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  • Original Article|Open Access

    CCEPAS: the creation and validation of a fast and sensitive clinical whole exome analysis pipeline based on gene and variant ranking

    C. Alexander Valencia, Abhinav Mathur, James Denton, Chao Wei, Xinjian Wang, Ammar Husami, Prakash Velayutham, Masaru Ryumae, Kejian Zhang
    Aim: Whole exome sequencing technology has permitted the discovery of genes that cause Mendelian disorders and was used in clinical laboratories. However, identifying the disease causing variant(s) for a specific disorder from thousands of variants is challenging. In this study, we describe the Cincinnati Clinical Exome Pipeline Analysis Suite (CCEPAS) that utilizes a four-level framework into one analysis procedure that rapidly identify the most likely causative gene variants to establish a clinical diagnosis. Methods: We developed and validated CCEPAS using 100 clinical exome cases. We... Read more
    J Transl Genet Genom 2018;2:1. | doi:10.20517/jtgg.2017.05
    Published on: 31 Jan 2018  | Viewed:3546  | Downloaded:237
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  • Topic: MicroRNAs in Allergic Diseases|Open Access

    MicroRNAs in atopic dermatitis: a review

    Neeti Bhardwaj
    Atopic dermatitis (AD) is a chronic and relapsing inflammatory skin disease, generally the first clinical manifestation of atopy and the start of atopic march. Effective treatment of AD could potentially interrupt the progression of atopic march. MicroRNAs (miRNAs), a recently described class of gene expression regulators in inflammatory conditions, affect expression of numerous proteins. The role of miRNAs has been investigated in several atopic conditions, including asthma, eosinophilic esophagitis, allergic rhinitis as well as atopic dermatitis. They have been shown to be involved in the... Read more
    J Transl Genet Genom 2017;1:15-22. | doi:10.20517/jtgg.2017.01
    Published on: 17 Nov 2017  | Viewed:2612  | Downloaded:206
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  • Topic: Reversing X Chromosome Inactivation as a New Therapeutic Treatment for X-linked Diseases|Open Access

    Reversal of X chromosome inactivation: lessons from pluripotent reprogramming of mouse and human somatic cells

    Irene Cantone
    X chromosome inactivation (XCI) is a strategy used by mammals to silence genes along one of the two female X chromosomes and equilibrate expression dosage between XY males and XX females. This epigenetically-inherited silencing is established during early embryonic development and maintained thereafter through cell divisions. Seeding of multiple repressive epigenetic marks along the inactive X chromosome (Xi) makes inactivation extremely robust and difficult to reverse upon single genetic perturbations. Reversal of XCI has, however, been observed when somatic cells are reprogrammed towards... Read more
    J Transl Genet Genom 2017;1:1-14. | doi:10.20517/jtgg.2017.19
    Published on: 16 Nov 2017  | Viewed:3428  | Downloaded:180
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  • Review|Open Access

    Novel molecular players of X chromosome inactivation: new technologies and new insights

    Piotr Przanowski, Urszula Waśko, Sanchita Bhatnagar
    The dosage compensation in placental mammals is achieved by silencing of one copy of the X chromosomes in a female cell by a process called X chromosome inactivation (XCI). XCI ensures equal gene dosage for X-linked genes between the two genders. Although the choice of X chromosome to be silenced is random, once the silencing of the X chromosome has been established, this process is highly regulated and maintained throughout subsequent cell divisions. A long non-coding RNA, Xist, and its interacting proteins execute this multistep process, but several of these regulatory proteins remain... Read more
    This article belongs to the Special Issue Reversing X Chromosome Inactivation as a New Therapeutic Treatment for X-linked Diseases
    J Transl Genet Genom 2018;2:2. | doi:10.20517/jtgg.2017.03
    Published on: 27 Feb 2018  | Viewed:2485  | Downloaded:169
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  • Letter to Editor|Open Access

    Gene dosage defects in primary immunodeficiencies and related disorders: a pilot study

    Lisa Dyer, Xia Li, James Denton, Brittany Jones, Emily Liston, Danielle Hilton, Abhinav Mathur, Kejian Zhang, C. Alexander Valencia
    J Transl Genet Genom 2017;1:23-7. | doi:10.20517/jtgg.2017.04
    Published on: 25 Dec 2017  | Viewed:1753  | Downloaded:134
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  • Editorial|Open Access

    Awakening the sleeping giant: methods for reactivating the inactive X chromosome as clinical treatment for X-linked disorders

    Andrea Cerase
    This article belongs to the Special Issue Reversing X Chromosome Inactivation as a New Therapeutic Treatment for X-linked Diseases
    J Transl Genet Genom 2018;2:3. | doi:10.20517/jtgg.2018.02
    Published on: 1 Mar 2018  | Viewed:1297  | Downloaded:109
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  • Review|Open Access

    MERRF and MELAS: current gene therapy trends and approaches

    Ciara Ann Agresti, Penelope Nicole Halkiadakis, Peter Tolias
    The mitochondrion is a unique organelle that predominantly functions to produce useful cellular energy in the form of adenosine triphosphate (ATP). Unlike other non-nuclear eukaryotic organelles (with the exception of chloroplasts), mitochondria have two lipid membranes that enclose their own mitochondrial DNA (mtDNA) and ribosomes for protein production. Similar to nuclear DNA, mtDNA is equally susceptible to mutations that may be classified as either pathogenic or nonpathogenic. Myoclonic Epilepsy with Ragged Red Fibers (MERRF) and Mitochondrial Encephalomyopathy, Lactic Acidosis, and... Read more
    This article belongs to the Special Issue Personalized genomic medicine: challenges and opportunities for the diagnosis and the treatment of human disease
    J Transl Genet Genom 2018;2:9. | doi:10.20517/jtgg.2018.05
    Published on: 3 Jul 2018  | Viewed:973  | Downloaded:64
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  • Review|Open Access

    Challenges in implementing genomic medicine: the 100,000 Genomes Project

    Julian G. Barwell, Rory B.G. O’Sullivan, Laura K. Mansbridge, Joanna M. Lowry, Huw R. Dorkins
    Many important medical conditions may be the result of an inherited mutation in one of a number of different genes. Technical advances have reduced the cost of whole genome sequencing and whole exome sequencing to a level where it is now feasible to analyse multiple genes in one test. Every human carries several hundred potentially pathogenic coding variants, so a major challenge is to understand which of these is relevant to the patient’s disease. This requires considerable computing power, the use of international unaffected “normal” population and disease cohort databases, clinical... Read more
    This article belongs to the Special Issue Personalized genomic medicine: challenges and opportunities for the diagnosis and the treatment of human disease
    J Transl Genet Genom 2018;2:13. | doi:10.20517/jtgg.2018.17
    Published on: 11 Sep 2018  | Viewed:836  | Downloaded:50
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  • Systematic Review|Open Access

    Clinical genomics of the relationship between ADAMTS7 and coronary artery calcification and atherosclerosis

    Simon W. Rabkin, Pavlos G. Koitsopoulos
    Aim: There are many coronary artery disease (CAD) cases in which the explanation for its development cannot be readily explained by traditional risk factors. The purpose of this study was to examine the data whether ADAMTS7 polymorphisms is related to the presence or severity of CAD. Methods: A systematic review of the literature was conducted to address the relationship between ADAMTS7 polymorphism and atherosclerosis. Results: Nine studies were evaluated that examined the relationship between ADAMTS7 and coronary atherosclerosis and 3 studies that examined the relationship between ADAMTS7... Read more
    J Transl Genet Genom 2018;2:4. | doi:10.20517/jtgg.2018.01
    Published on: 13 Apr 2018  | Viewed:998  | Downloaded:46
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  • Review|Open Access

    Molecular genetics of Ewing sarcoma, model systems and finding novel (immuno-) therapeutic targets

    Wietske van der Ent, Laurens G.L. Sand, Pancras C.W. Hogendoorn
    Ewing sarcoma (EWS) is a bone- and soft tissue tumour affecting primarily children and young adults. A quarter of patients present with metastases at the time of diagnosis and have a poor outlook in terms of overall survival. Efforts are made across the field to gain deeper insight in the genetics of this enigmatic neoplasm. EWS is characterized by presence of an oncogenic translocation gene, EWSR1-ETS. In addition, there are a limited number of known recurrent DNA copy number variations and mutations. Subsequent of the above, the epigenetic profile of EWS is subject of interest. In this... Read more
    This article belongs to the Special Issue Genetics and Genomics of Cancer
    J Transl Genet Genom 2018;2:10. | doi:10.20517/jtgg.2018.09
    Published on: 16 Jul 2018  | Viewed:946  | Downloaded:39
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  • Original Article|Open Access

    Exome sequencing identifies FLNC and ADD3 variants in a family with cardiomyopathy

    Alejandro J. Sanoja, Hua Li, F. Jay Fricker, Stephen F. Kingsmore, Margaret R. Wallace
    Aim: Idiopathic cardiomyopathy is often genetic in origin, typically autosomal dominant, and restrictive cardiomyopathy (RCM) is the rarest form. Clinically, RCM prognosis is poor with most patients requiring heart transplant due to impaired diastolic function leading to heart failure. In some cases, desminopathy is also observed, whereby desmin protein aggregates in the myocardium. Many genes are known to be involved in cardiomyopathy, and we sought to find the pathogenic mutation of a four-generation family with RCM and desminopathy. Methods: We employed whole exome sequence analysis of... Read more
    J Transl Genet Genom 2018;2:6. | doi:10.20517/jtgg.2017.13
    Published on: 30 May 2018  | Viewed:795  | Downloaded:36
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  • Review|Open Access

    Parathyroid carcinoma

    Jessica Costa-Guda
    Parathyroid carcinoma is a rare but clinically-aggressive tumor. While most cases are sporadic, parathyroid cancer is overrepresented in hyperparathyroidism-jaw tumor syndrome, or rarely other heritable syndromes. Evidence suggests that sporadic parathyroid carcinomas rarely, if ever, evolve through an identifiable benign tumor intermediate. A few genes have been directly implicated in the pathogenesis of sporadic parathyroid cancer; somatic (and less common germline) mutations in the CDC73 tumor suppressor gene are the most frequent finding and the only firmly established molecular drivers... Read more
    This article belongs to the Special Issue Genetics and Genomics of Cancer
    J Transl Genet Genom 2018;2:5. | doi:10.20517/jtgg.2018.08
    Published on: 22 May 2018  | Viewed:770  | Downloaded:34
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  • Review|Open Access

    Biomarkers and therapeutic targets: microRNA roles in the pathophysiology, diagnosis and management of eosinophilic esophagitis

    Kristin A. Lambert, Punit Jhaveri, Pooja Jhaveri
    Eosinophilic esophagitis (EoE) is a chronic inflammatory disease that is increasingly recognized as the cause of common gastrointestinal symptoms including dysphagia, chest and abdominal pain, heartburn, food impaction, and food refusal in children and adults. Often referred to as “asthma of the esophagus”, eosinophilic esophagitis, like its asthma counterpart, is an allergic disorder on the rise worldwide. Clinically managed by food avoidance, steroid therapy, recurring endoscopic evaluations and dilations as needed, eosinophilic esophagitis is a poorly understood disease process with... Read more
    This article belongs to the Special Issue MicroRNAs in Allergic Diseases
    J Transl Genet Genom 2018;2:11. | doi:10.20517/jtgg.2018.11
    Published on: 8 Aug 2018  | Viewed:343  | Downloaded:30
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  • Review|Open Access

    The failure of “engineered rejuvenation”: laboratory genomics do not translate into precision anti-aging therapies

    Marios Kyriazis
    There is a general failure of reductionist and mechanistic approaches to rejuvenation biomedical technologies which aim at providing treatments against aging (defined as “time-dependent dysfunction”). Importantly, it is becoming increasingly recognised that genomic research findings in animals may not adequately be translated into effective human anti-aging therapies. There exist translational impediments, which although individually formidable, can theoretically be overcome. However, the combined effects of these obstacles render this reductionist avenue of quest unattainable, at least for... Read more
    This article belongs to the Special Issue Personalized genomic medicine: challenges and opportunities for the diagnosis and the treatment of human disease
    J Transl Genet Genom 2018;2:7. | doi:10.20517/jtgg.2018.04
    Published on: 15 Jun 2018  | Viewed:784  | Downloaded:27
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  • Original Article|Open Access

    Which came first: validity or clinical testing? The example of long QT genes

    Lacey Boshe, A. Katherine M. Foreman, Jennifer L. Goldstein, Natasha T. Strande, Jonathan S. Berg, Julianne M. O’Daniel
    Aim: To investigate the potential relationship between the strength of evidence for a gene-disease association and inclusion of the gene on a targeted, indication-based gene panel test for hereditary long QT syndrome (LQTS) and to explore factors that may influence laboratory decisions about the inclusion or exclusion of genes from these clinical tests. Methods: A comprehensive literature search was performed to quantify existing evidence supporting putative LQTS gene-disease associations. This evidence included the year that the gene was first implicated in LQTS, the total number of... Read more
    This article belongs to the Special Issue Personalized genomic medicine: challenges and opportunities for the diagnosis and the treatment of human disease
    J Transl Genet Genom 2018;2:12. | doi:10.20517/jtgg.2018.18
    Published on: 30 Aug 2018  | Viewed:180  | Downloaded:12
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  • Case Report|Open Access

    Detection of leukocyte adhesion deficiency type 1 in an infant by high-throughput targeted exome sequencing

    Sha Hong, Li-Juan Xie, Qing-Nan Yang, Tian-Wen Zhu
    Leukocyte adhesion deficiency type 1 (LAD-I) characterized by immune-deficiency and leukocytosis is rare in infant patients. A 43-day-old boy with severe leukocytosis, recurrent infections, defective wound healing and hepatosplenomegaly associated with an acquired cytomegalovirus infection. To establish the diagnosis definitively, a high-throughput targeted exome sequencing was performed, which yielded the diagnosis of LAD-I. A homozygous mutation in integrin subunit beta 2 (ITGB2), c.817G>A (p.G273R) was identified. Though LAD-I has been thoroughly-studied, with more than 300 detailed... Read more
    This article belongs to the Special Issue Personalized genomic medicine: challenges and opportunities for the diagnosis and the treatment of human disease
    J Transl Genet Genom 2018;2:8. | doi:10.20517/jtgg.2018.06
    Published on: 28 Jun 2018  | Viewed:644  | Downloaded:12
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Journal of Translational Genetics and Genomics ISSN 2578-5281 (Online)
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