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Domrazek K, Jurka P. Application of Next-Generation Sequencing (NGS) Techniques for Selected Companion Animals. Animals (Basel) 2024; 14:1578. [PMID: 38891625 PMCID: PMC11171117 DOI: 10.3390/ani14111578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Next-Generation Sequencing (NGS) techniques have revolutionized veterinary medicine for cats and dogs, offering insights across various domains. In veterinary parasitology, NGS enables comprehensive profiling of parasite populations, aiding in understanding transmission dynamics and drug resistance mechanisms. In infectious diseases, NGS facilitates rapid pathogen identification, characterization of virulence factors, and tracking of outbreaks. Moreover, NGS sheds light on metabolic processes by elucidating gene expression patterns and metabolic pathways, essential for diagnosing metabolic disorders and designing tailored treatments. In autoimmune diseases, NGS helps identify genetic predispositions and molecular mechanisms underlying immune dysregulation. Veterinary oncology benefits from NGS through personalized tumor profiling, mutation analysis, and identification of therapeutic targets, fostering precision medicine approaches. Additionally, NGS plays a pivotal role in veterinary genetics, unraveling the genetic basis of inherited diseases and facilitating breeding programs for healthier animals. Physiological investigations leverage NGS to explore complex biological systems, unraveling gene-environment interactions and molecular pathways governing health and disease. Application of NGS in treatment planning enhances precision and efficacy by enabling personalized therapeutic strategies tailored to individual animals and their diseases, ultimately advancing veterinary care for companion animals.
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Affiliation(s)
- Kinga Domrazek
- Institute of Veterinary Medicine, Warsaw University of Life Sciences—SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland;
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2
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Vokač D, Stangler Herodež Š, Krgović D, Kokalj Vokač N. The Role of Next-Generation Sequencing in the Management of Patients with Suspected Non-Ischemic Cardiomyopathy after Syncope or Termination of Sudden Arrhythmic Death. Genes (Basel) 2024; 15:72. [PMID: 38254962 PMCID: PMC10815304 DOI: 10.3390/genes15010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Cardiac arrhythmias and sudden death are frequent in patients with non-ischemic cardiomyopathy and can precede heart failure or additional symptoms where malignant cardiac arrhythmias are mostly the consequence of advanced cardiomyopathy and heart failure. Finding these subgroups and making an early diagnosis could be lifesaving. In our retrospective study, we are presenting arrhythmic types of frequent cardiomyopathies where an arrhythmogenic substrate is less well defined, as in ischemic or structural heart disease. In the period of 2 years, next-generation sequencing (NGS) tests along with standard clinical tests were performed in 208 patients (67 women and 141 men; mean age, 51.2 ± 19.4 years) without ischemic or an overt structural heart disease after syncope or aborted sudden cardiac death. Genetic variants were detected in 34.4% of the study population, with a significant proportion of pathogenic variants (P) (14.4%) and variants of unknown significance (VUS) (20%). Regardless of genotype, all patients were stratified according to clinical guidelines for aggressive treatment of sudden cardiac death with an implantable cardioverter defibrillator (ICD). The P variant identified by NGS serves for an accurate diagnosis and, thus, better prevention and specific treatment of patients and their relatives. Results in our study suggest that targeted sequencing of genes associated with cardiovascular disease is an important addendum for final diagnosis, allowing the identification of a molecular genetic cause in a vast proportion of patients for a definitive diagnosis and a more specific way of treatment. VUS in this target population poses a high risk and should be considered possibly pathogenic in reanalysis.
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Affiliation(s)
- Damijan Vokač
- Department of Cardiology and Angiology, Division of Internal Medicine, University Medical Centre Maribor, 2000 Maribor, Slovenia;
| | - Špela Stangler Herodež
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Danijela Krgović
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
| | - Nadja Kokalj Vokač
- Clinical Institute for Genetic Diagnostics, University Medical Centre Maribor, 2000 Maribor, Slovenia; (Š.S.H.); (D.K.)
- Medical Faculty, University of Maribor, 2000 Maribor, Slovenia
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3
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Suwajanakorn O, Puangsricharern V, Kittipibul T, Chatsuwan T. Ocular surface microbiome in diabetes mellitus. Sci Rep 2022; 12:21527. [PMID: 36513692 PMCID: PMC9747965 DOI: 10.1038/s41598-022-25722-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
This cross-sectional, age- and gender-matched study included 20 eyes of non-diabetic subjects (non-DM group) and 60 eyes of type 2 diabetes mellitus (DM group). Subgroups of DM were classified by diabetic retinopathy (DR) staging into no DR (DM-no DR), non-proliferative DR (DM-NPDR), proliferative DR (DM-PDR), and by glycemic control (well-controlled DM; HbA1c < 7%, poorly controlled DM; HbA1c ≥ 7%). Conjunctival swabs were performed for ocular surface microbiome analysis using conventional culture and next-generation sequencing analysis (NGS). A higher culture-positive rate was found in DM (15%) than in non-DM group (5%) (p value = 0.437). Pathogenic organisms and antibiotic-resistant strains were detected in the DR groups (DM-NPDR and DM-PDR). The NGS analysis showed that potentially pathogenic bacteria such as Enterobacteriaceae, Neisseriaceae, Escherichia-Shigella, and Pseudomonas predominated in DM, especially in DR. There was dissimilarity in the ocular surface microbiome between DM and non-DM groups. The subgroup analysis showed that the DR group had significantly different microbial community from DM-no DR and non-DM groups (p value < 0.05). The microbial community in the poorly controlled DM was also significantly different from well-controlled DM and non-DM groups (p < 0.001). Using the NGS method, our study is the first to signify the importance of DR and glycemic control status, which affect the changes in the ocular surface microbiome.
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Affiliation(s)
- Orathai Suwajanakorn
- grid.7922.e0000 0001 0244 7875Cornea and Refractive Surgery Unit, Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.411628.80000 0000 9758 8584Excellence Center of Cornea and Limbal Stem Cell Transplantation, Department of Ophthalmology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Vilavun Puangsricharern
- grid.7922.e0000 0001 0244 7875Cornea and Refractive Surgery Unit, Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.411628.80000 0000 9758 8584Excellence Center of Cornea and Limbal Stem Cell Transplantation, Department of Ophthalmology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Thanachaporn Kittipibul
- grid.7922.e0000 0001 0244 7875Cornea and Refractive Surgery Unit, Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.411628.80000 0000 9758 8584Excellence Center of Cornea and Limbal Stem Cell Transplantation, Department of Ophthalmology, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Tanittha Chatsuwan
- grid.7922.e0000 0001 0244 7875Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Dlamini Z, Skepu A, Kim N, Mkhabele M, Khanyile R, Molefi T, Mbatha S, Setlai B, Mulaudzi T, Mabongo M, Bida M, Kgoebane-Maseko M, Mathabe K, Lockhat Z, Kgokolo M, Chauke-Malinga N, Ramagaga S, Hull R. AI and precision oncology in clinical cancer genomics: From prevention to targeted cancer therapies-an outcomes based patient care. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Martinez Velazquez LA, Ballios BG. The Next Generation of Molecular and Cellular Therapeutics for Inherited Retinal Disease. Int J Mol Sci 2021; 22:ijms222111542. [PMID: 34768969 PMCID: PMC8583900 DOI: 10.3390/ijms222111542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/26/2022] Open
Abstract
Inherited retinal degenerations (IRDs) are a diverse group of conditions that are often characterized by the loss of photoreceptors and blindness. Recent innovations in molecular biology and genomics have allowed us to identify the causative defects behind these dystrophies and to design therapeutics that target specific mechanisms of retinal disease. Recently, the FDA approved the first in vivo gene therapy for one of these hereditary blinding conditions. Current clinical trials are exploring new therapies that could provide treatment for a growing number of retinal dystrophies. While the field has had early success with gene augmentation strategies for treating retinal disease based on loss-of-function mutations, many novel approaches hold the promise of offering therapies that span the full spectrum of causative mutations and mechanisms. Here, we provide a comprehensive review of the approaches currently in development including a discussion of retinal neuroprotection, gene therapies (gene augmentation, gene editing, RNA modification, optogenetics), and regenerative stem or precursor cell-based therapies. Our review focuses on technologies that are being developed for clinical translation or are in active clinical trials and discusses the advantages and limitations for each approach.
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Affiliation(s)
| | - Brian G. Ballios
- Department of Ophthalmology and Vision Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5T 3A9, Canada
- Correspondence:
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Kittipibul T, Puangsricharern V. The Ocular Microbiome in Stevens-Johnson Syndrome. Front Med (Lausanne) 2021; 8:645053. [PMID: 34026783 PMCID: PMC8138458 DOI: 10.3389/fmed.2021.645053] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
The ocular surface microbiome is an essential factor that maintains ocular surface homeostasis. Since the ocular surface is continuously exposed to the external environment, its microbiome, tears, and local immunity are vital for maintaining normal conditions. Additionally, this microbiome helps prevent pathogen colonization, which commonly leads to opportunistic infection. The abnormal ocular surface microbiome has previously been reported in several conditions, including dry eyes, allergy, blepharitis, graft-versus-host disease (GVHD), and Stevens-Johnson syndrome (SJS). Several approaches were applied to identify the ocular microbiome, including conventional culture techniques and molecular sequencing techniques. By using 16s rRNA sequencing, alterations in the type, proportion, and composition of bacterial communities, described by alpha (α)-and beta (β)-diversity, were observed in SJS patients compared to the healthy group. Conventional culture techniques indicated a higher number of positive bacterial cultures in the SJS group, with a predominance of gram-positive cocci and gram-positive bacilli. Besides, there are increased variations and multiple detections of bacterial genera. Taken together, SJS causes structural changes in the ocular surface and significantly affects its microbiome. Further studies into the area of temporal relationship, metagenomics, proteomics, and metabolomics analysis of the microbiome will lead to a better understanding of this disease. Finally, the treatment using prebiotics and probiotics to re-establish the normal ocular ecosystem and bring back a healthy ocular surface await confirmation.
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Affiliation(s)
- Thanachaporn Kittipibul
- Excellence Center for Cornea and Limbal Stem Cell Transplantation, Department of Ophthalmology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand.,Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vilavun Puangsricharern
- Excellence Center for Cornea and Limbal Stem Cell Transplantation, Department of Ophthalmology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand.,Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Ballios BG, Pierce EA, Huckfeldt RM. Gene editing technology: Towards precision medicine in inherited retinal diseases. Semin Ophthalmol 2021; 36:176-184. [PMID: 33621144 DOI: 10.1080/08820538.2021.1887903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Purpose: To review preclinical and clinical advances in gene therapy, with a focus on gene editing technologies, and application to inherited retinal disease.Methods: A narrative overview of the literature, summarizing the state-of-the-art in clinical gene therapy for inherited retinal disease, as well as the science and application of new gene editing technology.Results: The last three years has seen the first FDA approval of an in vivo gene replacement therapy for a hereditary blinding eye disease and, recently, the first clinical application of an in vivo gene editing technique. Limitations and challenges in this evolving field are highlighted, as well as new technologies developed to address the multitude of molecular mechanisms of disease.Conclusion: Genetic therapy for the treatment of inherited retinal disease is a rapidly expanding area of ophthalmology. New technologies have revolutionized the field of genome engineering and rekindled an interest in precision medicines for these conditions.
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Affiliation(s)
- Brian G Ballios
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel M Huckfeldt
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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Dlamini Z, Francies FZ, Hull R, Marima R. Artificial intelligence (AI) and big data in cancer and precision oncology. Comput Struct Biotechnol J 2020; 18:2300-2311. [PMID: 32994889 PMCID: PMC7490765 DOI: 10.1016/j.csbj.2020.08.019] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023] Open
Abstract
Artificial intelligence (AI) and machine learning have significantly influenced many facets of the healthcare sector. Advancement in technology has paved the way for analysis of big datasets in a cost- and time-effective manner. Clinical oncology and research are reaping the benefits of AI. The burden of cancer is a global phenomenon. Efforts to reduce mortality rates requires early diagnosis for effective therapeutic interventions. However, metastatic and recurrent cancers evolve and acquire drug resistance. It is imperative to detect novel biomarkers that induce drug resistance and identify therapeutic targets to enhance treatment regimes. The introduction of the next generation sequencing (NGS) platforms address these demands, has revolutionised the future of precision oncology. NGS offers several clinical applications that are important for risk predictor, early detection of disease, diagnosis by sequencing and medical imaging, accurate prognosis, biomarker identification and identification of therapeutic targets for novel drug discovery. NGS generates large datasets that demand specialised bioinformatics resources to analyse the data that is relevant and clinically significant. Through these applications of AI, cancer diagnostics and prognostic prediction are enhanced with NGS and medical imaging that delivers high resolution images. Regardless of the improvements in technology, AI has some challenges and limitations, and the clinical application of NGS remains to be validated. By continuing to enhance the progression of innovation and technology, the future of AI and precision oncology show great promise.
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Affiliation(s)
- Zodwa Dlamini
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
| | - Flavia Zita Francies
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
| | - Rodney Hull
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
| | - Rahaba Marima
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
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9
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[Modern genetic counselling : Practical aspects exemplified by hypertrophic cardiomyopathy]. Internist (Berl) 2019; 59:790-798. [PMID: 29943241 DOI: 10.1007/s00108-018-0452-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Genetic counselling and subsequent molecular genetic testing should be performed in patients when an inherited monogenic form of heart disease is suspected. For the individual patient as well as for the (possibly asymptomatic) relatives, molecular diagnostics is important for an early diagnosis, (preventive) therapy and prognosis assessment. Using the example of hypertrophic cardiomyopathy (HCM), the most common monogenic form of structural heart disease, essential aspects of modern genetic counselling are elucidated. Specific examples of one case with a classical form of hypertrophic obstructive cardiomyopathy and one case of congenital HCM with Noonan's syndrome are discussed.
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10
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Czepluch FS, Hasenfuß G. [Inherited heart diseases and storage diseases with cardiac involvement]. Internist (Berl) 2018; 59:1063-1073. [PMID: 30178098 DOI: 10.1007/s00108-018-0485-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Rare diseases mostly have a genetic cause. Many rare cardiovascular diseases also have a genetic cause. For target-oriented cardiogenetic diagnostics, expert knowledge in human genetics as well as in clinical cardiology is needed. In recent years, the genetic cause of a number of heart diseases have been, at least in part, elucidated. Especially, certain arrhythmias and cardiomyopathy forms have a monogenetic cause. An early genetic diagnosis means that patients can be treated more effectively. Rare storage diseases also usually have a genetic cause and can manifest themselves in the heart; prominent examples are Fabry disease and amyloidosis. As patients with Fabry disease or amyloidosis suffer from a diverse and variable symptomatology, the correct diagnosis is often difficult.
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Affiliation(s)
- Frauke S Czepluch
- Klinik für Kardiologie und Pneumologie, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland.
| | - Gerd Hasenfuß
- Klinik für Kardiologie und Pneumologie, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland
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11
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Punetha J, Kesari A, Uapinyoying P, Giri M, Clarke NF, Waddell LB, North KN, Ghaoui R, O'Grady GL, Oates EC, Sandaradura SA, Bönnemann CG, Donkervoort S, Plotz PH, Smith EC, Tesi-Rocha C, Bertorini TE, Tarnopolsky MA, Reitter B, Hausmanowa-Petrusewicz I, Hoffman EP. Targeted Re-Sequencing Emulsion PCR Panel for Myopathies: Results in 94 Cases. J Neuromuscul Dis 2018; 3:209-225. [PMID: 27854218 DOI: 10.3233/jnd-160151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Molecular diagnostics in the genetic myopathies often requires testing of the largest and most complex transcript units in the human genome (DMD, TTN, NEB). Iteratively targeting single genes for sequencing has traditionally entailed high costs and long turnaround times. Exome sequencing has begun to supplant single targeted genes, but there are concerns regarding coverage and needed depth of the very large and complex genes that frequently cause myopathies. OBJECTIVE To evaluate efficiency of next-generation sequencing technologies to provide molecular diagnostics for patients with previously undiagnosed myopathies. METHODS We tested a targeted re-sequencing approach, using a 45 gene emulsion PCR myopathy panel, with subsequent sequencing on the Illumina platform in 94 undiagnosed patients. We compared the targeted re-sequencing approach to exome sequencing for 10 of these patients studied. RESULTS We detected likely pathogenic mutations in 33 out of 94 patients with a molecular diagnostic rate of approximately 35%. The remaining patients showed variants of unknown significance (35/94 patients) or no mutations detected in the 45 genes tested (26/94 patients). Mutation detection rates for targeted re-sequencing vs. whole exome were similar in both methods; however exome sequencing showed better distribution of reads and fewer exon dropouts. CONCLUSIONS Given that costs of highly parallel re-sequencing and whole exome sequencing are similar, and that exome sequencing now takes considerably less laboratory processing time than targeted re-sequencing, we recommend exome sequencing as the standard approach for molecular diagnostics of myopathies.
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Affiliation(s)
- Jaya Punetha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Akanchha Kesari
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Prech Uapinyoying
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Mamta Giri
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Nigel F Clarke
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Leigh B Waddell
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Kathryn N North
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, University of Melbourne, Melbourne, Australia
| | - Roula Ghaoui
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gina L O'Grady
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Emily C Oates
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Sarah A Sandaradura
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Sandra Donkervoort
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Paul H Plotz
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edward C Smith
- Department of Pediatrics, Division of Pediatric Neurology, Duke University Medical Center, Durham, NC, USA
| | - Carolina Tesi-Rocha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Tulio E Bertorini
- Department of Neurology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mark A Tarnopolsky
- Departments of Pediatrics and Medicine, McMaster University, Neuromuscular Disease Clinic, Health Sciences Centre, ON, Canada
| | - Bernd Reitter
- Children's Hospital, Johannes Gutenberg University, Mainz, Germany
| | | | - Eric P Hoffman
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
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Kalayinia S, Goodarzynejad H, Maleki M, Mahdieh N. Next generation sequencing applications for cardiovascular disease. Ann Med 2018; 50:91-109. [PMID: 29027470 DOI: 10.1080/07853890.2017.1392595] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The Human Genome Project (HGP), as the primary sequencing of the human genome, lasted more than one decade to be completed using the traditional Sanger's method. At present, next-generation sequencing (NGS) technology could provide the genome sequence data in hours. NGS has also decreased the expense of sequencing; therefore, nowadays it is possible to carry out both whole-genome (WGS) and whole-exome sequencing (WES) for the variations detection in patients with rare genetic diseases as well as complex disorders such as common cardiovascular diseases (CVDs). Finding new variants may contribute to establishing a risk profile for the pathology process of diseases. Here, recent applications of NGS in cardiovascular medicine are discussed; both Mendelian disorders of the cardiovascular system and complex genetic CVDs including inherited cardiomyopathy, channelopathies, stroke, coronary artery disease (CAD) and are considered. We also state some future use of NGS in clinical practice for increasing our information about the CVDs genetics and the limitations of this new technology. Key messages Traditional Sanger's method was the mainstay for Human Genome Project (HGP); Sanger sequencing has high fidelity but is slow and costly as compared to next generation methods. Within cardiovascular medicine, NGS has been shown to be successful in identifying novel causative mutations and in the diagnosis of Mendelian diseases which are caused by a single variant in a single gene. NGS has provided the opportunity to perform parallel analysis of a great number of genes in an unbiased approach (i.e. without knowing the underlying biological mechanism) which probably contribute to advance our knowledge regarding the pathology of complex diseases such as CVD.
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Affiliation(s)
- Samira Kalayinia
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | | | - Majid Maleki
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
| | - Nejat Mahdieh
- a Cardiogenetic Research Laboratory , Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences , Tehran , Iran
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Czepluch FS, Wollnik B, Hasenfuß G. Genetic determinants of heart failure: facts and numbers. ESC Heart Fail 2018; 5:211-217. [PMID: 29457878 PMCID: PMC5933969 DOI: 10.1002/ehf2.12267] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 12/22/2017] [Indexed: 12/20/2022] Open
Abstract
The relevance of gene mutations leading to heart diseases and hence heart failure has become evident. The risk for and the course of heart failure depends on genomic variants and mutations underlying the so‐called genetic predisposition. Genetic contribution to heart failure is highly heterogenous and complex. For any patient with a likely inherited heart failure syndrome, genetic counselling is recommended and important. In the last few years, novel sequencing technologies (named next‐generation sequencing – NGS) have dramatically improved the availability of molecular testing, the efficiency of genetic analyses, and moreover reduced the cost for genetic testing. Due to this development, genetic testing has become increasingly accessible and NGS‐based sequencing is now applied in clinical routine diagnostics. One of the most common reasons of heart failure are cardiomyopathies such as the dilated or the hypertrophic cardiomyopathy. Nearly 100 disease‐associated genes have been identified for cardiomyopathies. The knowledge of a pathogenic mutation can be used for genetic counselling, risk and prognosis determination, therapy guidance and hence for a more effective treatment. Besides, family cascade screening for a known familial, pathogenic mutation can lead to an early diagnosis in affected individuals. At that timepoint, a preventative intervention could be used to avoid or delay disease onset or delay disease progression. Understanding the cellular basis of genetic heart failure syndromes in more detail may provide new insights into the molecular biology of physiological and impaired cardiac (cell) function. As our understanding of the molecular and genetic pathophysiology of heart failure will increase, this might help to identify novel therapeutic targets and may lead to the development of new and specific treatment options in patients with heart failure.
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Affiliation(s)
- Frauke S Czepluch
- Department of Cardiology and Pulmonary Medicine, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Gerd Hasenfuß
- Department of Cardiology and Pulmonary Medicine, University Medical Center Göttingen, Göttingen, Germany
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Yehia L, Ni Y, Eng C. Germline TTN variants are enriched in PTEN-wildtype Bannayan-Riley-Ruvalcaba syndrome. NPJ Genom Med 2017; 2:37. [PMID: 29263846 PMCID: PMC5735137 DOI: 10.1038/s41525-017-0039-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/06/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022] Open
Abstract
Bannayan–Riley–Ruvalcaba syndrome (BRRS) is a rare congenital disorder classically characterized by macrocephaly in combination with intestinal hamartomatous polyposis, vascular malformations, lipomas, and genital lentiginosis. Germline PTEN mutations have been reported in up to 60% of BRRS patients. The remaining cases are of unknown genetic etiology. We exome-sequenced 35 unrelated PTEN-wildtype patients with classic presentation of BRRS and identified TTN germline missense variants in 12/35 (34%) patients. TTN encodes TITIN, a key structural and functional muscle protein. Exome and TTN-targeted sequencing in an additional unrelated series of 231 BRRS-like patients revealed 37 (16%) additional patients with germline TTN variants. All variants were predicted to be deleterious and equally distributed between the A-band and I-band protein domains. Rare TTN variants (MAF ≤ 0.0001) are enriched in classic BRRS patients compared to BRRS-like (OR = 2.7, 95% CI 1.21-5.94, p = 1.6 × 10-2) and multiple population controls (OR = 2.2, 95% CI 1.01-4.20, p = 4.7 × 10-2). Germline TTN mutations of different genotypes, inheritance patterns, and protein domain enrichment have been identified in multiple cardiac and/or skeletal muscular disorders. Functional interrogation of I-band variant p.Cys5096Arg identified in one of our classic BRRS patients, using CRISPR-Cas9 genome-edited cell lines, reveals an increased growth and lack of contact inhibition phenotype associated with increased levels of or phosphorylation of focal adhesion kinase (FAK) in mutant cells. These findings suggest that TITIN could play a role in overgrowth-relevant pathways and phenotypes. In summary, our observations suggest TTN as a candidate predisposing gene in classic PTEN-wildtype BRRS patients, perhaps suggesting this syndrome join the growing list of Titinopathies. TTN variants seem to explain many cases of a rare hereditary condition previously linked only to mutations in the unrelated gene PTEN. Charis Eng and team from the Cleveland Clinic, Ohio, USA, sequenced the protein-coding DNA from 35 patients with Bannayan-Riley-Ruvalcaba syndrome (BRRS), a disease characterized by large head size, tumors and other overgrowth problems. All of these individuals showed no mutations in PTEN, a tumor suppressor that explains 60% of BRRS cases. However, one-third had variants in TTN, which encodes a protein called TITIN that’s involved in muscle elasticity. Additional testing revealed more BRRS-like patients with TTN variants, and lab experiments indicated one possibility of how TTN variants lead to increased cellular growth. The authors suggest BRRS could be considered a “titinopathy” along with other cardiac and skeletal diseases caused by TTN mutations.
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Affiliation(s)
- Lamis Yehia
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195 USA.,Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Ying Ni
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195 USA.,Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 USA.,Center for Clinical Genomics, Cleveland Clinic, Cleveland, OH 44106 USA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195 USA.,Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195 USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA.,Germline High Risk Focus Group, CASE Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106 USA
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15
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Zhuang Y, Gong YJ, Zhong BF, Zhou Y, Gong L. Bioinformatics method identifies potential biomarkers of dilated cardiomyopathy in a human induced pluripotent stem cell-derived cardiomyocyte model. Exp Ther Med 2017; 14:2771-2778. [PMID: 28912841 DOI: 10.3892/etm.2017.4850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 02/10/2017] [Indexed: 12/23/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is the most common type of cardiomyopathy that account for the majority of heart failure cases. The present study aimed to reveal the underlying molecular mechanisms of DCM and provide potential biomarkers for detection of this condition. The public dataset of GSE35108 was downloaded, and 4 normal induced pluripotent stem cell (iPSC)-derived cardiomyocytes (N samples) and 4 DCM iPSC-derived cardiomyocytes (DCM samples) were utilized. Raw data were preprocessed, followed by identification of differentially expressed genes (DEGs) between N and DCM samples. Crucial functions and pathway enrichment analysis of DEGs were investigated, and protein-protein interaction (PPI) network analysis was conducted. Furthermore, a module network was extracted from the PPI network, followed by enrichment analysis. A set of 363 DEGs were identified, including 253 upregulated and 110 downregulated genes. Several biological processes (BPs), such as blood vessel development and vasculature development (FLT1 and MMP2), cell adhesion (CDH1, ITGB6, COL6A3, COL6A1 and LAMC2) and extracellular matrix (ECM)-receptor interaction pathway (CDH1, ITGB6, COL6A3, COL6A1 and LAMC2), were significantly enriched by these DEGs. Among them, MMP2, CDH1 and FLT1 were hub nodes in the PPI network, while COL6A3, COL6A1, LAMC2 and ITGB6 were highlighted in module 3 network. In addition, PENK and APLNR were two crucial nodes in module 2, which were linked to each other. In conclusion, several potential biomarkers for DCM were identified, such as MMP2, FLT1, CDH1, ITGB6, COL6A3, COL6A1, LAMC2, PENK and APLNR. These genes may serve significant roles in DCM via involvement of various BPs, such as blood vessel and vasculature development and cell adhesion, and the ECM-receptor interaction pathway.
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Affiliation(s)
- Yu Zhuang
- Department of Cardiovascular Surgery, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Yu-Jia Gong
- Stomatology Faculty, School of Medicine, Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Bei-Fen Zhong
- Department of Urology, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Yi Zhou
- Department of Cardiovascular Surgery, Shanghai First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Li Gong
- Department of Cardiothoracic Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
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16
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Nunn LM, Lopes LR, Syrris P, Murphy C, Plagnol V, Firman E, Dalageorgou C, Zorio E, Domingo D, Murday V, Findlay I, Duncan A, Carr-White G, Robert L, Bueser T, Langman C, Fynn SP, Goddard M, White A, Bundgaard H, Ferrero-Miliani L, Wheeldon N, Suvarna SK, O'Beirne A, Lowe MD, McKenna WJ, Elliott PM, Lambiase PD. Diagnostic yield of molecular autopsy in patients with sudden arrhythmic death syndrome using targeted exome sequencing. Europace 2015; 18:888-96. [PMID: 26498160 DOI: 10.1093/europace/euv285] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 07/20/2015] [Indexed: 11/13/2022] Open
Abstract
AIMS The targeted genetic screening of Sudden Arrhythmic Death Syndrome (SADS) probands in a molecular autopsy has a diagnostic yield of up to 35%. Exome sequencing has the potential to improve this yield. The primary aim of this study is to examine the feasibility and diagnostic utility of targeted exome screening in SADS victims, utilizing familial clinical screening whenever possible. METHODS AND RESULTS To determine the feasibility and diagnostic yield of targeted exome sequencing deoxyribonucleic acid (DNA) was isolated from 59 SADS victims (mean age 25 years, range 1-51 years). Targeted exome sequencing of 135 genes associated with cardiomyopathies and ion channelopathies was performed on the Illumina HiSeq2000 platform. Non-synonymous, loss-of-function, and splice-site variants with a minor allele frequency <0.02% in the NHLBI exome sequencing project and an internal set of control exomes were prioritized for analysis followed by <0.5% frequency threshold secondary analysis. First-degree relatives were offered clinical screening for inherited cardiac conditions. Seven probands (12%) carried very rare (<0.02%) or novel non-sense candidate mutations and 10 probands (17%) had previously published rare (0.02-0.5%) candidate mutations-a total yield of 29%. Co-segregation fully confirmed two private SCN5A Na channel mutations. Variants of unknown significance were detected in a further 34% of probands. CONCLUSION Molecular autopsy using targeted exome sequencing has a relatively low diagnostic yield of very rare potentially disease causing mutations. Candidate pathogenic variants with a higher frequency in control populations are relatively common and should be interpreted with caution.
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Affiliation(s)
- Laurence M Nunn
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Luis R Lopes
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Petros Syrris
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Cian Murphy
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Vincent Plagnol
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Eileen Firman
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Chrysoula Dalageorgou
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Esther Zorio
- Unit for Inherited Heart Diseases and Sudden Cardiac Death, Cardiology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Diana Domingo
- Unit for Inherited Heart Diseases and Sudden Cardiac Death, Cardiology Department, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Victoria Murday
- West of Scotland Clinical Genetics, Laboratory Medicine, Southern General Hospital, Edinburgh, UK
| | - Iain Findlay
- West of Scotland Clinical Genetics, Laboratory Medicine, Southern General Hospital, Edinburgh, UK
| | - Alexis Duncan
- West of Scotland Clinical Genetics, Laboratory Medicine, Southern General Hospital, Edinburgh, UK
| | | | | | | | | | | | | | | | - Henning Bundgaard
- Unit for Inherited Heart Diseases, The Heart Centre, National University Hospital, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Laura Ferrero-Miliani
- Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nigel Wheeldon
- South Yorkshire Regional Inherited Cardiac Conditions Service, South Yorkshire Cardiothoracic Centre, Sheffield, UK
| | - Simon K Suvarna
- South Yorkshire Regional Inherited Cardiac Conditions Service, South Yorkshire Cardiothoracic Centre, Sheffield, UK
| | - Aliceson O'Beirne
- South Yorkshire Regional Inherited Cardiac Conditions Service, South Yorkshire Cardiothoracic Centre, Sheffield, UK
| | - Martin D Lowe
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - William J McKenna
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Perry M Elliott
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
| | - Pier D Lambiase
- Institute of Cardiovascular Sciences, Barts Heart Centre, St Bartholomews Hospital and Institute of Cardiovascular Sciences, UCL, West Smithfield, London EC1A 7BE, UK
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17
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Zhao Y, Feng Y, Zhang YM, Ding XX, Song YZ, Zhang AM, Liu L, Zhang H, Ding JH, Xia XS. Targeted next-generation sequencing of candidate genes reveals novel mutations in patients with dilated cardiomyopathy. Int J Mol Med 2015; 36:1479-86. [PMID: 26458567 PMCID: PMC4678153 DOI: 10.3892/ijmm.2015.2361] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 09/16/2015] [Indexed: 12/23/2022] Open
Abstract
Dilated cardiomyopathy (DCM) is a major cause of sudden cardiac death and heart failure, and it is characterized by genetic and clinical heterogeneity, even for some patients with a very poor clinical prognosis; in the majority of cases, DCM necessitates a heart transplant. Genetic mutations have long been considered to be associated with this disease. At present, mutations in over 50 genes related to DCM have been documented. This study was carried out to elucidate the characteristics of gene mutations in patients with DCM. The candidate genes that may cause DCM include MYBPC3, MYH6, MYH7, LMNA, TNNT2, TNNI3, MYPN, MYL3, TPM1, SCN5A, DES, ACTC1 and RBM20. Using next-generation sequencing (NGS) and subsequent mutation confirmation with traditional capillary Sanger sequencing analysis, possible causative non-synonymous mutations were identified in ~57% (12/21) of patients with DCM. As a result, 7 novel mutations (MYPN, p.E630K; TNNT2, p.G180A; MYH6, p.R1047C; TNNC1, p.D3V; DES, p.R386H; MYBPC3, p.C1124F; and MYL3, p.D126G), 3 variants of uncertain significance (RBM20, p.R1182H; MYH6, p.T1253M; and VCL, p.M209L), and 2 known mutations (MYH7, p.A26V and MYBPC3, p.R160W) were revealed to be associated with DCM. The mutations were most frequently found in the sarcomere (MYH6, MYBPC3, MYH7, TNNC1, TNNT2 and MYL3) and cytoskeletal (MYPN, DES and VCL) genes. As genetic testing is a useful tool in the clinical management of disease, testing for pathogenic mutations is beneficial to the treatment of patients with DCM and may assist in predicting disease risk for their family members before the onset of symptoms.
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Affiliation(s)
- Yue Zhao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Yue Feng
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Yun-Mei Zhang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming 650034, P.R. China
| | - Xiao-Xue Ding
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming 650034, P.R. China
| | - Yu-Zhu Song
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - A-Mei Zhang
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Li Liu
- Faculty of Life Science and Technology, Research Center for Molecular Medicine in Yunnan Province, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Hong Zhang
- Department of Cardiology, The First Hospital of Yunnan Province, Kunming 650034, P.R. China
| | - Jia-Huan Ding
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Xue-Shan Xia
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, P.R. China
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Abstract
With the wider deployment of massively-parallel, next-generation sequencing, it is now possible to survey human genome data for research and clinical purposes. The reduced cost of producing short-read sequencing has now shifted the burden to data analysis. Analysis of genome sequencing remains challenged by the complexity of the human genome, including redundancy and the repetitive nature of genome elements and the large amount of variation in individual genomes. Public databases of human genome sequences greatly facilitate interpretation of common and rare genetic variation, although linking database sequence information to detailed clinical information is limited by privacy and practical issues. Genetic variation is a rich source of knowledge for cardiovascular disease because many, if not all, cardiovascular disorders are highly heritable. The role of rare genetic variation in predicting risk and complications of cardiovascular diseases has been well established for hypertrophic and dilated cardiomyopathy, where the number of genes that are linked to these disorders is growing. Bolstered by family data, where genetic variants segregate with disease, rare variation can be linked to specific genetic variation that offers profound diagnostic information. Understanding genetic variation in cardiomyopathy is likely to help stratify forms of heart failure and guide therapy. Ultimately, genetic variation may be amenable to gene correction and gene editing strategies.
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Affiliation(s)
- Elizabeth M McNally
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine
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19
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Ankala A, da Silva C, Gualandi F, Ferlini A, Bean LJH, Collins C, Tanner AK, Hegde MR. A comprehensive genomic approach for neuromuscular diseases gives a high diagnostic yield. Ann Neurol 2014; 77:206-14. [PMID: 25380242 DOI: 10.1002/ana.24303] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/31/2014] [Accepted: 11/02/2014] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Neuromuscular diseases (NMDs) are a group of >200 highly genetically as well as clinically heterogeneous inherited genetic disorders that affect the peripheral nervous and muscular systems, resulting in gross motor disability. The clinical and genetic heterogeneities of NMDs make disease diagnosis complicated and expensive, often involving multiple tests. METHODS To expedite the molecular diagnosis of NMDs, we designed and validated several next generation sequencing (NGS)-based comprehensive gene panel tests that include complementary deletion and duplication testing through comparative genomic hybridization arrays. Our validation established the targeted gene panel test to have 100% sensitivity and specificity for single nucleotide variant detection. To compare the clinical diagnostic yields of single gene (NMD-associated) tests with the various NMD NGS panel tests, we analyzed data from all clinical tests performed at the Emory Genetics Laboratory from October 2009 through May 2014. We further compared the clinical utility of the targeted NGS panel test with that of exome sequencing (ES). RESULTS We found that NMD comprehensive panel testing has a 3-fold greater diagnostic yield (46%) than single gene testing (15-19%). Sanger fill-in of low-coverage exons, copy number variation analysis, and thorough in-house validation of the assay all complement panel testing and allow the detection of all types of causative pathogenic variants, some of which (about 18%) may be missed by ES. INTERPRETATION Our results strongly indicate that for molecular diagnosis of heterogeneous disorders such as NMDs, targeted panel testing has the highest clinical yield and should therefore be the preferred first-tier approach.
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Affiliation(s)
- Arunkanth Ankala
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
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20
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Riazi S, Kraeva N, Muldoon SM, Dowling J, Ho C, Petre MA, Parness J, Dirksen RT, Rosenberg H. Malignant hyperthermia and the clinical significance of type-1 ryanodine receptor gene (RYR1) variants: proceedings of the 2013 MHAUS Scientific Conference. Can J Anaesth 2014; 61:1040-9. [PMID: 25189431 DOI: 10.1007/s12630-014-0227-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/11/2014] [Indexed: 01/07/2023] Open
Abstract
The Malignant Hyperthermia Association of the United States and the Department of Anesthesia at the University of Toronto sponsored a Scientific Conference on November 1-2, 2013 in Toronto, ON, Canada. The multidisciplinary group of experts, including clinicians, geneticists, and physiologists involved in research related to malignant hyperthermia (MH), shared new insights into the pathophysiology of diseases linked to the type-1 ryanodine receptor gene (RYR1) as well as the relationship between MH and "awake MH" conditions, such as exertional rhabdomyolysis and exertional heat illness. In addition, the molecular genetics of MH and clinical issues related to the diagnosis and management of disorders linked to RYR1 were presented. The conference also honoured Dr. David H. MacLennan for his contributions to our understanding of the genetics, pathogenesis, and treatment of MH and other RYR1-related myopathies. This report represents a summary of the proceedings of this conference.
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Affiliation(s)
- Sheila Riazi
- Malignant Hyperthermia Investigation Unit, Toronto General Hospital, UHN, 200 Elizabeth Street, Eaton 3-323, Toronto, ON, M5G 2C4, Canada,
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21
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Ankala A, Hegde M. Genomic Technologies and the New Era of Genomic Medicine. J Mol Diagn 2014; 16:7-10. [DOI: 10.1016/j.jmoldx.2013.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/08/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022] Open
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