Dercum's Disease and Roch-Leri Mesosomatous Lipomatosis
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Genetic Determinants Underlying Rare Diseases Identified Using Next-Generation Sequencing Technologies
Western University Scholarship@Western Electronic Thesis and Dissertation Repository 8-2-2018 1:30 PM Genetic determinants underlying rare diseases identified using next-generation sequencing technologies Rosettia Ho The University of Western Ontario Supervisor Hegele, Robert A. The University of Western Ontario Graduate Program in Biochemistry A thesis submitted in partial fulfillment of the equirr ements for the degree in Master of Science © Rosettia Ho 2018 Follow this and additional works at: https://ir.lib.uwo.ca/etd Part of the Medical Genetics Commons Recommended Citation Ho, Rosettia, "Genetic determinants underlying rare diseases identified using next-generation sequencing technologies" (2018). Electronic Thesis and Dissertation Repository. 5497. https://ir.lib.uwo.ca/etd/5497 This Dissertation/Thesis is brought to you for free and open access by Scholarship@Western. It has been accepted for inclusion in Electronic Thesis and Dissertation Repository by an authorized administrator of Scholarship@Western. For more information, please contact [email protected]. Abstract Rare disorders affect less than one in 2000 individuals, placing a huge burden on individuals, families and the health care system. Gene discovery is the starting point in understanding the molecular mechanisms underlying these diseases. The advent of next- generation sequencing has accelerated discovery of disease-causing genetic variants and is showing numerous benefits for research and medicine. I describe the application of next-generation sequencing, namely LipidSeq™ ‒ a targeted resequencing panel for the identification of dyslipidemia-associated variants ‒ and whole-exome sequencing, to identify genetic determinants of several rare diseases. Utilization of next-generation sequencing plus associated bioinformatics led to the discovery of disease-associated variants for 71 patients with lipodystrophy, two with early-onset obesity, and families with brachydactyly, cerebral atrophy, microcephaly-ichthyosis, and widow’s peak syndrome. -
Megalencephaly and Macrocephaly
277 Megalencephaly and Macrocephaly KellenD.Winden,MD,PhD1 Christopher J. Yuskaitis, MD, PhD1 Annapurna Poduri, MD, MPH2 1 Department of Neurology, Boston Children’s Hospital, Boston, Address for correspondence Annapurna Poduri, Epilepsy Genetics Massachusetts Program, Division of Epilepsy and Clinical Electrophysiology, 2 Epilepsy Genetics Program, Division of Epilepsy and Clinical Department of Neurology, Fegan 9, Boston Children’s Hospital, 300 Electrophysiology, Department of Neurology, Boston Children’s Longwood Avenue, Boston, MA 02115 Hospital, Boston, Massachusetts (e-mail: [email protected]). Semin Neurol 2015;35:277–287. Abstract Megalencephaly is a developmental disorder characterized by brain overgrowth secondary to increased size and/or numbers of neurons and glia. These disorders can be divided into metabolic and developmental categories based on their molecular etiologies. Metabolic megalencephalies are mostly caused by genetic defects in cellular metabolism, whereas developmental megalencephalies have recently been shown to be caused by alterations in signaling pathways that regulate neuronal replication, growth, and migration. These disorders often lead to epilepsy, developmental disabilities, and Keywords behavioral problems; specific disorders have associations with overgrowth or abnor- ► megalencephaly malities in other tissues. The molecular underpinnings of many of these disorders are ► hemimegalencephaly now understood, providing insight into how dysregulation of critical pathways leads to ► -
Unilateral Multiple Tuberous Xanthomas Mimicking Multiple Lipomatosis in Type Iia Hypercholesterolemia- a Case Report with Review
Jebmh.com Case Report Unilateral Multiple Tuberous Xanthomas Mimicking Multiple Lipomatosis in Type IIa Hypercholesterolemia- A Case Report with Review Madhuri K.1, Yugank Anand2, Vamseedhar Annam3, Prakash C. J.4, Shreya D. Prabhu5, Harshitha K. S.6 1Postgraduate Student, Department of Pathology, Rajarajeswari Medical College and Hospital, Bangalore, Karnataka. 2Postgraduate Student, Department of Pathology, Rajarajeswari Medical College and Hospital, Bangalore, Karnataka. 3Professor, Department of Pathology, Rajarajeswari Medical College and Hospital, Bangalore, Karnataka. 4Professor, Department of Pathology, Rajarajeswari Medical College and Hospital, Bangalore, Karnataka. 5Postgraduate Student, Department of Pathology, Rajarajeswari Medical College and Hospital, Bangalore, Karnataka. 6Postgradute Student, Department of Pathology, Rajarajeswari Medical College and Hospital, Bangalore, Karnataka. INTRODUCTION The term Xanthoma was derived from a Greek word “Xanthos” meaning yellow Corresponding Author: and was generally used to describe lipid deposits in the subcutaneous plane.1 They Dr. Vamseedhar Annam, do not represent a particular disease, but are cutaneous markers for dyslipidaemia Professor, or may even arise without any underlying metabolic defect.2 Tuberous xanthomas Department of Pathology, present as yellow or reddish nodules located mainly over the extensor surface of Rajarajeswari Medical College and the extremities and buttocks.1 They may be confused with lipomas. Early diagnosis Hospital, Bangalore- 560074, Karnataka. and treatment may help to prevent complications such as coronary artery disease, E-mail: [email protected] 3 myocardial infarction and pancreatitis. We here report a case of unilateral multiple tuberous xanthomas in a young lady with elevated Low density lipoprotein levels DOI: 10.18410/jebmh/2020/183 consistent with familial hypercholesterolemia Type IIa. Financial or Other Competing Interests: None. -
Cardiomyopathy Precision Panel Overview Indications
Cardiomyopathy Precision Panel Overview Cardiomyopathies are a group of conditions with a strong genetic background that structurally hinder the heart to pump out blood to the rest of the body due to weakness in the heart muscles. These diseases affect individuals of all ages and can lead to heart failure and sudden cardiac death. If there is a family history of cardiomyopathy it is strongly recommended to undergo genetic testing to be aware of the family risk, personal risk, and treatment options. Most types of cardiomyopathies are inherited in a dominant manner, which means that one altered copy of the gene is enough for the disease to present in an individual. The symptoms of cardiomyopathy are variable, and these diseases can present in different ways. There are 5 types of cardiomyopathies, the most common being hypertrophic cardiomyopathy: 1. Hypertrophic cardiomyopathy (HCM) 2. Dilated cardiomyopathy (DCM) 3. Restrictive cardiomyopathy (RCM) 4. Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) 5. Isolated Left Ventricular Non-Compaction Cardiomyopathy (LVNC). The Igenomix Cardiomyopathy Precision Panel serves as a diagnostic and tool ultimately leading to a better management and prognosis of the disease. It provides a comprehensive analysis of the genes involved in this disease using next-generation sequencing (NGS) to fully understand the spectrum of relevant genes. Indications The Igenomix Cardiomyopathy Precision Panel is indicated in those cases where there is a clinical suspicion of cardiomyopathy with or without the following manifestations: - Shortness of breath - Fatigue - Arrythmia (abnormal heart rhythm) - Family history of arrhythmia - Abnormal scans - Ventricular tachycardia - Ventricular fibrillation - Chest Pain - Dizziness - Sudden cardiac death in the family 1 Clinical Utility The clinical utility of this panel is: - The genetic and molecular diagnosis for an accurate clinical diagnosis of a patient with personal or family history of cardiomyopathy, channelopathy or sudden cardiac death. -
Whole Exome Sequencing Gene Package Intellectual Disability, Version 9.1, 31-1-2020
Whole Exome Sequencing Gene package Intellectual disability, version 9.1, 31-1-2020 Technical information DNA was enriched using Agilent SureSelect DNA + SureSelect OneSeq 300kb CNV Backbone + Human All Exon V7 capture and paired-end sequenced on the Illumina platform (outsourced). The aim is to obtain 10 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate and non-unique reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA-MEM algorithm (reference: http://bio-bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x A2ML1 {Otitis media, susceptibility to}, 166760 610627 66 100 100 96 AARS1 Charcot-Marie-Tooth disease, axonal, type 2N, 613287 601065 63 100 97 90 Epileptic encephalopathy, early infantile, 29, 616339 AASS Hyperlysinemia, -
Lipoprotein Lipase: a General Review Moacir Couto De Andrade Júnior1,2*
Review Article iMedPub Journals Insights in Enzyme Research 2018 www.imedpub.com Vol.2 No.1:3 ISSN 2573-4466 DOI: 10.21767/2573-4466.100013 Lipoprotein Lipase: A General Review Moacir Couto de Andrade Júnior1,2* 1Post-Graduation Department, Nilton Lins University, Manaus, Amazonas, Brazil 2Department of Food Technology, Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Amazonas, Brazil *Corresponding author: MC Andrade Jr, Post-Graduation Department, Nilton Lins University, Manaus, Amazonas, Brazil, Tel: +55 (92) 3633-8028; E-mail: [email protected] Rec date: March 07, 2018; Acc date: April 10, 2018; Pub date: April 17, 2018 Copyright: © 2018 Andrade Jr MC. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Citation: Andrade Jr MC (2018) Lipoprotein Lipase: A General Review. Insights Enzyme Res Vol.2 No.1:3 Abstract Lipoprotein Lipase: Historical Hallmarks, Enzymatic Activity, Characterization, and Carbohydrates (e.g., glucose) and lipids (e.g., free fatty acids or FFAs) are the most important sources of energy Present Relevance in Human for most organisms, including humans. Lipoprotein lipase (LPL) is an extracellular enzyme (EC 3.1.1.34) that is Pathophysiology and Therapeutics essential in lipoprotein metabolism. LPL is a glycoprotein that is synthesized and secreted in several tissues (e.g., Macheboeuf, in 1929, first described chemical procedures adipose tissue, skeletal muscle, cardiac muscle, and for the isolation of a plasma protein fraction that was very rich macrophages). At the luminal surface of the vascular in lipids but readily soluble in water, such as a lipoprotein [1]. -
Noonan Spectrum Disorders Panel, Sequencing ARUP Test Code 2010772 Noonan Disorders Sequencing Specimen Whole Blood
Patient Report |FINAL Client: Example Client ABC123 Patient: Patient, Example 123 Test Drive Salt Lake City, UT 84108 DOB 12/9/2011 UNITED STATES Gender: Female Patient Identifiers: 01234567890ABCD, 012345 Physician: Doctor, Example Visit Number (FIN): 01234567890ABCD Collection Date: 01/01/2017 12:34 Noonan Spectrum Disorders Panel, Sequencing ARUP test code 2010772 Noonan Disorders Sequencing Specimen Whole Blood Noonan Disorders Sequencing Interp Positive INDICATION FOR TESTING Short stature and facial features suggestive of Noonan syndrome. RESULT One pathogenic variant was detected in the PTPN11 gene. PATHOGENIC VARIANT Gene: PTPN11 (NM_002834.3) Nucleic Acid Change: c.188A>G; Heterozygous Amino Acid Alteration: p.Tyr63Cys Inheritance: Autosomal Dominant INTERPRETATION One pathogenic variant, c.188A>G; p.Tyr63Cys, was detected in the PTPN11 gene by massively parallel sequencing and confirmed by Sanger sequencing. Pathogenic PTPN11 variants are inherited in an autosomal dominant manner, and are associated with Noonan syndrome 1 (MIM: 163950), metachondromatosis (MIM: 156250), and LEOPARD syndrome 1 (MIM: 151100). No additional pathogenic variants were identified in the other targeted genes by massively parallel sequencing. Please refer to the background information included in this report for a list of the genes analyzed and limitations of this test. Evidence for variant classification: The PTPN11 c.188A>G, p.Tyr63Cys variant (rs121918459) has been reported in multiple patients diagnosed with Noonan syndrome (Tartaglia 2001, Jongmans 2011, Martinelli 2012, Hashida 2013, Lepri 2014, Okamoto 2015). This variant is located in a structurally important region of the catalytic N-terminal SH2 domain of PTPN11 (Hof 1998), and several additional variants in neighboring codons have also been identified in Noonan patients (Jongmans 2011, Tartaglia 2002, Tartaglia 2006). -
Difference Between Dyslipidemia and Hyperlipidemia Key Difference – Dyslipidemia Vs Hyperlipidemia
Difference Between Dyslipidemia and Hyperlipidemia www.differenebetween.com Key Difference – Dyslipidemia vs Hyperlipidemia Dyslipidemia and hyperlipidemia are two medical conditions that affect the lipid levels of the body. Any deviation of the lipid level of the body from the normal and clinically appropriate values is identified as dyslipidemia. Hyperlipidemia is a form of dyslipidemia where the lipid levels are abnormally elevated. The key difference between dyslipidemia and hyperlipidemia is that dyslipidemia refers to any abnormality in the lipid levels whereas hyperlipidemia refers to an abnormal elevation in the lipid level. What is Dyslipidemia? Any abnormality in the lipid levels of the body is identified as dyslipidemia. Different forms of dyslipidemia include Hyperlipidemia Hypolipidemia Lipid levels of the body are abnormally reduced in this condition. Severe protein energy malnutrition, severe malabsorption, and intestinal lymphangiectasia are the causes. Hypolipoproteinemia This disease is caused by genetic or acquired causes. The familial form of hypolipoproteinemia is asymptomatic and does not require treatments. But there are some other forms of this condition which are extremely severe. Genetic disorders associated with this condition are, Abeta lipoproteinemia Familial hypobetalipoproteinemia Chylomicron retention disease Lipodystrophy Lipomatosis Dyslipidemia in pregnancy What is Hyperlipidemia? Hyperlipidemia is a form of dyslipidemia that is characterized by abnormally elevated lipid levels. Primary Hyperlipidemia Primary hyperlipidemias are due to a primary defect in the lipid metabolism. Classification Disorders of VLDL and chylomicrons- hypertriglyceridemia alone The commonest cause of these disorders is the genetic defects in multiple genes. There is a modest increase in the VLDL level. Disorders of LDL- hypercholesterolemia alone There are several subgroups of this category Heterozygous Familial Hypercholesterolemia This is a fairly common autosomal dominant monogenic disorder. -
NGS Panels 2020
NGS Panels 2020 BENEFIT FROM OUR MEDICAL EXPERTISE AND STREAMLINED GENETIC TESTING NGS Panels 2020 Benefit from our Medical Expertise and Streamlined Genetic Testing CENTOGENE is fully committed to bringing the best possible diagnostic solutions to our patients and their families. We always strive to incorporate the latest in-house findings and medical research in our products to improve and ease the diagnostic odyssey of rare disease patients. To reflect the fast-growing knowledge of complex associations of genes with diseases as well as to maximize clinical sensitivity, we have updated and significantly redesigned our Next Generation Sequencing (NGS) gene panels. The gene composition of each panel has been revised to meet the latest gene discoveries as well as to provide the highest clinical validity. Additionally, we have minimized complexity and removed redundancy in the panel portfolio by creating phenotype-directed diagnostic panels, which are the most comprehensive and include all relevant genes necessary for differential diagnosis of syndromes with overlapping phenotype, therefore allowing the diagnosis of diseases that otherwise would be missed. This principle increases the clinical utility, de-risks panel choice, increases cost-effectiveness, and ultimately simplifies the diagnostic process. When choosing one of our NGS panels, feel confident that you will receive high-quality sequencing combined with best data analysis and interpretation, which are documented in comprehensive medical reports. As always, CENTOGENE and our Customer -
Revista2vol87ingle Snaza Layout 1
324 SYNDROME IN QUESTION ▲ Do you know this syndrome? * Você conhece esta síndrome? Aristóteles Rosmaninho 1 Teresa Pinto-Almeida 2 Iolanda Conde Fernandes 3 Susana Machado 4 Manuela Selores 5 CASE REPORT A 65 year-old man presented for evaluation of lesions were observed in his two brothers and father. multiple widespread nodules in his body. The lesions Some lesions were surgically excised because they were long standing and began during his childhood. caused functional discomfort. The histopathological More lesions appeared over time. On physical exami- examination showed the presence of globules of nation multiple, subcutaneous, soft, mobile and non mature white adipose tissue surrounded by thin painful nodules and tumors were observed in the fibrous capsules. The analytical study showed no sig- arms, legs and abdomen distorting the affected areas nificant abnormalities including lipid abnormalities. (Figures 1, 2 and 3). His past medical history was Based on the characteristic clinical history, family his- remarkable for diabetes mellitus and hepatocarcino- tory and histopathology the diagnosis of familial mul- ma secondary to chronic HBV infection. He denied tiple lipomatosis (FML) was made. alcohol consumption. Similar but less extensive A B C FIGURE 1: Multiple subcutaneous lesions in the abdomen FIGURE 2: Multiple subcutaneous lesions in the arms A B C FIGURE 3: Subcutaneous lesions in the legs Received on 03.08.2011. Approved by the Advisory Board and accepted for publication on 22.11.2011. * Work carried out at the Centro Hospitalar do Porto-Hospital de Santo António (EPE-HSA) - Porto, Portugal. Conflict of interest: None / Conflito de interesse: Nenhum Financial funding: None / Suporte financeiro: Nenhum 1 Intern in Dermatovenereology - Centro Hospitalar do Porto-Hospital de Santo António (EPE-HSA) - Porto, Portugal. -
Blueprint Genetics Noonan Syndrome Panel
Noonan Syndrome Panel Test code: CA0501 Is a 35 gene panel that includes assessment of non-coding variants. Is ideal for patients with a clinical suspicion of a RASopathy including Noonan syndrome with or without lentigines, cardio- facio-cutaneous (CFC) syndrome, Costello syndrome, Noonan-like syndromes or other syndromes causing differential diagnostic challenges such as Legius syndrome, Baraitser-Winter syndromes and neurofibromatosis. About Noonan Syndrome Noonan syndrome is one of the most common syndromes with an estimated prevalence of 1 in 1,000 to 1 in 2,500 live births. It is clinically and genetically heterogeneous condition characterized by cardiovascular abnormalities, distinctive facial features, chest deformity, short stature, and other co-morbidities. Among the Noonan syndrome associated genes, many different genotype-phenotype correlations have been established although no phenotypic features are exclusively associated with one genotype. There are, however, significant differences in the risk of various Noonan syndrome manifestations based on the causative gene. Availability 4 weeks Gene Set Description Genes in the Noonan Syndrome Panel and their clinical significance Gene Associated phenotypes Inheritance ClinVar HGMD ACTB* Baraitser-Winter syndrome AD 55 60 ACTG1* Deafness, Baraitser-Winter syndrome AD 27 47 BRAF* LEOPARD syndrome, Noonan syndrome, Cardiofaciocutaneous syndrome AD 134 65 CBL Noonan syndrome-like disorder with or without juvenile myelomonocytic AD 24 43 leukemia CCNK Intellectual disability AD CDC42 -
Sequence Diversity in Genes of Lipid Metabolism Christine Kim Garcia,1 Gabriele Mues,2 Yuanlan Liao,1 Tommy Hyatt,1 Nila Patil,3 Jonathan C
Downloaded from genome.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Sequence Diversity in Genes of Lipid Metabolism Christine Kim Garcia,1 Gabriele Mues,2 Yuanlan Liao,1 Tommy Hyatt,1 Nila Patil,3 Jonathan C. Cohen,1 andHelen H. Hobbs 1,4 Departments of 1Internal Medicine and Molecular Genetics and 2Pathology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9046, USA; 3Affymetrix, Inc., Santa Clara, California 95051, USA Elevated plasma lipoprotein levels play a crucial role in the development of coronary artery disease. Genetic factors strongly influence the levels of plasma lipoproteins, but the genes and sequence variations contributing to the most common forms of dyslipidemias are not known. We used GeneChip probe arrays to resequence the coding regions of 10 key genes of lipid metabolism. The sequences of these genes were analyzed in 80 dyslipidemic individuals. Fourteen nonsynonymous and twenty-two synonymous single nucleotide changes were identified that could be confirmed by conventional sequencing. Seven of the fourteen nonsynonymous sequence variants were polymorphisms with allele frequency >1% in the general population. The remaining seven were not found in normolipidemic controls (25 Caucasians and 25 African-Americans). The relationship between nonsynonymous sequence variations and various dyslipidemias was explored in association and family studies. No evidence was found for coding sequence variations in any of the 10 genes contributing to dyslipidemia. Only a single sequence variation, a missense mutation in the low density lipoprotein receptor gene, co-segregated with hyperlipidemia in the proband’s family. This study illustrates some of the difficulties associated with identifying sequence variations contributing to complex traits.