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Lannoy N, Hermans C. Accessibility and visibility of genetic testing for haemophilia across Europe: Where do we stand? Haemophilia 2023; 29:256-273. [PMID: 36222225 DOI: 10.1111/hae.14672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 09/06/2022] [Accepted: 09/18/2022] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Haemophilia is characterized by bleeding complications resulting from clotting factor VIII (FVIII) or IX (FIX) deficiency. Identifying the causal pathogenic genetic variant denotes a vital aspect of haemophilia management. AIM This study evaluated the accessibility and performances of genetic testing for haemophilia across Europe. The types of genetic analyses, techniques used, turn-around time (TAT) and costs were collected and analysed, as were data updating and quality control. METHODS Reported data were retrieved from open access resources, including international databases, Google, laboratory websites, PubMed and government organizations. RESULTS Overall, 51 genetic laboratories across 15 European countries providing recently updated molecular haemophilia testing were identified. Gene sequencing for small variants of both F8 and F9 genes was provided in most surveyed laboratories. Almost two-thirds of them offer analysis for inversions using a polymerase chain reaction (PCR) method and detection of copy number variation (CNV) using multiplex ligation-dependent probe amplification (MLPA). Cost and TAT were found to vary considerably. In total, 74% of laboratories exhibited a last modified date or change history. The same percentage of laboratories was in possession of an ISO 15189 standard accreditation, whereas only few of them recently performed external quality assessment schemes (EQA) for haemophilia. CONCLUSION Despite several initiatives to improve access to genetic testing for haemophilia, such access must still be improved. Our study similarly revealed the large heterogeneity of the variants tested, techniques employed, TAT, cost and quality among the surveyed laboratories.
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Affiliation(s)
- Nathalie Lannoy
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Saint-Luc University Hospital, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Cedric Hermans
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Saint-Luc University Hospital, Université catholique de Louvain (UCLouvain), Brussels, Belgium
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Pezeshkpoor B, Oldenburg J, Pavlova A. Insights into the Molecular Genetic of Hemophilia A and Hemophilia B: The Relevance of Genetic Testing in Routine Clinical Practice. Hamostaseologie 2022; 42:390-399. [PMID: 36549291 PMCID: PMC9779947 DOI: 10.1055/a-1945-9429] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hemophilia A and hemophilia B are rare congenital, recessive X-linked disorders caused by lack or deficiency of clotting factor VIII (FVIII) or IX (FIX), respectively. The severity of the disease depends on the reduction of coagulation FVIII or FIX activity levels, which is determined by the type of the pathogenic variants in the genes encoding the two factors (F8 and F9, respectively). Molecular genetic analysis is widely applied in inherited bleeding disorders. The outcome of genetic analysis allows genetic counseling of affected families and helps find a link between the genotype and the phenotype. Genetic analysis in hemophilia has tremendously improved in the last decades. Many new techniques and modifications as well as analysis softwares became available, which made the genetic analysis and interpretation of the data faster and more accurate. Advances in genetic variant detection strategies facilitate identification of the causal variants in up to 97% of patients. In this review, we discuss the milestones in genetic analysis of hemophilia and highlight the importance of identification of the causative genetic variants for genetic counseling and particularly for the interpretation of the clinical presentation of hemophilia patients.
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Affiliation(s)
- Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, Medical Faculty, University of Bonn, University Hospital Bonn, Bonn, Germany,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, Medical Faculty, University of Bonn, University Hospital Bonn, Bonn, Germany,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - Anna Pavlova
- Institute of Experimental Hematology and Transfusion Medicine, Medical Faculty, University of Bonn, University Hospital Bonn, Bonn, Germany,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany,Address for correspondence Anna Pavlova, MD, PhD Institute of Experimental Hematology and Transfusion Medicine, University of BonnVenusberg Campus 1, 53127, BonnGermany
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3
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[Research progress of Molecular diagnostic technique in Venous Thromboembolism]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2022; 43:964-968. [PMID: 36709191 PMCID: PMC9808858 DOI: 10.3760/cma.j.issn.0253-2727.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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4
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Egido-Turrión C, Rossi E, Ollauri-Ibáñez C, Pérez-García ML, Sevilla MA, Bastida JM, González-Porras JR, Rodríguez-Barbero A, Bernabeu C, Lopez-Novoa JM, Pericacho M. Functional Alterations Involved in Increased Bleeding in Hereditary Hemorrhagic Telangiectasia Mouse Models. Front Med (Lausanne) 2022; 9:871903. [PMID: 35665360 PMCID: PMC9160577 DOI: 10.3389/fmed.2022.871903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Hereditary Hemorrhagic Telangiectasia (HHT) is an autosomal-dominant genetic disorder involving defects in two predominant genes known as endoglin (ENG; HHT-1) and activin receptor-like kinase 1 (ACVRL1/ALK1; HHT-2). It is characterized by mucocutaneous telangiectases that, due to their fragility, frequently break causing recurrent epistaxis and gastrointestinal bleeding. Because of the severity of hemorrhages, the study of the hemostasis involved in these vascular ruptures is critical to find therapies for this disease. Our results demonstrate that HHT patients with high bleeding, as determined by a high Epistaxis Severity Score (ESS), do not have prolonged clotting times or alterations in clotting factors. Considering that coagulation is only one of the processes involved in hemostasis, the main objective of this study was to investigate the overall mechanisms of hemostasis in HHT-1 (Eng+/−) and HHT-2 (Alk1+/−) mouse models, which do not show HHT vascular phenotypes in the meaning of spontaneous bleeding. In Eng+/− mice, the results of in vivo and in vitro assays suggest deficient platelet-endothelium interactions that impair a robust and stable thrombus formation. Consequently, the thrombus could be torn off and dragged by the mechanical force exerted by the bloodstream, leading to the reappearance of hemorrhages. In Alk1+/− mice, an overactivation of the fibrinolysis system was observed. These results support the idea that endoglin and Alk1 haploinsufficiency leads to a common phenotype of impaired hemostasis, but through different mechanisms. This contribution opens new therapeutic approaches to HHT patients' epistaxis.
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Affiliation(s)
- Cristina Egido-Turrión
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Elisa Rossi
- Université de Paris, Innovative Therapies in Haemostasis, INSERM, Paris, France
| | - Claudia Ollauri-Ibáñez
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - María L. Pérez-García
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Department of Internal Medicine, Complejo Asistencial Universitario de Salamanca (CAUSA)-SACYL, Salamanca, Spain
| | - María A. Sevilla
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - José María Bastida
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Department of Hematology, Complejo Asistencial Universitario de Salamanca (CAUSA)-SACYL, Salamanca, Spain
| | - José Ramón González-Porras
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Department of Hematology, Complejo Asistencial Universitario de Salamanca (CAUSA)-SACYL, Salamanca, Spain
| | - Alicia Rodríguez-Barbero
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Carmelo Bernabeu
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - José M. Lopez-Novoa
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Miguel Pericacho
- Department of Physiology and Pharmacology, Universidad de Salamanca, Salamanca, Spain
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- *Correspondence: Miguel Pericacho
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5
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New approaches to the genetic study of bleeding diathesis in our center: from sanger to next-generation sequencing. Blood Coagul Fibrinolysis 2022; 33:S19-S21. [PMID: 35088770 DOI: 10.1097/mbc.0000000000001107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Ver Donck F, Labarque V, Freson K. Hemostatic phenotypes and genetic disorders. Res Pract Thromb Haemost 2021; 5:e12637. [PMID: 34964017 PMCID: PMC8677882 DOI: 10.1002/rth2.12637] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/26/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
This review is focused on genetic regulators of bleeding and thrombosis with a focus on next-generation sequencing (NGS) technologies for diagnosis and research of patients with inherited disorders. The molecular diagnosis of hemostatic phenotypes relies on the detection of genetic variants in the 99 curated disease-causing genes implicated for bleeding, platelet, and thrombotic disorders through the use of multigene panel tests. In this review, we will provide an overview of the advantages and disadvantages of using such multigene panel tests for diagnostics. During the past decade, NGS technologies have also been used for the gene discovery of 32 novel genes involved in inherited hemostatic phenotypes. We will provide a brief overview of these genes and discuss what information (eg, linkage, consanguinity, multiple index cases with similar phenotypes, mouse models, and more) was used to support the gene discovery process. Next, we provide examples on how RNA sequencing is useful to explore disease mechanisms of novel and often unexpected genes. This review will summarize the important findings concerning NGS technologies for diagnostics and gene discovery that were presented at the ISTH 2021 conference. Finally, future perspectives in our field mainly deal with finding the needle in the haystack for some still unexplained patients and the need for exploring the noncoding gene space and rapid disease validation models.
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Affiliation(s)
- Fabienne Ver Donck
- Department of Cardiovascular SciencesCenter for Molecular and Vascular BiologyUniversity of LeuvenLeuvenBelgium
| | - Veerle Labarque
- Department of Cardiovascular SciencesCenter for Molecular and Vascular BiologyUniversity of LeuvenLeuvenBelgium
- Department of Pediatrics, Pediatric Hemato‐OncologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Kathleen Freson
- Department of Cardiovascular SciencesCenter for Molecular and Vascular BiologyUniversity of LeuvenLeuvenBelgium
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Borràs N, Castillo-González D, Comes N, Martin-Fernandez L, Rivero-Jiménez RA, Chang-Monteagudo A, Ruiz-Moleón V, Garrote-Santana H, Vidal F, Macías-Abraham C. Molecular study of a large cohort of 109 haemophilia patients from Cuba using a gene panel with next generation sequencing-based technology. Haemophilia 2021; 28:125-137. [PMID: 34708896 DOI: 10.1111/hae.14438] [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: 07/07/2021] [Revised: 09/10/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION In several countries, molecular diagnosis of haemophilia A (HA) and B (HB) is hampered by a lack of resources for DNA analysis. The advent of next-generation sequencing (NGS) has enabled gene analysis at a reasonable cost. AIM Describe a collaboration between Cuban and Spanish researchers to identify candidate variants and investigate the molecular epidemiology of 106 Cuban haemophilia patients using NGS. PATIENTS/METHODS The molecular analysis protocol included well-established LR-PCR procedures to detect F8 inversions, NGS with a 30-gene panel to sequence F8 and F9, and multiplex ligation-dependent probe amplification to identify large structural variants. RESULTS One-hundred and thirty-one candidate variants were identified along F8, F9, and VWF; 72 were unique and 28 (39%) had not been previously recorded. Putative variants were identified in 105/106 patients. Molecular characterization enabled confirmation and reclassification of: 90 HA (85%), 15 HB (14%), and one type 2N VWD (1%). Null variants leading to non-production of FVIII or FIX were common in severe HA (64%), moderate HA (74%), and severe HB (60%), whereas missense variants were frequent in mild HA (57%) and moderate or mild HB (83%). Additional variants in VWF were identified in 16 patients. CONCLUSION This is the first description of the molecular epidemiology of HA and HB in Cuba. Variants identified in index cases will be of value for local implementation of familial studies and prenatal diagnosis using the molecular approaches available in Cuba. The results of this protocolled genetic study improved the accuracy of the clinical diagnosis and will facilitate management of these patients.
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Affiliation(s)
- Nina Borràs
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain
| | | | - Natalia Comes
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain
| | - Laura Martin-Fernandez
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain
| | | | | | | | | | - Francisco Vidal
- Congenital Coagulopathies Laboratory, Blood and Tissue Bank, Barcelona, Spain.,Transfusion Medicine, Universitat Autònoma de Barcelona (VHIR-UAB), Vall d'Hebron Research Institute, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Instituto Carlos III (ISCIII), Madrid, Spain
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8
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Zaninetti C, Wolff M, Greinacher A. Diagnosing Inherited Platelet Disorders: Modalities and Consequences. Hamostaseologie 2021; 41:475-488. [PMID: 34391210 DOI: 10.1055/a-1515-0813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Inherited platelet disorders (IPDs) are a group of rare conditions featured by reduced circulating platelets and/or impaired platelet function causing variable bleeding tendency. Additional hematological or non hematological features, which can be congenital or acquired, distinctively mark the clinical picture of a subgroup of patients. Recognizing an IPD is challenging, and diagnostic delay or mistakes are frequent. Despite the increasing availability of next-generation sequencing, a careful phenotyping of suspected patients-concerning the general clinical features, platelet morphology, and function-is still demanded. The cornerstones of IPD diagnosis are clinical evaluation, laboratory characterization, and genetic testing. Achieving a diagnosis of IPD is desirable for several reasons, including the possibility of tailored therapeutic strategies and individual follow-up programs. However, detailed investigations can also open complex scenarios raising ethical issues in case of IPDs predisposing to hematological malignancies. This review offers an overview of IPD diagnostic workup, from the interview with the proband to the molecular confirmation of the suspected disorder. The main implications of an IPD diagnosis are also discussed.
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Affiliation(s)
- Carlo Zaninetti
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany.,Department of Internal Medicine, University of Pavia, Pavia, Italy
| | - Martina Wolff
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Andreas Greinacher
- Institut für Immunologie und Transfusionsmedizin, Universitätsmedizin Greifswald, Greifswald, Germany
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9
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Molecular classification of blood and bleeding disorder genes. NPJ Genom Med 2021; 6:62. [PMID: 34272389 PMCID: PMC8285395 DOI: 10.1038/s41525-021-00228-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
The advances and development of sequencing techniques and data analysis resulted in a pool of informative genetic data, that can be analyzed for informing decision making in designing national screening, prevention programs, and molecular diagnostic tests. The accumulation of molecular data from different populations widen the scope of utilization of this information. Bleeding disorders are a heterogeneous group of clinically overlapping disorders. We analyzed the targeted sequencing data from ~1285 Saudi individuals in 17 blood and bleeding disorders genes, to determine the frequency of mutations and variants. We used a replication set of ~5000 local exomes to validate pathogenicity and determine allele frequencies. We identified a total of 821 variants, of these 98 were listed in HGMD as disease related variants and 140 were novel variants. The majority of variants were present in VWF, followed by F5, F8, and G6PD genes, while FGG, FGB, and HBA1 had the lowest number of variants. Our analysis generated a priority list of genes, mutations and novel variants. This data will have an impact on informing decisions for screening and prevention programs and in management of vulnerable patients admitted to emergency, surgery, or interventions with bleeding side effects.
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Athar M, Ghita IS, Albagenny AA, Abduljaleel Z, Shadab G, Elsendiony A, Halawani SH, Alkazmi MM, Alquthami K, Alkhuzae MM, Althebyani AA, Bogari NM, Dannoun A, Al-Allaf FA. Targeted next-generation sequencing reveals novel and known variants of thrombophilia associated genes in Saudi patients with venous thromboembolism. Clin Chim Acta 2021; 519:247-254. [PMID: 34015304 DOI: 10.1016/j.cca.2021.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/25/2021] [Accepted: 05/13/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Thrombophilia is a substantial source of indisposition and mortality in several countries, including Arab populations. Deep venous thrombosis (DVT) with or without pulmonary embolism (PE) is the prevalent clinical manifestation of thrombophilia. While many genetic risk factors for DVT are known, almost all associated with hemostasis, many genetic factors remain unexplained. Nowadays, Next Generation Sequencing (NGS) offers a potential solution that allows several candidate genes to be analyzed simultaneously at a reasonable expense. METHODS We performed variant screening in the thrombophilia associated genes in Factor V Leiden (FVL) mutation-negative patients using Ion Torrent Next-generation sequencing (NGS). Ion AmpliSeq panel for 18 genes was designed. Twenty-nine unrelated patients with idiopathic VTE were recruited for NGS. RESULTS We were able to identify 19 variants (1 novel and 18 previously reported) in 10 out of 18 targeted genes. Pathogenic variants were identified in 22 patients demonstrating mutation detection rates of 76%. Previously reported variants in the F5, MTHFR, PROS1, PROC, F8, F9, SERPINA10, SERPIND1, and HRG genes were recognized in 21 patients. More than one variant in the targeted genes was detected in some of the patients with VTE. We identified SERPINA10 recurrent variant p.(R88*) in seven patients representing 32% of VTE cases. Additionally, we report one novel variant c.356G > T, p.(G119V) in the F7 gene, considered to be pathogenic in this study. CONCLUSIONS Our studies finding illustrates the ability of targeted next-generation sequencing to uncover uncommon/unknown genetic variants that may predispose to thrombophilia. The finding of the novel variant in the F7 gene extends the spectrum of variants affecting thrombosis. While a comparatively small number of subjects have been included in our cohort, the findings summarize the possible genetic features of thrombophilia.
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Affiliation(s)
- Mohammad Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Ibrahim S Ghita
- Hematology Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Amani A Albagenny
- Laboratory and Blood Bank Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Zainularifeen Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia; Science and Technology Unit, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ghulam Shadab
- Cytogenetics and Molecular Toxicology Laboratory, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Ahmed Elsendiony
- Laboratory and Blood Bank Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Saeed H Halawani
- Department of Hematology and Immunology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohammad M Alkazmi
- Hematology Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Khalid Alquthami
- Laboratory and Blood Bank Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | - Mohammad M Alkhuzae
- Laboratory and Blood Bank Department, Al-Noor Specialist Hospital, Makkah, Saudi Arabia
| | | | - Neda M Bogari
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Anas Dannoun
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faisal A Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
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Use of a Comprehensive 66-Gene Cholestasis Sequencing Panel in 2171 Cholestatic Infants, Children, and Young Adults. J Pediatr Gastroenterol Nutr 2021; 72:654-660. [PMID: 33720099 DOI: 10.1097/mpg.0000000000003094] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVES Cholestasis is caused by a wide variety of etiologies, often genetic in origin. Broad overlap in clinical presentations, particularly in newborns, renders prioritizing diagnostic investigations challenging. In this setting, a timely, comprehensive assessment using a multigene panel by a clinical diagnostic laboratory would likely prove useful. We summarize initial findings from a testing program designed to discover genetic causes of cholestasis. METHODS A neonatal/adult sequencing panel containing 66 genes (originally 57; nine added March 2017) relevant to cholestasis was used. A broad range of eligible patients were enrolled with current/history of cholestasis without an identified cause, or unexplained chronic liver disease. DNA sequencing utilized a custom-designed capture library, and variants were classified and reported as benign, likely benign, variant of unknown significance (VOUS), likely pathogenic (LP), or pathogenic (P), according to the clinical interpretation workflow at EGL Genetics (Tucker, GA). RESULTS A total of 2433 samples were submitted between February 2016 and December 2017; 2171 results were reported. Median turnaround time was 21 days. Results from the 2171 subjects (57% <1 year old) included 583 P variants, 79 LP variants, and 3117 VOUS; 166 P/LP variants and 415 VOUS were novel. The panel's overall diagnostic yield was 12% (n = 265/2171) representing 32 genes. The top five genetic diagnoses for the group, in order: JAG1 + NOTCH2 (Alagille syndrome), ABCB11, SERPINA1, ABCB4, and POLG. CONCLUSIONS These findings support the utility of comprehensive rapid multigene testing in diagnosing cholestasis and highlight the evolving understanding of genetic variants contributing to the pathogenesis of cholestasis.
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Hausman-Kedem M, Malinger G, Modai S, Kushner SA, Shiran SI, Ben-Sira L, Roth J, Constantini S, Fattal-Valevski A, Ben-Shachar S. Monogenic Causes of Apparently Idiopathic Perinatal Intracranial Hemorrhage. Ann Neurol 2021; 89:813-822. [PMID: 33527515 DOI: 10.1002/ana.26033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/26/2021] [Accepted: 01/26/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Perinatal intracranial hemorrhage (pICH) is a rare event that occurs during the fetal/neonatal period with potentially devastating neurological outcome. However, the etiology of pICH is frequently hard to depict. We investigated the role of rare genetic variations in unexplained cases of pICH. METHODS We performed whole-exome sequencing (WES) in fetuses and term neonates with otherwise unexplained pICH and their parents. Variant causality was determined according to the American College of Medical Genetics and Genomics (ACMG) criteria, consistency between suggested genes and phenotypes, and mode of inheritance. RESULTS Twenty-six probands (25 families) were included in the study (9 with a prenatal diagnosis and 17 with a postnatal diagnosis). Intraventricular hemorrhage (IVH) was the most common type of hemorrhage (n = 16, 62%), followed by subpial (n = 4, 15%), subdural (n = 4, 15%), and parenchymal (n = 2, 8%) hemorrhage. Causative/likely causative variants were found in 4 subjects from 3 of the 25 families (12%) involving genes related to the brain microenvironment (COL4A1, COL4A2, and TREX-1). Additionally, potentially causative variants were detected in genes related to coagulation (GP1BA, F11, Von Willebrand factor [VWF], FGA, and F7; n = 4, 16%). A potential candidate gene for phenotypic expansion related to microtubular function (DNAH5) was identified in 1 case (4%). Fifty-five percent of the variants were inherited from an asymptomatic parent. Overall, these findings showed a monogenic cause for pICH in 12% to 32% of the families. INTERPRETATION Our findings reveal a clinically significant diagnostic yield of WES in apparently idiopathic pICH and support the use of WES in the evaluation of these cases. ANN NEUROL 2021;89:813-822.
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Affiliation(s)
- Moran Hausman-Kedem
- Pediatric Neurology Institute, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gustavo Malinger
- Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Division of Obstetrics and Gynecology Ultrasound, Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | | | - Steven A Kushner
- Department of Psychiatry, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Shelly I Shiran
- Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Radiology Department, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Liat Ben-Sira
- Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Radiology Department, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jonathan Roth
- Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Neurosurgery Department, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Shlomi Constantini
- Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Neurosurgery Department, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Aviva Fattal-Valevski
- Pediatric Neurology Institute, Dana-Dwek Children's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shay Ben-Shachar
- Sackler Faulty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Schneider Children's Medical Center, Petah Tikva, Israel.,Clalit Research Institute, Ramat Gan, Israel
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13
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Grover SP, Mackman N. Description of the first mutation in the human tissue factor gene associated with a bleeding tendency. J Thromb Haemost 2021; 19:3-6. [PMID: 33225609 DOI: 10.1111/jth.15151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Steven P Grover
- UNC Blood Research Center, Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nigel Mackman
- UNC Blood Research Center, Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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14
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Manderstedt E, Nilsson R, Ljung R, Lind‐Halldén C, Astermark J, Halldén C. Detection of mosaics in hemophilia A by deep Ion Torrent sequencing and droplet digital PCR. Res Pract Thromb Haemost 2020; 4:1121-1130. [PMID: 33134778 PMCID: PMC7590296 DOI: 10.1002/rth2.12425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The occurrence of mosaicism in hemophilia A (HA) has been investigated in several studies using different detection methods. OBJECTIVES To characterize and compare the ability of AmpliSeq/Ion Torrent sequencing and droplet digital polymerase chain reaction (ddPCR) for mosaic detection in HA. METHODS Ion Torrent sequencing and ddPCR were used to analyze 20 healthy males and 16 mothers of sporadic HA patients. RESULTS An error-rate map over all coding positions and all positions reported as mutated in the F8-specific mutation database was produced. The sequencing produced a mean read depth of >1500X where >97% of positions were covered by >100 reads. Higher error frequencies were observed in positions with A or T as reference allele and in positions surrounded on both sides with C or G. Seventeen of 9319 positions had a mean substitution error frequency >1%. The ability to identify low-level mosaicism was determined primarily by read depth and error rate of each specific position. Limit of detection (LOD) was <1% for 97% of positions with substitutions and 90% of indel positions. The positions with LOD >1% require repeated testing and mononucleotide repeats with more than four repeat units need an alternative analysis strategy. Mosaicism was detected in 1 of 16 mothers and confirmed using ddPCR. CONCLUSIONS Deep sequencing using an AmpliSeq/Ion Torrent strategy allows for simultaneous identification of disease-causing mutations in patients and mosaicism in mothers. ddPCR has high sensitivity but is hampered by the need for mutation-specific design.
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Affiliation(s)
- Eric Manderstedt
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
| | - Rosanna Nilsson
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
| | - Rolf Ljung
- Department of Clinical Sciences‐Pediatrics, Lund and Malmö Center for Thrombosis and HemostasisLund UniversitySkåne University HospitalMalmöSweden
| | - Christina Lind‐Halldén
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
| | - Jan Astermark
- Department for Hematology, Oncology and Radiation PhysicsCenter for Thrombosis and HemostasisSkåne University HospitalMalmöSweden
| | - Christer Halldén
- Department of Environmental Science and BioscienceKristianstad UniversityKristianstadSweden
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15
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Ver Donck F, Downes K, Freson K. Strengths and limitations of high-throughput sequencing for the diagnosis of inherited bleeding and platelet disorders. J Thromb Haemost 2020; 18:1839-1845. [PMID: 32521110 DOI: 10.1111/jth.14945] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/27/2020] [Accepted: 05/31/2020] [Indexed: 12/23/2022]
Abstract
Inherited bleeding and platelet disorders (BPD) are highly heterogeneous and their diagnosis involves a combination of clinical investigations, laboratory tests, and genetic screening. This review will outline some of the challenges that geneticists and experts in clinical hemostasis face when implementing high-throughput sequencing (HTS) for patient care. We will provide an overview of the strengths and limitations of the different HTS techniques that can be used to diagnose BPD. An HTS test is cost-efficient and expected to increase the diagnostic rate with a possibility to detect unexpected diagnoses and decrease the turnaround time to diagnose patients. On the other hand, technical shortcomings, variant interpretation difficulties, and ethical issues related to HTS for BPD will also be documented. Delivering a genetic diagnosis to patients is highly desirable to improve clinical management and allow family counseling, but making incorrect assumptions about variants and providing insufficient information to patients before initiating the test could be harmful. Data-sharing and improved HTS guidelines are essential to limit these major drawbacks of HTS.
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Affiliation(s)
- Fabienne Ver Donck
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Kate Downes
- East Midlands and East of England Genomics Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
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16
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Li H, Ma RQ, Cheng HY, Ye X, Zhu HL, Chang XH. Fibrinogen alpha chain promotes the migration and invasion of human endometrial stromal cells in endometriosis through focal adhesion kinase/protein kinase B/matrix metallopeptidase 2 pathway†. Biol Reprod 2020; 103:779-790. [PMID: 32697296 DOI: 10.1093/biolre/ioaa126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/04/2020] [Accepted: 07/14/2020] [Indexed: 12/27/2022] Open
Abstract
Fibrinogen alpha chain (FGA), a cell adhesion molecule, contains two arginyl-glycyl-aspartic acid (RGD) cell adhesion sequences. Our previous study demonstrated that FGA, as an up-regulated protein in endometriosis (EM), was closely related to disease severity and involved in the development of EM. However, the biological functions and underlying mechanism of FGA in EM have not been fully understood. To explore the roles of FGA in EM, we analyzed the effects of FGA on the biological behaviors of human primary eutopic endometrial stromal cells (EuESC). The results indicated FGA knockdown suppressed the migration and invasion ability of EuESC, which also altered the distribution of cytoskeletal filamentous and cell morphology. Western blot analysis demonstrated that knockdown of FGA attenuated the migration-related protein levels of vimentin and matrix metallopeptidase 2 (MMP-2), but not integrin subunit alpha V (ITGAV) and integrin subunit beta 3 (ITGB3). Meanwhile, integrin-linked transduction pathways were detected. We found FGA knockdown significantly suppressed the expression of focal adhesion kinase (FAK) level and protein kinase B (AKT) phosphorylation, without extracellular-signal-regulated kinase (ERK) dependent pathways. Treatment with the AKT inhibitor MK2206 or RGD antagonist highly decreased the effects of FGA on the migration and invasion of EuESC. RGD antagonist treatment strongly inhibited FAK- and AKT-dependent pathways, but not ERK pathways. Our data indicated that FGA may enhance the migration and invasion of EuESC through RGD sequences binding integrin and activating the FAK/AKT/MMP-2 signaling pathway. This novel finding suggests that FGA may provide a novel potential approach to the treatment of EM, which provides a new way to understand the pathogenesis of EM.
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Affiliation(s)
- Hui Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.,Center of Gynecological Oncology, Peking University People's Hospital, Beijing, China
| | - Rui-Qiong Ma
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.,Center of Gynecological Oncology, Peking University People's Hospital, Beijing, China
| | - Hong-Yan Cheng
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.,Center of Gynecological Oncology, Peking University People's Hospital, Beijing, China
| | - Xue Ye
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.,Center of Gynecological Oncology, Peking University People's Hospital, Beijing, China
| | - Hong-Lan Zhu
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China
| | - Xiao-Hong Chang
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing, China.,Center of Gynecological Oncology, Peking University People's Hospital, Beijing, China
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17
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Srivastava A. Diagnosis of haemophilia and other inherited bleeding disorders ‐ Is a new paradigm needed? Haemophilia 2020; 27 Suppl 3:14-20. [DOI: 10.1111/hae.14042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Alok Srivastava
- Department of Haematology Christian Medical College Vellore India
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18
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Zhang X, Wang G, Chen K, Zhang C, Qin X, Zhang Y, Liu X, Yang L. Identification of five novel variants of haemophilia B in 32 patients in Shanxi province, China. Haemophilia 2020; 26:e217-e219. [PMID: 32311179 DOI: 10.1111/hae.14007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Xialin Zhang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Gang Wang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Kun Chen
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Cuiming Zhang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiuyu Qin
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yaofang Zhang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiue Liu
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Linhua Yang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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19
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Favaloro EJ, Lippi G. Understanding the extent of the diagnostic potential of coagulation factors. Expert Rev Mol Diagn 2020; 20:273-276. [PMID: 31903796 DOI: 10.1080/14737159.2020.1711735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Emmanuel J Favaloro
- Haematology, Institute of Clinical Pathology and Medical Research (ICPMR), NSW Health Pathology, Westmead Hospital, Westmead, Australia.,Sydney Centres for Thrombosis and Haemostasis, Westmead Hospital, Westmead, Australia
| | - Giuseppe Lippi
- Section of Clinical Biochemistry, University of Verona, Verona, Italy
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20
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Bastida JM, Girós ML, Benito R, Janusz K, Hernández-Rivas JM, González-Porras JR. Sitosterolemia: Diagnosis, Metabolic and Hematological Abnormalities, Cardiovascular Disease and Management. Curr Med Chem 2019; 26:6766-6775. [DOI: 10.2174/0929867325666180705145900] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/27/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022]
Abstract
Sitosterolemia is a recessive inherited metabolic disorder of unknown prevalence,
characterized by increased levels of plasma plant sterols. It is caused by 28 and 31 variants in
ABCG5 and ABCG8 genes, respectively, and is characterized by a predisposition to hyperabsorption
and accumulation of toxic levels of plant sterols in plasma. Its clinical picture is extremely
heterogeneous. The main clinical features are tendinous and cutaneous xanthomas, arthritis
or arthralgia, premature cardiovascular disease and atherosclerosis. These characteristics
are shared with familial hypercholesterolemia (FH), making it possible for sitosterolemia to be
misdiagnosed as homozygous FH, especially in pediatric patients. In such cases, a specific
chromatography-based laboratory method is essential to differentiate sitosterol and cholesterol.
Hematological abnormalities (hemolytic anemia and macrothrombocytopenia) may be present in
25-35% of patients, in whom it is usually associated with the main clinical features, as occurs in
the 70% of the cases. In this context, the peripheral blood smear is essential and reveals giant
platelets and stomatocytes. Only 21 causative variants in ABCG5/ABCG8 are associated with
macrothrombocytopenia. Most physicians still do not recognize these hematological abnormalities
or relate them to sitosterolemia. Patients may suffer long-term misdiagnosis of immune
thrombocytopenia and be at high risk of receiving harmful therapies or of not benefitting from a
low-cholesterol diet and/or from the gold standard treatment with ezetimibe. This drug reduces
the levels of plasma plant sterols, provokes regression of xanthomas, and can alleviate hematological
abnormalities. Finally, to identify genetic defects, recent advances in high-throughput
sequencing, especially in the use of targeted sequencing of pre-specified genes, have begun to be
incorporated in the first-line approach in the field of genetic disorders.
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Affiliation(s)
- Jose María Bastida
- Department of Hematology, Hospital Universitario de Salamanca-IBSAL-USAL, Salamanca, Spain
| | - María Luisa Girós
- Seccio d'Errors Congenits del Metabolisme-IBC, Servei de Bioquimica i Genetica Molecular Hospital Clínic, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rocío Benito
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Salamanca, Spain
| | - Kamila Janusz
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Salamanca, Spain
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21
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The next(gen) step in coagulation testing. Blood 2019; 134:2002-2003. [PMID: 31805193 DOI: 10.1182/blood.2019001414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Clinical and laboratory diagnosis of rare coagulation disorders (RCDs). Thromb Res 2019; 196:603-608. [PMID: 31515069 DOI: 10.1016/j.thromres.2019.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/17/2022]
Abstract
Rare coagulation disorders (RCDs) are a group of diseases due to coagulation factors deficiency leading to life-long bleeding diathesis. The diagnosis of RCDs is challenging due to the limited knowledge of these disorders and the large heterogeneity of their bleeding patterns. The clinical symptoms of RCDs are extremely diverse in terms of bleeding type, site, severity, age at onset, and duration. The strength of the association between clotting factor activity level in plasma and clinical symptoms is also variable within each RCD. The clinical evaluation of RCDs starts with a detailed collection of clinical history and has been facilitated by bleeding assessment tools, however their effectiveness in diagnosing RCDs requires further investigation. The following laboratory diagnosis of RCDs involves coagulation screening tests, including activated partial thromboplastin time, prothrombin time, and thrombin time. After ruling out the presence of an inhibitor by mixing studies, in case of abnormal results, the specific deficiency is identified by performing one-stage clotting assays using the specific factor-depleted plasmas as substrate. In fibrinogen and FXIII deficiencies coagulation screening tests are not informative, therefore additional tests are needed. Global assays have been developed and are thought to aid in patient management, however, they are not well standardized yet. In addition to outlining the principles of clinical and laboratory diagnosis, this review explores molecular basis of RCDs and laboratory techniques for genetic analysis, and discusses the importance and effectiveness of quality control programs to ensure standardized laboratory results.
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23
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Ma S, Chen C, Liang Q, Wu X, Wang X, Wu W, Liu Y, Ding Q. Phenotype and genotype of FXIII deficiency in two unrelated probands: identification of a novel F13A1 large deletion mediated by complex rearrangement. Orphanet J Rare Dis 2019; 14:182. [PMID: 31340840 PMCID: PMC6657060 DOI: 10.1186/s13023-019-1144-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/25/2019] [Indexed: 01/27/2023] Open
Abstract
Background Inherited Factor XIII deficiency (FXIIID) is one of the most severe and under-diagnosed rare bleeding disorders. Only 5 large deletions involving one or more exons in F13A1 have been reported, and lacking of multiplex ligation-dependent probe amplification (MLPA) assay might underestimate the copy number variations (CNVs) in F13A1 and F13B. We had characterized the clinical presentation of two unrelated severe FXIIID probands and explored the pathogenic mechanisms. Results Both probands experienced several episodes of fatal bleeding and delayed wound healings prior to diagnosis. FXIII activity was measured by the ammonia release assay, and FXIII-A and FXIII-B antigens were determined by ELISA. All the exons including exon-intron boundaries and promoter regions of F13A1 and F13B were amplified and directly sequenced. Copy number variations (CNVs) of F13A1 and F13B were detected by the CNVplex® method. Breakpoints of the F13A1 large deletion were identified by quantitative primer walking combined long-range PCR (LR-PCR) strategies. Proband 1 was found to have compound heterozygous mutations of a novel small deletion (c.1147del) and a missense mutation p.Arg383Ser. Proband 2 was compound heterozygous for a novel large deletion (g.[77815_112815del;112837_116628del]) and a missense mutation p.Arg716Gly in F13A1. Bioinformatics analysis of the large deletion breakpoints predicted that two fork stalling and template switching and/or microhomology-mediated break-induced replication (FoSTeS/MMBIR) events with two homologies of TCT and C might be responsible for the complex rearrangement. Prophylactic replacement therapy was immediately administered for the two probands upon establishment of the diagnosis. Conclusions We detected two type I FXIIID pedigrees and adopted CNVplex® method to detect CNVs of F13A1 and F13B for the first time. A large heterozygous deletion of g.[77815_112815del;112837_116628del] in F13A1, mediated by two FoSTeS/MMBIR events, was identified. Electronic supplementary material The online version of this article (10.1186/s13023-019-1144-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siyu Ma
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China.,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wenman Wu
- Faculty of Medical Laboratory Science, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China. .,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Yan Liu
- Department of Burns and Plastic Surgery, Ruijin Hospital Affiliated to Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Second Road, Shanghai, 200025, China. .,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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24
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Ferraresi P, Balestra D, Guittard C, Buthiau D, Pan-Petesh B, Maestri I, Farah R, Pinotti M, Giansily-Blaizot M. Next-generation sequencing and recombinant expression characterized aberrant splicing mechanisms and provided correction strategies in factor VII deficiency. Haematologica 2019; 105:829-837. [PMID: 31273093 PMCID: PMC7049351 DOI: 10.3324/haematol.2019.217539] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023] Open
Abstract
Despite the exhaustive screening of F7 gene exons and exon-intron boundaries and promoter region, a significant proportion of mutated alleles remains unidentified in patients with coagulation factor VII deficiency. Here, we applied next-generation sequencing to 13 FVII-deficient patients displaying genotype-phenotype discrepancies upon conventional sequencing, and identified six rare intronic variants. Computational analysis predicted splicing effects for three of them, which would strengthen (c.571+78G>A; c.806-329G>A) or create (c.572-392C>G) intronic 5′ splice sites (5′ss). In F7 minigene assays, the c.806-329G>A was ineffective while the c.571+78G>A change led to usage of the +79 cryptic 5′ss with only trace levels of correct transcripts (3% of wild-type), in accordance with factor VII activity levels in homozygotes (1-3% of normal). The c.572-392C>G change led to pseudo-exonization and frame-shift, but also substantial levels of correct transcripts (approx. 70%). However, this variant was associated with the common F7 polymorphic haplotype, predicted to further decrease factor VII levels; this provided some kind of explanation for the 10% factor VII levels in the homozygous patient. Intriguingly, the effect of the c.571+78G>A and c.572-392C>G changes, and particularly of the former (the most severe and well-represented in our cohort), was counteracted by antisense U7snRNA variants targeting the intronic 5′ss, thus demonstrating their pathogenic role. In conclusion, the combination of next-generation sequencing of the entire F7 gene with the minigene expression studies elucidated the molecular bases of factor VII deficiency in 10 of 13 patients, thus improving diagnosis and genetic counseling. It also provided a potential therapeutic approach based on antisense molecules that has been successfully exploited in other disorders.
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Affiliation(s)
- Paolo Ferraresi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Caroline Guittard
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | - Delphine Buthiau
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
| | | | - Iva Maestri
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Roula Farah
- Department of Pediatrics, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Muriel Giansily-Blaizot
- Department of Biological Haematology, CHU Montpellier, Université Montpellier, Montpellier, France
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25
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Manderstedt E, Nilsson R, Lind-Halldén C, Ljung R, Astermark J, Halldén C. Targeted re-sequencing of F8, F9 and VWF: Characterization of Ion Torrent data and clinical implications for mutation screening. PLoS One 2019; 14:e0216179. [PMID: 31026269 PMCID: PMC6485758 DOI: 10.1371/journal.pone.0216179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Mutations are not identified in ~5% of hemophilia A and 10–35% of type 1 VWD patients. The bleeding tendency also varies among patients carrying the same causative mutation, potentially indicating variants in additional genes modifying the phenotype that cannot be identified by routine single-gene analysis. The F8, F9 and VWF genes were analyzed in parallel using an AmpliSeq strategy and Ion Torrent sequencing. Targeting all exonic positions showed an average read depth of >2000X and coverage close to 100% in 24 male patients with known disease-causing mutations. Discrimination between reference alleles and alternative/indel alleles was adequate at a 25% frequency threshold. In F8, F9 and VWF there was an absolute majority of all reference alleles at allele frequencies >95% and the average alternative allele and indel frequencies never reached above 10% and 15%, respectively. In VWF, 4–5 regions showed lower reference allele frequencies; in two regions covered by the pseudogene close to the 25% cut-off for reference alleles. All known mutations, including indels, gross deletions and substitutions, were identified. Additional VWF variants were identified in three hemophilia patients. The presence of additional mutations in 2 out of 16 (12%) randomly selected hemophilia patients indicates a potential mutational contribution that may affect the disease phenotype and counseling in these patients. Parallel identification of disease-causing mutations in all three genes not only confirms the deficiency, but differentiates phenotypic overlaps and allows for correct genetic counseling.
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Affiliation(s)
- Eric Manderstedt
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
| | - Rosanna Nilsson
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
- * E-mail:
| | - Christina Lind-Halldén
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
| | - Rolf Ljung
- Department of Clinical Sciences–Pediatrics and Malmö Center for Thrombosis and Hemostasis, Skåne University Hospital, Malmö, Sweden
| | - Jan Astermark
- Department for Hematology Oncology and Radiation Physics, Center for Thrombosis and Hemostasis, Skåne University Hospital, Malmö, Sweden
| | - Christer Halldén
- Department of Environmental Science and Bioscience, Kristianstad University, Kristianstad, Sweden
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26
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Bastida JM, Morais S, Palma-Barqueros V, Benito R, Bermejo N, Karkucak M, Trapero-Marugan M, Bohdan N, Pereira M, Marin-Quilez A, Oliveira J, Yucel Y, Santos R, Padilla J, Janusz K, Lau C, Martin-Izquierdo M, Couto E, Francisco Ruiz-Pividal J, Vicente V, Hernández-Rivas JM, González-Porras JR, Luisa Lozano M, Lima M, Rivera J. Identification of novel variants in ten patients with Hermansky-Pudlak syndrome by high-throughput sequencing. Ann Med 2019; 51:141-148. [PMID: 30990103 PMCID: PMC7857454 DOI: 10.1080/07853890.2019.1587498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Background: Hermansky-Pudlak syndrome (HPS) is a rare inherited platelet disorder characterized by bleeding diathesis, oculocutaneous albinism (OCA) and a myriad of often-serious clinical complications. Methods: We established the clinical and laboratory phenotype and genotype of six unrelated pedigrees comprising ten patients with clinical suspicion of HPS; including platelet aggregation, flow cytometry, platelet dense granule content, electron microscopy and high-throughput sequencing (HTS). Results: The clinical presentation showed significant heterogeneity and no clear phenotype-genotype correlations. HTS revealed two known and three novel disease-causing variants. The Spanish patients carried a homozygous p.Pro685Leufs17* deletion (n = 2) in HPS4, or the novel p.Arg822* homozygous variant (n = 1) in HPS3. In the case of two Turkish sisters, a novel missense homozygous HPS4 variant (p.Leu91Pro) was found. In two Portuguese families, genetic studies confirmed a previously reported nonsense variant (p.Gln103*) in DTNBP1 in three patients and a novel duplication (p.Leu22Argfs*33) in HPS6 in two unrelated patients. Conclusions: Our findings expand the mutational spectrum of HPS, which may help in investigating phenotype-genotype relationships and assist genetic counselling for affected individuals. This approach is a proof of principle that HTS can be considered and used in the first-line diagnosis of patients with biological and clinical manifestations suggestive of HPS. Key messages We established the relationships between the clinical and laboratory phenotype and genotype of six unrelated pedigrees comprising ten patients with clinical suspicion of HPS. Molecular analysis is useful in confirming the diagnosis and may offer some prognostic information that will aid in optimizing monitoring and surveillance for early detection of end-organ damage. This approach is a proof of principle that HTS can be considered and used in the first-line diagnosis of patients with biological and clinical manifestations suggestive of HPS.
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Affiliation(s)
- Jose María Bastida
- a Department of Hematology , University Hospital of Salamanca-IBSAL , Salamanca , Spain
| | - Sara Morais
- b Department of Hematology, University Hospital of Porto-UMIB/ICBAS/UP , Porto , Portugal
| | - Veronica Palma-Barqueros
- c Department of Hematology and Oncology, University Hospital of Morales Meseguer, Centro Regional de Hemodonación, University of Murcia , Murcia , Spain
| | - Rocio Benito
- d IBSAL, IBMCC, CIC, University of Salamanca-CSIC , Salamanca , Spain
| | - Nuria Bermejo
- e Department of Hematology , Hospital of San Pedro de Alcantara , Cáceres , Spain
| | - Mutlu Karkucak
- f Department of Medical Genetics , Sakarya University Training and Research Hospital , Sakarya , Turkey
| | - Maria Trapero-Marugan
- g Department of Hematology , University Hospital of Puerta de Hierro , Majadahonda , Spain
| | - Natalia Bohdan
- c Department of Hematology and Oncology, University Hospital of Morales Meseguer, Centro Regional de Hemodonación, University of Murcia , Murcia , Spain
| | - Mónica Pereira
- b Department of Hematology, University Hospital of Porto-UMIB/ICBAS/UP , Porto , Portugal
| | - Ana Marin-Quilez
- d IBSAL, IBMCC, CIC, University of Salamanca-CSIC , Salamanca , Spain
| | - Jorge Oliveira
- h Department of Molecular Genetics, Medical Center of Genetics Dr. Jacinto Magalhães, University Hospital of Porto-UMIB/ICBAS/UP , Porto , Portugal
| | - Yusuf Yucel
- f Department of Medical Genetics , Sakarya University Training and Research Hospital , Sakarya , Turkey
| | - Rosario Santos
- h Department of Molecular Genetics, Medical Center of Genetics Dr. Jacinto Magalhães, University Hospital of Porto-UMIB/ICBAS/UP , Porto , Portugal
| | - Jose Padilla
- c Department of Hematology and Oncology, University Hospital of Morales Meseguer, Centro Regional de Hemodonación, University of Murcia , Murcia , Spain
| | - Kamila Janusz
- d IBSAL, IBMCC, CIC, University of Salamanca-CSIC , Salamanca , Spain
| | - Catarina Lau
- b Department of Hematology, University Hospital of Porto-UMIB/ICBAS/UP , Porto , Portugal
| | | | - Eduarda Couto
- b Department of Hematology, University Hospital of Porto-UMIB/ICBAS/UP , Porto , Portugal
| | - Juan Francisco Ruiz-Pividal
- c Department of Hematology and Oncology, University Hospital of Morales Meseguer, Centro Regional de Hemodonación, University of Murcia , Murcia , Spain
| | - Vicente Vicente
- c Department of Hematology and Oncology, University Hospital of Morales Meseguer, Centro Regional de Hemodonación, University of Murcia , Murcia , Spain
| | - Jesus Maria Hernández-Rivas
- a Department of Hematology , University Hospital of Salamanca-IBSAL , Salamanca , Spain.,d IBSAL, IBMCC, CIC, University of Salamanca-CSIC , Salamanca , Spain
| | | | - Maria Luisa Lozano
- c Department of Hematology and Oncology, University Hospital of Morales Meseguer, Centro Regional de Hemodonación, University of Murcia , Murcia , Spain
| | - Margarida Lima
- b Department of Hematology, University Hospital of Porto-UMIB/ICBAS/UP , Porto , Portugal
| | - Jose Rivera
- c Department of Hematology and Oncology, University Hospital of Morales Meseguer, Centro Regional de Hemodonación, University of Murcia , Murcia , Spain
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Owaidah T, Saleh M, Baz B, Abdulaziz B, Alzahrani H, Tarawah A, Almusa A, AlNounou R, AbaAlkhail H, Al-Numair N, Altahan R, Abouelhoda M, Alamoudi T, Monies D, Jabaan A, Al Tassan N. Molecular yield of targeted sequencing for Glanzmann thrombasthenia patients. NPJ Genom Med 2019; 4:4. [PMID: 30792900 PMCID: PMC6375963 DOI: 10.1038/s41525-019-0079-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/23/2019] [Indexed: 12/19/2022] Open
Abstract
Glanzmann thrombasthenia (GT) is a rare autosomal recessive bleeding disorder. Around 490 mutations in ITGA2B and ITGB3 genes were reported. We aimed to use targeted next-generation sequencing (NGS) to identify variants in patients with GT. We screened 72 individuals (including unaffected family members) using a panel of 393 genes (SHGP heme panel). Validation was done by Sanger sequencing and pathogenicity was predicted using multiple tools. In 83.5% of our cohort, 17 mutations were identified in ITGA2B and ITGB3 (including 6 that were not previously reported). In addition to variants in the two known genes, we found variants in ITGA2, VWF and F8. The SHGP heme panel can be used as a high-throughput molecular diagnostic assay to screen for mutations and variants in GT cases and carriers. Our findings expand the molecular landscape of GT and emphasize the robustness and usefulness of this panel.
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Affiliation(s)
- Tarek Owaidah
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mahasen Saleh
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Batoul Baz
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Basma Abdulaziz
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hazza Alzahrani
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Ahmed Tarawah
- Medina Maternity and Children Hospital, Medina, Saudi Arabia
| | - Abdulrahman Almusa
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Randa AlNounou
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hala AbaAlkhail
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Nouf Al-Numair
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Rahaf Altahan
- 1Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohammed Abouelhoda
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Thamer Alamoudi
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Amjad Jabaan
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- 2Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,3Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
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28
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Saes JL, Simons A, de Munnik SA, Nijziel MR, Blijlevens NMA, Jongmans MC, van der Reijden BA, Smit Y, Brons PP, van Heerde WL, Schols SEM. Whole exome sequencing in the diagnostic workup of patients with a bleeding diathesis. Haemophilia 2018; 25:127-135. [PMID: 30431218 DOI: 10.1111/hae.13638] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/26/2018] [Accepted: 10/27/2018] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Bleeding assessment tools and laboratory phenotyping often remain inconclusive in patients with a haemorrhagic diathesis. AIM To describe the phenotype and genetic profile of patients with a bleeding tendency. METHODS Whole exome sequencing (WES) was incorporated in the routine diagnostic pathway of patients with thrombocytopenia (n = 17), platelet function disorders (n = 19) and an unexplained bleeding tendency (n = 51). The analysis of a panel of 126 OMIM (Online Mendelian Inheritance in Man) genes involved in thrombosis and haemostasis was conducted, and if negative, further exome-wide analysis was performed if informed consent given. RESULTS Eighteen variants were detected in 15 patients from a total of 87 patients (17%). Causative variants were observed in MYH9 (two cases), SLFN14, P2RY12 and GP9. In addition, one case was considered solved due to combined carriership of F7 and F13A1 variants and one with combined carriership of F2, F8 and VWF, all variants related to secondary haemostasis protein aberrations. Two variants of uncertain significance (VUS) were found in two primary haemostasis genes: GFI1B and VWF. Eight patients were carriers of autosomal recessive disorders. Exome-wide analysis was performed in 54 cases and identified three variants in candidate genes. CONCLUSION Based on our findings, we conclude that performing WES at the end of the diagnostic trajectory can be of additive value to explain the complete bleeding phenotype in patients without a definite diagnosis after conventional laboratory tests. Discovery of combinations of (novel) genes that predispose to bleeding will increase the diagnostic yield in patients with an unexplained bleeding diathesis.
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Affiliation(s)
- Joline L Saes
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands.,Hemophilia Treatment Center, Nijmegen-Eindhoven-Maastricht, Nijmegen, The Netherlands
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marten R Nijziel
- Department of Hematology, Catharina Hospital, Eindhoven, The Netherlands
| | - Nicole M A Blijlevens
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.,Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Haematology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Yolba Smit
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul P Brons
- Hemophilia Treatment Center, Nijmegen-Eindhoven-Maastricht, Nijmegen, The Netherlands.,Department of Pediatric Hemato-Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Waander L van Heerde
- Hemophilia Treatment Center, Nijmegen-Eindhoven-Maastricht, Nijmegen, The Netherlands
| | - Saskia E M Schols
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands.,Hemophilia Treatment Center, Nijmegen-Eindhoven-Maastricht, Nijmegen, The Netherlands
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29
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A novel type 2N VWF gene mutation. Blood Coagul Fibrinolysis 2018; 29:651-652. [DOI: 10.1097/mbc.0000000000000761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Wang Q, Cao L, Sheng G, Shen H, Ling J, Xie J, Ma Z, Yin J, Wang Z, Yu Z, Chen S, Zhao Y, Ruan C, Xia L, Jiang M. Application of High-Throughput Sequencing in the Diagnosis of Inherited Thrombocytopenia. Clin Appl Thromb Hemost 2018; 24:94S-103S. [PMID: 30103613 PMCID: PMC6714838 DOI: 10.1177/1076029618790696] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Inherited thrombocytopenia is a group of hereditary diseases with a reduction in platelet
count as the main clinical manifestation. Clinically, there is an urgent need for a
convenient and rapid diagnosis method. We introduced a high-throughput, next-generation
sequencing (NGS) platform into the routine diagnosis of patients with unexplained
thrombocytopenia and analyzed the gene sequencing results to evaluate the value of NGS
technology in the screening and diagnosis of inherited thrombocytopenia. From a cohort of
112 patients with thrombocytopenia, we screened 43 patients with hereditary features. For
the blood samples of these 43 patients, a gene sequencing platform for hemorrhagic and
thrombotic diseases comprising 89 genes was used to perform gene detection using NGS
technology. When we combined the screening results with clinical features and other
findings, 15 (34.9%) of 43patients were diagnosed with inherited thrombocytopenia. In
addition, 19 pathogenic variants, including 8 previously unreported variants, were
identified in these patients. Through the use of this detection platform, we expect to
establish a more effective diagnostic approach to such disorders.
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Affiliation(s)
- Qi Wang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Lijuan Cao
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Guangying Sheng
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Hongjie Shen
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jing Ling
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Jundan Xie
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Zhenni Ma
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Jie Yin
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Zhaoyue Wang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Ziqiang Yu
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Suning Chen
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yiming Zhao
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Changgeng Ruan
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Lijun Xia
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.,Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Miao Jiang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China.,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
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31
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He X, Xiong Z, Shen N, Lu Y, Wang X. Performance of next-generation sequencing in the detection of large exon deletion in patients of haemophilia A. Haemophilia 2018; 24:e296-e300. [PMID: 30004153 DOI: 10.1111/hae.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 11/29/2022]
Affiliation(s)
- X. He
- Department of Laboratory Medicine; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Z. Xiong
- Department of Laboratory Medicine; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - N. Shen
- Department of Laboratory Medicine; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Y. Lu
- Department of Laboratory Medicine; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - X. Wang
- Department of Laboratory Medicine; Tongji Hospital; Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
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32
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Dunkley S, Lam JCM, John MJ, Wong RSM, Tran H, Yang R, Nair SC, Shima M, Street A, Srivastava A. Principles of haemophilia care: The Asia-Pacific perspective. Haemophilia 2018; 24:366-375. [DOI: 10.1111/hae.13425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2017] [Indexed: 01/08/2023]
Affiliation(s)
- S. Dunkley
- Haemophilia Treatment Centre; Royal Prince Alfred Hospital; Sydney NSW Australia
| | - J. C. M. Lam
- Department of Paediatric Subspecialties; KK Women's and Children's Hospital; Singapore Singapore
| | - M. J. John
- Department of Clinical Haematology; Christian Medical College; Ludhiana Punjab India
| | - R. S. M. Wong
- Department of Medicine & Therapeutics; Sir Y.K. Pao Centre for Cancer; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong Hong Kong
| | - H. Tran
- Ronald Sawers Haemophilia Centre; The Alfred Hospital Melbourne; Melbourne Vic Australia
| | - R. Yang
- State Key Laboratory of Experimental Hematology; Institute of Hematology and Hospital of Blood Disease; Chinese Academy of Medical Sciences & Peking Union Medical College; Tianjin China
| | - S. C. Nair
- Department of Immunohematology & Transfusion Medicine; Christian Medical College; Vellore Tamil Nadu India
| | - M. Shima
- Department of Paediatrics; Nara Medical University; Kashihara Japan
| | - A. Street
- Department of Immunology and Pathology; Monash University; Melbourne Vic Australia
| | - A. Srivastava
- Department of Hematology; Christian Medical College; Vellore Tamil Nadu India
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33
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Koko M, Abdallah MOE, Amin M, Ibrahim M. Challenges imposed by minor reference alleles on the identification and reporting of clinical variants from exome data. BMC Genomics 2018; 19:46. [PMID: 29334895 PMCID: PMC5769444 DOI: 10.1186/s12864-018-4433-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 01/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references. This hinders the correct identification of variants with minor and/or pathogenic reference alleles warranting additional approaches for variant calling. Results More than 26,000 Exome Aggregation Consortium (ExAC) variants have a minor reference allele including variants with known ClinVar disease alleles. For instance, in a number of variants related to clotting disorders, the phenotype-associated allele is a human genome reference allele (rs6025, rs6003, rs1799983, and rs2227564 using the assembly hg19). We highlighted how the current variant calling standards miss homozygous reference disease variants in these sites and provided a bioinformatic panel that can be used to screen these variants using commonly available variant callers. We present exome sequencing results from an individual with venous thrombosis to emphasize how pathogenic alleles in clinically relevant variants escape variant calling while non-pathogenic alleles are detected. Conclusions This article highlights the importance of specialized variant calling strategies in clinical variants with minor reference alleles especially in the context of personal genomes and exomes. We provide here a simple strategy to screen potential disease-causing variants when present in homozygous reference state. Electronic supplementary material The online version of this article (10.1186/s12864-018-4433-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahmoud Koko
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, P. O. Box 102, Army Road, 11111, Khartoum, Sudan. .,Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, Tübingen, Germany.
| | - Mohammed O E Abdallah
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, P. O. Box 102, Army Road, 11111, Khartoum, Sudan
| | - Mutaz Amin
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, P. O. Box 102, Army Road, 11111, Khartoum, Sudan.,Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Muntaser Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, P. O. Box 102, Army Road, 11111, Khartoum, Sudan.
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34
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González-Porras J, Jiménez C, Benito R, Ordoñez GR, Álvarez-Román M, Fontecha ME, Janusz K, Castillo D, Fisac R, García-Frade L, Aguilar C, Martínez P, Bermejo N, Herrero S, Balanzategui A, Martin-Antorán J, Ramos R, Cebeiro M, Pardal E, Aguilera C, Pérez-Gutierrez B, Prieto M, Riesco S, Mendoza M, Benito A, Benito-Sendin A, Jimenez-Yuste V, Hernández-Rivas J, García-Sanz R, González-Díaz M, Sarasquete M, Bastida J. Application of a molecular diagnostic algorithm for haemophilia A and B using next-generation sequencing of entire F8, F9 and VWF genes. Thromb Haemost 2017; 117:66-74. [DOI: 10.1160/th16-05-0375] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/17/2016] [Indexed: 12/30/2022]
Abstract
SummaryCurrently, molecular diagnosis of haemophilia A and B (HA and HB) highlights the excess risk-inhibitor development associated with specific mutations, and enables carrier testing of female relatives and prenatal or preimplantation genetic diagnosis. Molecular testing for HA also helps distinguish it from von Willebrand disease (VWD). Next-generation sequencing (NGS) allows simultaneous investigation of several complete genes, even though they may span very extensive regions. This study aimed to evaluate the usefulness of a molecular algorithm employing an NGS approach for sequencing the complete F8, F9 and VWF genes. The proposed algorithm includes the detection of inversions of introns 1 and 22, an NGS custom panel (the entire F8, F9 and VWF genes), and multiplex ligation-dependent probe amplification (MLPA) analysis. A total of 102 samples (97 FVIII- and FIX-deficient patients, and five female carriers) were studied. IVS-22 screening identified 11 out of 20 severe HA patients and one female carrier. IVS-1 analysis did not reveal any alterations. The NGS approach gave positive results in 88 cases, allowing the differential diagnosis of mild/moderate HA and VWD in eight cases. MLPA confirmed one large exon deletion. Only one case did have no pathogenic variants. The proposed algorithm had an overall success rate of 99 %. In conclusion, our evaluation demonstrates that this algorithm can reliably identify pathogenic variants and diagnose patients with HA, HB or VWD.Supplementary Material to this article is available online at www.thrombosis-online.com.
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35
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Bastida JM, Lozano ML, Benito R, Janusz K, Palma-Barqueros V, Del Rey M, Hernández-Sánchez JM, Riesco S, Bermejo N, González-García H, Rodriguez-Alén A, Aguilar C, Sevivas T, López-Fernández MF, Marneth AE, van der Reijden BA, Morgan NV, Watson SP, Vicente V, Hernández-Rivas JM, Rivera J, González-Porras JR. Introducing high-throughput sequencing into mainstream genetic diagnosis practice in inherited platelet disorders. Haematologica 2017; 103:148-162. [PMID: 28983057 PMCID: PMC5777202 DOI: 10.3324/haematol.2017.171132] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/29/2017] [Indexed: 12/30/2022] Open
Abstract
Inherited platelet disorders are a heterogeneous group of rare diseases, caused by inherited defects in platelet production and/or function. Their genetic diagnosis would benefit clinical care, prognosis and preventative treatments. Until recently, this diagnosis has usually been performed via Sanger sequencing of a limited number of candidate genes. High-throughput sequencing is revolutionizing the genetic diagnosis of diseases, including bleeding disorders. We have designed a novel high-throughput sequencing platform to investigate the unknown molecular pathology in a cohort of 82 patients with inherited platelet disorders. Thirty-four (41.5%) patients presented with a phenotype strongly indicative of a particular type of platelet disorder. The other patients had clinical bleeding indicative of platelet dysfunction, but with no identifiable features. The high-throughput sequencing test enabled a molecular diagnosis in 70% of these patients. This sensitivity increased to 90% among patients suspected of having a defined platelet disorder. We found 57 different candidate variants in 28 genes, of which 70% had not previously been described. Following consensus guidelines, we qualified 68.4% and 26.3% of the candidate variants as being pathogenic and likely pathogenic, respectively. In addition to establishing definitive diagnoses of well-known inherited platelet disorders, high-throughput sequencing also identified rarer disorders such as sitosterolemia, filamin and actinin deficiencies, and G protein-coupled receptor defects. This included disease-causing variants in DIAPH1 (n=2) and RASGRP2 (n=3). Our study reinforces the feasibility of introducing high-throughput sequencing technology into the mainstream laboratory for the genetic diagnostic practice in inherited platelet disorders.
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Affiliation(s)
- José M Bastida
- Servicio de Hematología, Hospital Universitario de Salamanca-IBSAL-USAL, Spain .,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - María L Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain.,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - Rocío Benito
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - Kamila Janusz
- IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - Verónica Palma-Barqueros
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain
| | | | | | - Susana Riesco
- Servicio de Pediatría, Hospital Universitario de Salamanca-IBSAL, Spain
| | - Nuria Bermejo
- Servicio de Hematología, Complejo Hospitalario San Pedro Alcántara, Cáceres, Spain
| | | | - Agustín Rodriguez-Alén
- Servicio de Hematología y Hemoterapia, Hospital Virgen de la Salud, Complejo Hospitalario de Toledo, Spain
| | - Carlos Aguilar
- Servicio de Hematología, Complejo Asistencial de Soria, Spain
| | - Teresa Sevivas
- Serviço de Imunohemoterapia, Sangue e Medicina Transfusional do Centro Hospitalar e Universitário de Coimbra, EPE, Portugal
| | | | - Anna E Marneth
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Neil V Morgan
- Birmingham Platelet Group, Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Steve P Watson
- Birmingham Platelet Group, Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, UK
| | - Vicente Vicente
- On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
| | - Jesús M Hernández-Rivas
- Servicio de Hematología, Hospital Universitario de Salamanca-IBSAL-USAL, Spain.,IBSAL, IBMCC, CIC, Universidad de Salamanca-CSIC, Spain
| | - José Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, CB15/00055-CIBERER, Spain.,On behalf of the Project "Functional and Molecular Characterization of Patients with Inherited Platelet Disorders" of the Hemorrhagic Diathesis Working Group of the Spanish Society of Thrombosis and Haemostasis
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36
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Sivapalaratnam S, Collins J, Gomez K. Diagnosis of inherited bleeding disorders in the genomic era. Br J Haematol 2017; 179:363-376. [PMID: 28612396 DOI: 10.1111/bjh.14796] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inherited bleeding disorders affect between 1 in 1000 individuals for the most common disorder, von Willebrand Disease, to only 8 reported cases worldwide of alpha-2-antiplasmin deficiency. Those with an identifiable abnormality can be divided into disorders of coagulation factors (87%), platelet count and function (8%) and the fibrinolytic system (3%). Of the patients registered in the UK with a bleeding disorder, the remaining 2% are unclassifiable. In addition to bleeding symptoms, patients with an inherited bleeding disorder can manifest other abnormalities, making an accurate and complete diagnosis that reflects the underlying molecular pathology important. Although some inherited bleeding disorders can still be easily diagnosed through a combination of careful clinical assessment and laboratory assays of varying degrees of complexity, there are many where conventional approaches are inadequate. Improvements in phenotyping assays have enhanced our diagnostic armoury but genotyping now offers the most accurate and complete diagnosis for some of these conditions. The advent of next generation sequencing technology has meant that many genes can now be analysed routinely in clinical practice. Here, we discuss the different diagnostic tools currently available for inherited bleeding disorders and suggest that genotyping should be incorporated at an early stage in the diagnostic pathway.
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Affiliation(s)
- Suthesh Sivapalaratnam
- Department of Haematology, University of Cambridge, Cambridge, UK.,The Royal London Haemophilia Centre, The Royal London Hospital, London, UK
| | - Janine Collins
- Department of Haematology, University of Cambridge, Cambridge, UK.,The Royal London Haemophilia Centre, The Royal London Hospital, London, UK
| | - Keith Gomez
- Katherine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
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37
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Johnsen JM, Fletcher SN, Huston H, Roberge S, Martin BK, Kircher M, Josephson NC, Shendure J, Ruuska S, Koerper MA, Morales J, Pierce GF, Aschman DJ, Konkle BA. Novel approach to genetic analysis and results in 3000 hemophilia patients enrolled in the My Life, Our Future initiative. Blood Adv 2017; 1:824-834. [PMID: 29296726 PMCID: PMC5727804 DOI: 10.1182/bloodadvances.2016002923] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/22/2017] [Indexed: 01/05/2023] Open
Abstract
Hemophilia A and B are rare, X-linked bleeding disorders. My Life, Our Future (MLOF) is a collaborative project established to genotype and study hemophilia. Patients were enrolled at US hemophilia treatment centers (HTCs). Genotyping was performed centrally using next-generation sequencing (NGS) with an approach that detected common F8 gene inversions simultaneously with F8 and F9 gene sequencing followed by confirmation using standard genotyping methods. Sixty-nine HTCs enrolled the first 3000 patients in under 3 years. Clinically reportable DNA variants were detected in 98.1% (2357/2401) of hemophilia A and 99.3% (595/599) of hemophilia B patients. Of the 924 unique variants found, 285 were novel. Predicted gene-disrupting variants were common in severe disease; missense variants predominated in mild-moderate disease. Novel DNA variants accounted for ∼30% of variants found and were detected continuously throughout the project, indicating that additional variation likely remains undiscovered. The NGS approach detected >1 reportable variants in 36 patients (10 females), a finding with potential clinical implications. NGS also detected incidental variants unlikely to cause disease, including 11 variants previously reported in hemophilia. Although these genes are thought to be conserved, our findings support caution in interpretation of new variants. In summary, MLOF has contributed significantly toward variant annotation in the F8 and F9 genes. In the near future, investigators will be able to access MLOF data and repository samples for research to advance our understanding of hemophilia.
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Affiliation(s)
- Jill M Johnsen
- Bloodworks Northwest, Seattle, WA
- Department of Medicine and
| | | | | | | | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Chevy Chase, MD
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38
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Swystun LL, James PD. Genetic diagnosis in hemophilia and von Willebrand disease. Blood Rev 2017; 31:47-56. [DOI: 10.1016/j.blre.2016.08.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 11/24/2022]
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39
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Bariana TK, Ouwehand WH, Guerrero JA, Gomez K. Dawning of the age of genomics for platelet granule disorders: improving insight, diagnosis and management. Br J Haematol 2016; 176:705-720. [PMID: 27984638 DOI: 10.1111/bjh.14471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inherited disorders of platelet granules are clinically heterogeneous and their prevalence is underestimated because most patients do not undergo a complete diagnostic work-up. The lack of a genetic diagnosis limits the ability to tailor management, screen family members, aid with family planning, predict clinical progression and detect serious consequences, such as myelofibrosis, lung fibrosis and malignancy, in a timely manner. This is set to change with the introduction of high throughput sequencing (HTS) as a routine clinical diagnostic test. HTS diagnostic tests are now available, affordable and allow parallel screening of DNA samples for variants in all of the 80 known bleeding, thrombotic and platelet genes. Increased genetic diagnosis and curation of variants is, in turn, improving our understanding of the pathobiology and clinical course of inherited platelet disorders. Our understanding of the genetic causes of platelet granule disorders and the regulation of granule biogenesis is a work in progress and has been significantly enhanced by recent genomic discoveries from high-powered genome-wide association studies and genome sequencing projects. In the era of whole genome and epigenome sequencing, new strategies are required to integrate multiple sources of big data in the search for elusive, novel genes underlying granule disorders.
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Affiliation(s)
- Tadbir K Bariana
- Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK.,Department of Haematology, University College London Cancer Institute, London, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.,NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.,Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Jose A Guerrero
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Keith Gomez
- Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
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40
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Bastida Bermejo JM, Hernández-Rivas JM, González-Porras JR. Novel approaches for diagnosing inherited platelet disorders. Med Clin (Barc) 2016; 148:71-77. [PMID: 28218058 DOI: 10.1016/j.medcli.2016.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 12/20/2022]
Abstract
Inherited platelet disorders diagnosis is based on the clinical history and bleeding assessment tools. The laboratory functional assays as well as the molecular test to identify the pathogenic genetic variant are essential to confirm the accurate diagnosis of these disorders. Nowadays, the main challenges to developing a new diagnostic system are involved in reducing the samples' volume, and faster and more helpful analysis. Moreover, there are no widely available and standardised global tests. High throughput genetic testing such as next-generation sequencing has revolutionised DNA sequencing technologies as it allows the simultaneous and faster investigation of multiple genes at a manageable cost. This technology has improved the molecular characterisation of inherited platelet disorders and has been implemented in the research studies and the clinical routine practice.
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Affiliation(s)
- José María Bastida Bermejo
- Servicio de Hematología, Hospital Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca (USAL), Salamanca, España.
| | - Jesús María Hernández-Rivas
- Servicio de Hematología, Hospital Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca (USAL), Salamanca, España
| | - José Ramón González-Porras
- Servicio de Hematología, Hospital Universitario de Salamanca, Instituto de Investigación Biomédica de Salamanca (IBSAL), Universidad de Salamanca (USAL), Salamanca, España
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