finger binding model predicts that 3 of the variants alter DNA recognition. Expression studies showed that chromatin binding was disrupted in mutant compared with wild-type IKZF5, and electron microscopy revealed a reduced quantity of α granules in normally sized platelets. Proplatelet formation was reduced in megakaryocytes from 7 cases relative to 6 controls. Comparison of RNA-sequencing data from platelets, monocytes, neutrophils, and CD4+ T cells from 3 cases and 14 healthy controls showed 1194 differentially expressed genes in platelets but only 4 differentially expressed genes in each of the other blood cell types. In conclusion, IKZF5 is a novel transcriptional regulator of megakaryopoiesis and the eighth transcription factor associated with dominant thrombocytopenia in humans.
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35
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Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders. Blood 2020; 134:2082-2091. [PMID: 31064749 DOI: 10.1182/blood.2018891192] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/22/2019] [Indexed: 12/17/2022] Open
Abstract
A targeted high-throughput sequencing (HTS) panel test for clinical diagnostics requires careful consideration of the inclusion of appropriate diagnostic-grade genes, the ability to detect multiple types of genomic variation with high levels of analytic sensitivity and reproducibility, and variant interpretation by a multidisciplinary team (MDT) in the context of the clinical phenotype. We have sequenced 2396 index patients using the ThromboGenomics HTS panel test of diagnostic-grade genes known to harbor variants associated with rare bleeding, thrombotic, or platelet disorders (BTPDs). The molecular diagnostic rate was determined by the clinical phenotype, with an overall rate of 49.2% for all thrombotic, coagulation, platelet count, and function disorder patients and a rate of 3.2% for patients with unexplained bleeding disorders characterized by normal hemostasis test results. The MDT classified 745 unique variants, including copy number variants (CNVs) and intronic variants, as pathogenic, likely pathogenic, or variants of uncertain significance. Half of these variants (50.9%) are novel and 41 unique variants were identified in 7 genes recently found to be implicated in BTPDs. Inspection of canonical hemostasis pathways identified 29 patients with evidence of oligogenic inheritance. A molecular diagnosis has been reported for 894 index patients providing evidence that introducing an HTS genetic test is a valuable addition to laboratory diagnostics in patients with a high likelihood of having an inherited BTPD.
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36
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Park ES. When to suspect inherited platelet disorders and how to diagnose them. Clin Exp Pediatr 2020; 63:98-99. [PMID: 32023406 PMCID: PMC7073383 DOI: 10.3345/cep.2019.01207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/31/2019] [Indexed: 11/27/2022] Open
Affiliation(s)
- Eun Sil Park
- Department of Pediatrics, Institute of Health Science, Gyeongsang National University College of Medicine, Jinju, Korea
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37
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Cacheiro P, Muñoz-Fuentes V, Murray SA, Dickinson ME, Bucan M, Nutter LMJ, Peterson KA, Haselimashhadi H, Flenniken AM, Morgan H, Westerberg H, Konopka T, Hsu CW, Christiansen A, Lanza DG, Beaudet AL, Heaney JD, Fuchs H, Gailus-Durner V, Sorg T, Prochazka J, Novosadova V, Lelliott CJ, Wardle-Jones H, Wells S, Teboul L, Cater H, Stewart M, Hough T, Wurst W, Sedlacek R, Adams DJ, Seavitt JR, Tocchini-Valentini G, Mammano F, Braun RE, McKerlie C, Herault Y, de Angelis MH, Mallon AM, Lloyd KCK, Brown SDM, Parkinson H, Meehan TF, Smedley D. Human and mouse essentiality screens as a resource for disease gene discovery. Nat Commun 2020; 11:655. [PMID: 32005800 PMCID: PMC6994715 DOI: 10.1038/s41467-020-14284-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.
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Grants
- UM1 HG008900 NHGRI NIH HHS
- UM1 HG006504 NHGRI NIH HHS
- MC_UP_1502/1 Medical Research Council
- UM1 HG006542 NHGRI NIH HHS
- UM1 OD023221 NIH HHS
- MC_U142684171 Medical Research Council
- MR/S006753/1 Medical Research Council
- UM1 HG006370 NHGRI NIH HHS
- UM1 HG006493 NHGRI NIH HHS
- U54 HG006370 NHGRI NIH HHS
- U54 HG006364 NHGRI NIH HHS
- MC_U142684172 Medical Research Council
- UM1 HG006348 NHGRI NIH HHS
- U42 OD011174 NIH HHS
- U42 OD011175 NIH HHS
- Wellcome Trust
- This work was supported by NIH grant U54 HG006370. IMPC-related mouse production and phenotyping was funded by the Government of Canada through Genome Canada and Ontario Genomics (OGI-051) for NorCOMM2 (C.M.) and the National Institutes of Health and OD, NCRR, NIDDK and NHLBI for KOMP and KOMP2 Projects U42 OD011175 and UM1OD023221 (C.M., K.C.K.L), Infrafrontier grant 01KX1012, EU Horizon2020: IPAD-MD funding 653961 (M.H.d.A); EUCOMM: LSHM-CT-2005-018931, EUCOMMTOOLS: FP7-HEALTH-F4-2010-261492 (W.G.W). UM1 HG006348; U42 OD011174; U54 HG005348 (A.L.B), NIH U54706HG006364 (A.L.B). Wellcome Trust grants WT098051 and WT206194 (D.A). The French National Centre for Scientific Research (CNRS), the French National Institute of Health and Medical Research (INSERM), the University of Strasbourg and the “Centre Europeen de Recherche en Biomedecine”, and the French state funds through the “Agence Nationale de la Recherche” under the frame programme Investissements d’Avenir labelled (ANR-10-IDEX-0002-02, ANR-10-LABX-0030-INRT, ANR-10-INBS-07 PHENOMIN (J.H.). This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. We are also grateful for the data access provided by the DDD and CMG projects. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund [grant number HICF-1009-003], a parallel funding partnership between Wellcome and the Department of Health, and the Wellcome Sanger Institute [grant number WT098051]. The views expressed in this publication are those of the author(s) and not necessarily those of Wellcome or the Department of Health. The study has UK Research Ethics Committee approval (10/H0305/83, granted by the Cambridge South REC, and GEN/284/12 granted by the Republic of Ireland REC). The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network. The Centers for Mendelian Genomics are funded by the National Human Genome Research Institute, the National Heart, Lung, and Blood Institute, and the National Eye Institute. Broad Institute (UM1 HG008900), Johns Hopkins University School of Medicine/Baylor College of Medicine (UM1 HG006542), University of Washington (UM1 HG006493), Yale University (UM1 HG006504).
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Affiliation(s)
- Pilar Cacheiro
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - Mary E Dickinson
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | | | - Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ann M Flenniken
- The Centre for Phenogenomics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5T 3H7, Canada
| | - Hugh Morgan
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Henrik Westerberg
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tomasz Konopka
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Chih-Wei Hsu
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Audrey Christiansen
- Departments of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Denise G Lanza
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jason D Heaney
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS, 67404, Illkirch, France
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - Vendula Novosadova
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | | | | | - Sara Wells
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Lydia Teboul
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Heather Cater
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Michelle Stewart
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Tertius Hough
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764, Neuherberg, Germany
- Department of Developmental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85764, Neuherberg, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, 80336, Munich, Germany
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, 252 50, Prague, Czech Republic
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - John R Seavitt
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Glauco Tocchini-Valentini
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Institute of Cell Biology and Neurobiology, 00015, Monterotondo Scalo, Italy
| | | | - Colin McKerlie
- The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, ON, M5T 3H7, Canada
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS, 67404, Illkirch, France
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Ann-Marie Mallon
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, CA, 95618, USA
| | - Steve D M Brown
- Medical Research Council Harwell Institute (Mammalian Genetics Unit and Mary Lyon Centre), Harwell, Oxfordshire, OX11 0RD, UK
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Terrence F Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Damian Smedley
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
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38
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Vincenot A, Saultier P, Kunishima S, Poggi M, Hurtaud-Roux MF, Roussel A, Actn Study Coinvestigators, Schlegel N, Alessi MC. Novel ACTN1 variants in cases of thrombocytopenia. Hum Mutat 2019; 40:2258-2269. [PMID: 31237726 PMCID: PMC6900141 DOI: 10.1002/humu.23840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 11/11/2022]
Abstract
The ACTN1 gene has been implicated in inherited macrothrombocytopenia. To decipher the spectrum of variants and phenotype of ACTN1‐related thrombocytopenia, we sequenced the ACTN1 gene in 272 cases of unexplained chronic or familial thrombocytopenia. We identified 15 rare, monoallelic, nonsynonymous and likely pathogenic ACTN1 variants in 20 index cases from 20 unrelated families. Thirty‐one family members exhibited thrombocytopenia. Targeted sequencing was carried out on 12 affected relatives, which confirmed presence of the variant. Twenty‐eight of 32 cases with monoallelic ACTN1 variants had mild to no bleeding complications. Eleven cases harbored 11 different unreported ACTN1 variants that were monoallelic and likely pathogenic. Nine variants were located in the α‐actinin‐1 (ACTN1) rod domain and were predicted to hinder dimer formation. These variants displayed a smaller increase in platelet size compared with variants located outside the rod domain. In vitro expression of the new ACTN1 variants induced actin network disorganization and led to increased thickness of actin fibers. These findings expand the repertoire of ACTN1 variants associated with thrombocytopenia and highlight the high frequency of ACTN1‐related thrombocytopenia cases. The rod domain, like other ACTN1 functional domains, may be mutated resulting in actin disorganization in vitro and thrombocytopenia with normal platelet size in most cases.
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Affiliation(s)
- Anne Vincenot
- CHU Robert Debré, National Reference Center for Inherited Platelet Disorders and Biological Hematology Service, AP-HP, Paris, France
| | - Paul Saultier
- Aix-Marseille Univ, INSERM, INRA, C2VN, Marseille, France
| | - Shinji Kunishima
- Department of Medical Technology, Gifu University of Medical Science, Seki, Gifu, Japan
| | - Marjorie Poggi
- Aix-Marseille Univ, INSERM, INRA, C2VN, Marseille, France
| | - Marie-Françoise Hurtaud-Roux
- CHU Robert Debré, National Reference Center for Inherited Platelet Disorders and Biological Hematology Service, AP-HP, Paris, France
| | - Alain Roussel
- Aix Marseille University, CNRS, AFMB, Marseille, France
| | | | - Nicole Schlegel
- CHU Robert Debré, National Reference Center for Inherited Platelet Disorders and Biological Hematology Service, AP-HP, Paris, France
| | - Marie-Christine Alessi
- Aix-Marseille Univ, INSERM, INRA, C2VN, Marseille, France.,APHM, CHU Timone, French Reference Center for Inherited Platelet Disorders, Marseille, France
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39
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Salnikova LE, Chernyshova EV, Anastasevich LA, Larin SS. Gene- and Disease-Based Expansion of the Knowledge on Inborn Errors of Immunity. Front Immunol 2019; 10:2475. [PMID: 31695696 PMCID: PMC6816315 DOI: 10.3389/fimmu.2019.02475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 12/31/2022] Open
Abstract
The recent report of the International Union of Immunological Societies (IUIS) has provided the categorized list of 354 inborn errors of immunity. We performed a systematic analysis of genes and diseases from the IUIS report with the use of the OMIM, ORPHANET, and HPO resources. To measure phenotypic similarity we applied the Jaccard/Tanimoto (J/T) coefficient for HPO terms and top-level categories. Low J/T coefficients for HPO terms for OMIM or ORPHANET disease pairs associated with the same genes indicated high pleiotropy of these genes. Gene ORGANizer enrichment analysis demonstrated that gene sets related to HPO top-level categories were most often enriched in immune, lymphatic, and corresponding body systems (for example, genes from the category "Cardiovascular" were enriched in cardiovascular system). We presented available data on frequent and very frequent clinical signs and symptoms in inborn errors of immunity. With the use of DisGeNET, we generated the list of 25 IUIS/OMIM diseases with two or more relatively high score gene-disease associations, found for unrelated genes and/or for clusters of genes coding for interacting proteins. Our study showed the enrichment of gene sets related to several IUIS categories with neoplastic and autoimmune diseases from the GWAS Catalog and reported individual genes with phenotypic overlap between inborn errors of immunity and GWAS diseases/traits. We concluded that genetic background may play a role in phenotypic diversity of inborn errors of immunity.
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Affiliation(s)
- Lyubov E Salnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,The Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Ekaterina V Chernyshova
- The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Lyudmila A Anastasevich
- The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Sergey S Larin
- The Laboratory of Molecular Immunology, Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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40
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Bury L, Megy K, Stephens JC, Grassi L, Greene D, Gleadall N, Althaus K, Allsup D, Bariana TK, Bonduel M, Butta NV, Collins P, Curry N, Deevi SVV, Downes K, Duarte D, Elliott K, Falcinelli E, Furie B, Keeling D, Lambert MP, Linger R, Mangles S, Mapeta R, Millar CM, Penkett C, Perry DJ, Stirrups KE, Turro E, Westbury SK, Wu J, BioResource N, Gomez K, Freson K, Ouwehand WH, Gresele P, Simeoni I. Next-generation sequencing for the diagnosis of MYH9-RD: Predicting pathogenic variants. Hum Mutat 2019; 41:277-290. [PMID: 31562665 PMCID: PMC6972977 DOI: 10.1002/humu.23927] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/19/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022]
Abstract
The heterogeneous manifestations of MYH9‐related disorder (MYH9‐RD), characterized by macrothrombocytopenia, Döhle‐like inclusion bodies in leukocytes, bleeding of variable severity with, in some cases, ear, eye, kidney, and liver involvement, make the diagnosis for these patients still challenging in clinical practice. We collected phenotypic data and analyzed the genetic variants in more than 3,000 patients with a bleeding or platelet disorder. Patients were enrolled in the BRIDGE‐BPD and ThromboGenomics Projects and their samples processed by high throughput sequencing (HTS). We identified 50 patients with a rare variant in MYH9. All patients had macrothrombocytes and all except two had thrombocytopenia. Some degree of bleeding diathesis was reported in 41 of the 50 patients. Eleven patients presented hearing impairment, three renal failure and two elevated liver enzymes. Among the 28 rare variants identified in MYH9, 12 were novel. HTS was instrumental in diagnosing 23 patients (46%). Our results confirm the clinical heterogeneity of MYH9‐RD and show that, in the presence of an unclassified platelet disorder with macrothrombocytes, MYH9‐RD should always be considered. A HTS‐based strategy is a reliable method to reach a conclusive diagnosis of MYH9‐RD in clinical practice.
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Affiliation(s)
- Loredana Bury
- Department of Internal Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Jonathan C Stephens
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Luigi Grassi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Daniel Greene
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,Department of Haematology, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nick Gleadall
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Karina Althaus
- Institute for Immunology and Transfusion Medicine, Universitätsmedizin Greifswald Ernst-Moritz-Arndt University Greifswald, Greifswald, Germany.,Transfusion Medicine, Medical Faculty Tübingen, Tübingen, Germany
| | - David Allsup
- Hull York Medical School, University of Hull, York, UK
| | - Tadbir K Bariana
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
| | - Mariana Bonduel
- Hematology/Oncology Department, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Buenos Aires, Argentina
| | - Nora V Butta
- Servicio de Hematología y Hemoterapia Hospital, Universitario La Paz-IDIPaz, Madrid, Spain
| | - Peter Collins
- Arthur Bloom Haemophilia Centre, Institute of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Nicola Curry
- Department of Clinical Haematology, Oxford Haemophilia and Thrombosis Centre, Oxford University Hospitals NHS Trust, Churchill Hospital, Oxford, UK
| | - Sri V V Deevi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Daniel Duarte
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Kim Elliott
- Oxford Haemophilia & Thrombosis Centre, Department of Haematology, Oxford University Hospitals NHS Trust, Churchill Hospital, Oxford and the NIHR BRC, Blood Theme, Oxford Centre for Haematology, Oxford, UK
| | - Emanuela Falcinelli
- Department of Internal Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Bruce Furie
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | | | - Michele P Lambert
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rachel Linger
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Sarah Mangles
- Basingstoke and Hampshire Hospital, NHS Foundation Trust, UK
| | - Rutendo Mapeta
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Carolyn M Millar
- Hampshire Hospital NHS Foundation Trust, UK.,Centre for Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, UK
| | - Christopher Penkett
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - David J Perry
- Department of Haematology, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kathleen E Stirrups
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge Institute of Public Health, Cambridge, UK
| | - Sarah K Westbury
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - John Wu
- British Columbia Children's Hospital, Vancouver, Canada
| | - Nihr BioResource
- NIHR BioResource, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
| | - Keith Gomez
- Transfusion Medicine, Medical Faculty Tübingen, Tübingen, Germany
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK.,NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.,Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Paolo Gresele
- Department of Internal Medicine, Section of Internal and Cardiovascular Medicine, University of Perugia, Perugia, Italy
| | - Ilenia Simeoni
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource - Rare Diseases, Cambridge Biomedical Campus, Cambridge University Hospitals, Cambridge, UK
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41
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Phenotype description and response to thrombopoietin receptor agonist in DIAPH1-related disorder. Blood Adv 2019; 2:2341-2346. [PMID: 30232087 DOI: 10.1182/bloodadvances.2018020370] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/01/2018] [Indexed: 12/13/2022] Open
Abstract
Key Points
DIAPH1-related disorder has a bilineage hematological phenotype of macrothrombocytopenia and neutropenia associated with hearing loss. Eltrombopag increased proplatelet formation from cultured DIAPH1-related disorder megakaryocytes and improved platelet counts in vivo.
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42
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O'Sullivan LR, Ajaykumar AP, Dembicka KM, Murphy A, Grennan EP, Young PW. Investigation of calmodulin-like and rod domain mutations suggests common molecular mechanism for α-actinin-1-linked congenital macrothrombocytopenia. FEBS Lett 2019; 594:161-174. [PMID: 31365757 DOI: 10.1002/1873-3468.13562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/22/2019] [Accepted: 07/29/2019] [Indexed: 11/11/2022]
Abstract
Actinin-1 mutations cause dominantly inherited congenital macrothrombocytopenia (CMTP), with mutations in the actin-binding domain increasing actinin's affinity for F-actin. In this study, we examined nine CMTP-causing mutations in the calmodulin-like and rod domains of actinin-1. These mutations increase, to varying degrees, actinin's ability to bundle actin filaments in vitro. Mutations within the calmodulin-like domain decrease its thermal stability slightly but do not dramatically affect calcium binding, with mutant proteins retaining calcium-dependent regulation of filament bundling in vitro. The G764S and E769K mutations increase cytoskeletal association of actinin in cells, and all mutant proteins colocalize with F-actin in cultured HeLa cells. Thus, CMTP-causing actinin-1 mutations outside the actin-binding domain also increase actin association, suggesting a common molecular mechanism underlying actinin-1 related CMTP.
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Affiliation(s)
- Leanne Rose O'Sullivan
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | | | - Kornelia Maria Dembicka
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | - Aidan Murphy
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | - Eamonn Paul Grennan
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
| | - Paul William Young
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, Ireland
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43
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Su S, Zhang L, Liu J. An Effective Method to Measure Disease Similarity Using Gene and Phenotype Associations. Front Genet 2019; 10:466. [PMID: 31164903 PMCID: PMC6536643 DOI: 10.3389/fgene.2019.00466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Motivation: In order to create controlled vocabularies for shared use in different biomedical domains, a large number of biomedical ontologies such as Disease Ontology (DO) and Human Phenotype Ontology (HPO), etc., are created in the bioinformatics community. Quantitative measures of the associations among diseases could help researchers gain a deep insight of human diseases, since similar diseases are usually caused by similar molecular origins or have similar phenotypes, which is beneficial to reveal the common attributes of diseases and improve the corresponding diagnoses and treatment plans. Some previous are proposed to measure the disease similarity using a particular biomedical ontology during the past few years, but for a newly discovered disease or a disease with few related genetic information in Disease Ontology (i.e., a disease with less disease-gene associations), these previous approaches usually ignores the joint computation of disease similarity by integrating gene and phenotype associations. Results: In this paper we propose a novel method called GPSim to effectively deduce the semantic similarity of diseases. In particular, GPSim calculates the similarity by jointly utilizing gene, disease and phenotype associations extracted from multiple biomedical ontologies and databases. We also explore the phenotypic factors such as the depth of HPO terms and the number of phenotypic associations that affect the evaluation performance. A final experimental evaluation is carried out to evaluate the performance of GPSim and shows its advantages over previous approaches.
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Affiliation(s)
- Shuhui Su
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Lei Zhang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Jian Liu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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44
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Nurden AT, Nurden P. High-throughput sequencing for rapid diagnosis of inherited platelet disorders: a case for a European consensus. Haematologica 2019; 103:6-8. [PMID: 29290630 DOI: 10.3324/haematol.2017.182295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alan T Nurden
- Institut de Rythmologie et de Modélisation Cardiaque, Plateforme Technologique d'Innovation Biomédicale, Hôpital Xavier Arnozan, Pessac, France
| | - Paquita Nurden
- Institut de Rythmologie et de Modélisation Cardiaque, Plateforme Technologique d'Innovation Biomédicale, Hôpital Xavier Arnozan, Pessac, France
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45
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Nessle CN, Ghosal S, Mathews C, Taylor D, Myers J, Raj A, Panigrahi A. Weak correlation of bleeding scores to platelet electron microscopy: A retrospective chart review of pediatric patients with delta-storage pool disorder. Pediatr Blood Cancer 2019; 66:e27505. [PMID: 30345617 DOI: 10.1002/pbc.27505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/11/2018] [Accepted: 09/24/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Delta granule storage pool deficiency (δ-SPD) is a rare platelet disorder in which a deficiency of platelet granules leads to poor aggregation, resulting in varying clinical bleeding phenotypes. Children with δ-SPD have variable laboratory results, making the proper diagnosis and evaluation controversial. OBJECTIVES To describe the demographic and laboratory trends of this population and to assess the value of electron microscopy in diagnostic evaluation and its correlation to bleeding symptoms. METHODS We performed a retrospective review of 109 pediatric patients diagnosed with δ-SPD. We collected demographic information and bleeding scores using a validated bleeding assessment tool. A descriptive and exploratory analysis was performed. RESULTS The majority of patients were female, with an average age at diagnosis of 11.61 years. Females were diagnosed at a significantly older age presenting most often with menorrhagia, while males presented most commonly with epistaxis. The majority showed normal lumiaggregometry, the mean platelet electron microscopy (PEM) value was 2.37, and the mean bleeding score was 6. Bleeding assessment tool and PEM had a significantly weak correlation. CONCLUSIONS Patients with more dense granules per platelet had higher bleeding scores than those with fewer dense granules per platelet. The current body of evidence does not favor the use of PEM in routine clinical practice, and results are difficult to interpret. In patients with severe mucocutaneous bleeding symptoms and normal platelet aggregation studies, consideration should be given to an alternative diagnosis and further evaluation is warranted.
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Affiliation(s)
- C N Nessle
- Department of Pediatrics, University of Louisville, Louisville, Kentucky
| | - S Ghosal
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky
| | - C Mathews
- Department of Pediatrics, University of Louisville, Louisville, Kentucky
| | - D Taylor
- Department of Pediatrics, University of Louisville, Louisville, Kentucky
| | - J Myers
- Department of Pediatrics, University of Louisville, Louisville, Kentucky.,Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky
| | - A Raj
- Department of Pediatrics, University of Louisville, Louisville, Kentucky.,Department of Pediatric Hematology Oncology, University of Louisville, Louisville, Kentucky
| | - A Panigrahi
- Department of Pediatric Hematology Oncology, University of California-Davis, Davis, California
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46
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Andres O, König EM, Althaus K, Bakchoul T, Bugert P, Eber S, Knöfler R, Kunstmann E, Manukjan G, Meyer O, Strauß G, Streif W, Thiele T, Wiegering V, Klopocki E, Schulze H. Use of Targeted High-Throughput Sequencing for Genetic Classification of Patients with Bleeding Diathesis and Suspected Platelet Disorder. TH OPEN 2018; 2:e445-e454. [PMID: 31249973 PMCID: PMC6524924 DOI: 10.1055/s-0038-1676813] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
Inherited platelet disorders (IPD) form a rare and heterogeneous disease entity that is present in about 8% of patients with non-acquired bleeding diathesis. Identification of the defective cellular pathway is an important criterion for stratifying the patient's individual risk profile and for choosing personalized therapeutic options. While costs of high-throughput sequencing technologies have rapidly declined over the last decade, molecular genetic diagnosis of bleeding and platelet disorders is getting more and more suitable within the diagnostic algorithms. In this study, we developed, verified, and evaluated a targeted, panel-based next-generation sequencing approach comprising 59 genes associated with IPD for a cohort of 38 patients with a history of recurrent bleeding episodes and functionally suspected, but so far genetically undefined IPD. DNA samples from five patients with genetically defined IPD with disease-causing variants in
WAS
,
RBM8A
,
FERMT3
,
P2YR12
, and
MYH9
served as controls during the validation process. In 40% of 35 patients analyzed, we were able to finally detect 15 variants, eight of which were novel, in 11 genes,
ACTN1
,
AP3B1
,
GFI1B
,
HPS1
,
HPS4
,
HPS6
,
MPL
,
MYH9
,
TBXA2R
,
TPM4
, and
TUBB1
, and classified them according to current guidelines. Apart from seven variants of uncertain significance in 11% of patients, nine variants were classified as likely pathogenic or pathogenic providing a molecular diagnosis for 26% of patients. This report also emphasizes on potentials and pitfalls of this tool and prospectively proposes its rational implementation within the diagnostic algorithms of IPD.
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Affiliation(s)
- Oliver Andres
- University Children's Hospital, University of Würzburg, Würzburg, Germany
| | - Eva-Maria König
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Karina Althaus
- Centre for Clinical Transfusion Medicine, University Hospital of Tübingen, Tübingen, Germany.,Institute for Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Tamam Bakchoul
- Centre for Clinical Transfusion Medicine, University Hospital of Tübingen, Tübingen, Germany.,Institute for Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Peter Bugert
- DRK-Blutspendedienst Baden-Württemberg-Hessen, Institute for Transfusion Medicine and Immunology, Heidelberg University, Mannheim, Germany
| | - Stefan Eber
- University Children's Hospital, Technical University Munich, Munich, Germany
| | - Ralf Knöfler
- Department of Pediatrics, Carl Gustav Carus University Hospital, Dresden, Germany
| | - Erdmute Kunstmann
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Georgi Manukjan
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Oliver Meyer
- Institute for Transfusion Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriele Strauß
- Department for Pediatric Oncology and Hematology, HELIOS Klinikum Berlin-Buch, Berlin, Germany
| | - Werner Streif
- Department of Pediatrics, Medical University Innsbruck, Innsbruck, Austria
| | - Thomas Thiele
- Institute for Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Verena Wiegering
- University Children's Hospital, University of Würzburg, Würzburg, Germany
| | - Eva Klopocki
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Harald Schulze
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
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47
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van Oorschot R, Marneth AE, Bergevoet SM, van Bergen MGJM, Peerlinck K, Lentaigne CE, Millar CM, Westbury SK, Favier R, Erber WN, Turro E, Jansen JH, Ouwehand WH, McKinney HL, Downes K, Freson K, van der Reijden BA. Inherited missense variants that affect GFI1B function do not necessarily cause bleeding diatheses. Haematologica 2018; 104:e260-e264. [PMID: 30573501 DOI: 10.3324/haematol.2018.207712] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Rinske van Oorschot
- Department of Laboratory Medicine, Laboratory of Hematology, Radboudumc, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
| | - Anna E Marneth
- Department of Laboratory Medicine, Laboratory of Hematology, Radboudumc, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
| | - Saskia M Bergevoet
- Department of Laboratory Medicine, Laboratory of Hematology, Radboudumc, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
| | - Maaike G J M van Bergen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboudumc, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
| | - Kathelijne Peerlinck
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Belgium
| | - Claire E Lentaigne
- Centre for Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, UK
| | - Carolyn M Millar
- Centre for Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, UK.,Imperial College Healthcare NHS Trust, London, UK
| | - Sarah K Westbury
- School of Cellular and Molecular Medicine, University of Bristol, UK
| | - Remi Favier
- Service d'Hematologie Biologique, Assistance-Publique Hôpitaux de Paris, Centre de Référence des Pathologies Plaquettaires, Hôpital Armand Trousseau, Paris, France
| | - Wendy N Erber
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia, Australia.,PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, UK.,NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, UK.,Medical Research Council Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, UK
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboudumc, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, UK.,NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, UK.,Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, UK.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, UK
| | - Harriet L McKinney
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, UK.,NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, UK
| | | | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, UK.,NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Belgium.,NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, UK
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboudumc, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen, the Netherlands
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48
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Faleschini M, Melazzini F, Marconi C, Giangregorio T, Pippucci T, Cigalini E, Pecci A, Bottega R, Ramenghi U, Siitonen T, Seri M, Pastore A, Savoia A, Noris P. ACTN1 mutations lead to a benign form of platelet macrocytosis not always associated with thrombocytopenia. Br J Haematol 2018; 183:276-288. [PMID: 30351444 DOI: 10.1111/bjh.15531] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/19/2018] [Indexed: 12/27/2022]
Abstract
The inherited thrombocytopenias (IT) are a heterogeneous group of diseases resulting from mutations in more than 30 different genes. Among them, ACTN1-related thrombocytopenia (ACTN1-RT; Online Mendelian Inheritance in Man: 615193) is one of the most recently identified forms. It has been described as a mild autosomal dominant macrothrombocytopenia caused by mutations in ACTN1, a gene encoding for one of the two non-muscle isoforms of α-actinin. We recently identified seven new unrelated families with ACTN1-RT caused by different mutations. Two of them are novel missense variants (p.Trp128Cys and p.Pro233Leu), whose pathogenic role has been confirmed by in vitro studies. Together with the 10 families we have previously described, our cohort of ACTN1-RT now consists of 49 individuals carrying ACTN1 mutations. This is the largest case series ever collected and enabled a critical evaluation of the clinical aspects of the disease. We concluded that ACTN1-RT is the fourth most frequent form of IT worldwide and it is characterized by platelet macrocytosis in all affected subjects and mild thrombocytopenia in less than 80% of cases. The risk of bleeding, either spontaneous or upon haemostatic challenge, is negligible and there are no other associated defects, either congenital or acquired. Therefore, ACTN1-RT is a benign form of IT, whose diagnosis provides affected individuals and their families with a good prognosis.
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Affiliation(s)
- Michela Faleschini
- Institute for Maternal and Child Health - "IRCCS Burlo Garofolo", Trieste, Italy
| | - Federica Melazzini
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Caterina Marconi
- Department of Medical Science, Medical Genetics Unit, Policlinico Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | | | - Tommaso Pippucci
- Department of Medical Science, Medical Genetics Unit, Policlinico Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Elena Cigalini
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Alessandro Pecci
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health - "IRCCS Burlo Garofolo", Trieste, Italy
| | - Ugo Ramenghi
- Pediatric Department, Hematology Unit, University of Torino, Torino, Italy
| | - Timo Siitonen
- Department of Medicine, Oulu University Hospital, Oulu, Finland
| | - Marco Seri
- Department of Medical Science, Medical Genetics Unit, Policlinico Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Annalisa Pastore
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health - "IRCCS Burlo Garofolo", Trieste, Italy.,Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Patrizia Noris
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
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Heremans J, Freson K. High-throughput sequencing for diagnosing platelet disorders: lessons learned from exploring the causes of bleeding disorders. Int J Lab Hematol 2018; 40 Suppl 1:89-96. [PMID: 29741246 DOI: 10.1111/ijlh.12812] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 02/07/2018] [Indexed: 12/21/2022]
Abstract
Inherited platelet disorders (IPDs) are a heterogeneous group of disorders caused by multiple genetic defects. Obtaining a molecular diagnosis for IPD patients using a phenotype- and laboratory-based approach is complex, expensive, time-consuming, and not always successful. High-throughput sequencing (HTS) methods offer a genotype-based approach to facilitate molecular diagnostics. Such approaches are expected to decrease time to diagnosis, increase the diagnostic rate, and they have provided novel insights into the genotype-phenotype correlation of IPDs. Some of these approaches have also focused on the discovery of novel genes and unexpected molecular pathways which modulate megakaryocyte and platelet biology were discovered. A growing number of genetic defects underlying IPDs have been identified and we will here provide an overview of the diverse molecular players. Screening of these genes will deliver a genetic diagnosis for about 40%-50% of the IPDs patients and we will compare different HTS applications that have been developed. A brief focus on gene variant interpretation and classification in a diagnostic setting will be given. Although it is true that successes in diagnostics and gene discovery have been reached, a large fraction of patients still remains without a conclusive diagnosis. In these patients, the sum of non-diagnostic variants in known genes or in potential novel genes might only be proven informative in future studies with larger patient cohorts and by data sharing among the diverse genome medicine initiatives. Finally, we still do not understand the role of the non-coding genome space for IPDs.
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Affiliation(s)
- J Heremans
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
| | - K Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium
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Valdeolivas A, Tichit L, Navarro C, Perrin S, Odelin G, Levy N, Cau P, Remy E, Baudot A. Random walk with restart on multiplex and heterogeneous biological networks. Bioinformatics 2018; 35:497-505. [DOI: 10.1093/bioinformatics/bty637] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 07/16/2018] [Indexed: 01/04/2023] Open
Affiliation(s)
- Alberto Valdeolivas
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
- ProGeLife, Marseille
| | - Laurent Tichit
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Claire Navarro
- ProGeLife, Marseille
- Aix Marseille Univ, INSERM, MMG, Marseille, France
| | - Sophie Perrin
- ProGeLife, Marseille
- Aix Marseille Univ, INSERM, MMG, Marseille, France
| | - Gaëlle Odelin
- ProGeLife, Marseille
- Aix Marseille Univ, INSERM, MMG, Marseille, France
| | - Nicolas Levy
- Aix Marseille Univ, INSERM, MMG, Marseille, France
| | - Pierre Cau
- ProGeLife, Marseille
- Aix Marseille Univ, INSERM, MMG, Marseille, France
| | - Elisabeth Remy
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
| | - Anaïs Baudot
- Aix Marseille Univ, CNRS, Centrale Marseille, I2M, Marseille, France
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