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The Advantage of Genome-Wide Microarrays Over Targeted Approaches
PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/70828 Please be advised that this information was generated on 2021-09-24 and may be subject to change. COPY NUMBER VARIATION AND MENTAL RETARDATION opmaak koolen.indd 1 10-09-2008 10:11:31 Copy number variation and mental retardation The studies presented in this thesis were performed at the Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands. The research was supported by a grant from the Netherlands Organization for Health Research and Development (ZonMw). Publication of this thesis was financially supported by the Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands. ISBN/EAN 978-90-6464-290-6 © 2008 D.A. Koolen All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, by print or otherwise, without permission in writing from the author. Cover photo: Printed by: Ponsen & Looijen B.V., Wageningen opmaak koolen.indd 2 10-09-2008 10:11:31 Copy number variation and mental retardation Een wetenschappelijke proeve op het gebied van de Medische Wetenschappen Proefschrift ter verkrijging van de graad doctor aan de Radboud Universiteit Nijmegen op gezag van de rector magnificus prof. mr. S.C.J.J. Kortmann, volgens besluit van het College van Decanen in het openbaar te verdedigen op donderdag 6 november 2008 om 15.30 uur precies door David Aljosja Koolen geboren op 22 juni 1976 te ‘s-Gravenhage opmaak koolen.indd 3 10-09-2008 10:11:32 Promotor: Prof. -
Soft Tissue Cytopathology: a Practical Approach Liron Pantanowitz, MD
4/1/2020 Soft Tissue Cytopathology: A Practical Approach Liron Pantanowitz, MD Department of Pathology University of Pittsburgh Medical Center [email protected] What does the clinician want to know? • Is the lesion of mesenchymal origin or not? • Is it begin or malignant? • If it is malignant: – Is it a small round cell tumor & if so what type? – Is this soft tissue neoplasm of low or high‐grade? Practical diagnostic categories used in soft tissue cytopathology 1 4/1/2020 Practical approach to interpret FNA of soft tissue lesions involves: 1. Predominant cell type present 2. Background pattern recognition Cell Type Stroma • Lipomatous • Myxoid • Spindle cells • Other • Giant cells • Round cells • Epithelioid • Pleomorphic Lipomatous Spindle cell Small round cell Fibrolipoma Leiomyosarcoma Ewing sarcoma Myxoid Epithelioid Pleomorphic Myxoid sarcoma Clear cell sarcoma Pleomorphic sarcoma 2 4/1/2020 CASE #1 • 45yr Man • Thigh mass (fatty) • CNB with TP (DQ stain) DQ Mag 20x ALT –Floret cells 3 4/1/2020 Adipocytic Lesions • Lipoma ‐ most common soft tissue neoplasm • Liposarcoma ‐ most common adult soft tissue sarcoma • Benign features: – Large, univacuolated adipocytes of uniform size – Small, bland nuclei without atypia • Malignant features: – Lipoblasts, pleomorphic giant cells or round cells – Vascular myxoid stroma • Pitfalls: Lipophages & pseudo‐lipoblasts • Fat easily destroyed (oil globules) & lost with preparation Lipoma & Variants . Angiolipoma (prominent vessels) . Myolipoma (smooth muscle) . Angiomyolipoma (vessels + smooth muscle) . Myelolipoma (hematopoietic elements) . Chondroid lipoma (chondromyxoid matrix) . Spindle cell lipoma (CD34+ spindle cells) . Pleomorphic lipoma . Intramuscular lipoma Lipoma 4 4/1/2020 Angiolipoma Myelolipoma Lipoblasts • Typically multivacuolated • Can be monovacuolated • Hyperchromatic nuclei • Irregular (scalloped) nuclei • Nucleoli not typically seen 5 4/1/2020 WD liposarcoma Layfield et al. -
Whole Chromosome Gain Does Not in Itself Confer Cancer-Like Chromosomal Instability
Whole chromosome gain does not in itself confer cancer-like chromosomal instability Anders Valinda,1, Yuesheng Jina, Bo Baldetorpb, and David Gisselssona aDepartment of Clinical Genetics, Lund University, University and Regional Laboratories, Biomedical Center B13, Lund SE22184, Sweden; and bDepartment of Oncology, Lund University, Skåne University Hospital, Lund SE22185, Sweden Edited* by George Klein, Karolinska Institutet, Stockholm, Sweden, and approved November 4, 2013 (received for review June 12, 2013) Constitutional aneuploidy is typically caused by a single-event and chromosomal instability in humans is using constitutional meiotic or early mitotic error. In contrast, somatic aneuploidy, aneuploidy syndromes as a model. Cells from patients with these found mainly in neoplastic tissue, is attributed to continuous syndromes provide a good experimental system for studying the chromosomal instability. More debated as a cause of aneuploidy effects of aneuploidy on overall genome stability on representative is aneuploidy itself; that is, whether aneuploidy per se causes human material. Such cells typically only have a single or a limited chromosomal instability, for example, in patients with inborn set of stem-line chromosome aberrations compared with tumor aneuploidy. We have addressed this issue by quantifying the level cell lines, which typically harbor a multitude of genetic lesions, as of somatic mosaicism, a proxy marker of chromosomal instability, well as a cancer phenotype. The few earlier studies performed on in patients with -
Well-Differentiated Spindle Cell Liposarcoma
Modern Pathology (2010) 23, 729–736 & 2010 USCAP, Inc. All rights reserved 0893-3952/10 $32.00 729 Well-differentiated spindle cell liposarcoma (‘atypical spindle cell lipomatous tumor’) does not belong to the spectrum of atypical lipomatous tumor but has a close relationship to spindle cell lipoma: clinicopathologic, immunohistochemical, and molecular analysis of six cases Thomas Mentzel1, Gabriele Palmedo1 and Cornelius Kuhnen2 1Dermatopathologie, Friedrichshafen, Germany and 2Institute of Pathology, Medical Center, Mu¨nster, Germany Well-differentiated spindle cell liposarcoma represents a rare atypical/low-grade malignant lipogenic neoplasm that has been regarded as a variant of atypical lipomatous tumor. However, well-differentiated spindle cell liposarcoma tends to occur in subcutaneous tissue of the extremities, the trunk, and the head and neck region, contains slightly atypical spindled tumor cells often staining positively for CD34, and lacks an amplification of MDM2 and/or CDK4 in most of the cases analyzed. We studied a series of well-differentiated spindle cell liposarcomas arising in two female and four male patients (age of the patients ranged from 59 to 85 years). The neoplasms arose on the shoulder, the chest wall, the thigh, the lower leg, the back of the hand, and in paratesticular location. The size of the neoplasms ranged from 1.5 to 10 cm (mean: 6.0 cm). All neoplasms were completely excised. The neoplasms were confined to the subcutis in three cases, and in three cases, an infiltration of skeletal muscle was seen. Histologically, the variably cellular neoplasms were composed of atypical lipogenic cells showing variations in size and shape, and spindled tumor cells with slightly enlarged, often hyperchromatic nuclei. -
TERT Promoter Mutations Occur Frequently in Gliomas and a Subset of Tumors Derived from Cells with Low Rates of Self-Renewal
TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal Patrick J. Killelaa,1, Zachary J. Reitmana,1, Yuchen Jiaob,1, Chetan Bettegowdab,c,1, Nishant Agrawalb,d, Luis A. Diaz, Jr.b, Allan H. Friedmana, Henry Friedmana, Gary L. Galliac,d, Beppino C. Giovanellae, Arthur P. Grollmanf, Tong-Chuan Heg, Yiping Hea, Ralph H. Hrubanh, George I. Jalloc, Nils Mandahli, Alan K. Meekerh,m, Fredrik Mertensi, George J. Nettoh,l, B. Ahmed Rasheeda, Gregory J. Rigginsc, Thomas A. Rosenquistf, Mark Schiffmanj, Ie-Ming Shihh, Dan Theodorescuk, Michael S. Torbensonh, Victor E. Velculescub, Tian-Li Wangh, Nicolas Wentzensenj, Laura D. Woodh, Ming Zhangb, Roger E. McLendona, Darell D. Bignera, Kenneth W. Kinzlerb, Bert Vogelsteinb,2, Nickolas Papadopoulosb, and Hai Yana,2 aThe Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, NC 27710; bLudwig Center for Cancer Genetics and Howard Hughes Medical Institutions, Johns Hopkins Kimmel Cancer Center, Johns Hopkins Medical Institutions, Baltimore, MD 21231; Departments of cNeurosurgery, dOtolaryngology—Head and Neck Surgery, hPathology, lUrology, and mOncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231; eChristus Stehlin Foundation for Cancer Research, Houston, TX 77025; fDepartment of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794; gMolecular Oncology Laboratory, Department of Orthopaedic -
Spindle Cell Liposarcoma with a TRIO-TERT Fusion Transcript
Virchows Archiv (2019) 475:391–394 https://doi.org/10.1007/s00428-019-02545-5 BRIEF REPORTS Spindle cell liposarcoma with a TRIO-TERT fusion transcript David I. Suster1 & Vikram Deshpande1 & Ivan Chebib1 & Martin S. Taylor1 & John Mullen2 & Miriam A. Bredella3 & G. Petur Nielsen1 Received: 7 January 2019 /Revised: 8 February 2019 /Accepted: 11 February 2019 /Published online: 22 February 2019 # Springer-Verlag GmbH Germany, part of Springer Nature 2019 Abstract Conventional well-differentiated, dedifferentiated, and myxoid liposarcomas have long been known to harbor numerous typical genetic alterations that allow for diagnosis of these tumors. These include MDM2 and CDK4 amplification in well-differentiated and dedifferentiated liposarcomas as well as FUS-DDIT3 rearrangements in myxoid liposarcoma. More recently, in-frame TRIO- TERT fusion genes have been described in a subset of non-translocation-related sarcomas including myxofibrosarcoma, dedifferentiated liposarcoma, undifferentiated pleomorphic sarcoma, pleomorphic rhabdomyosarcoma, and leiomyosarcoma. These genetic rearrangements lead to TERT mRNA expression levels hundreds of times higher than normal, causing increased telomerase activation in these tumors. Herein, we describe an unusual case of a liposarcoma with spindle cell features and a TRIO-TERT fusion transcript identified through next-generation sequencing. Keywords Liposarcoma . TRIO-TERT . Fusion transcript The current classification of spindle cell lipomatous neoplasms Recently, a novel in-frame TRIO-TERT fusion has been is still evolving. In the literature, the term Bspindle cell identified in some non-translocation-related sarcomas [6]. liposarcoma^ has been used to describe many tumors including TRIO plays an important role in cell adhesion and nuclear spindled variants of well-differentiated liposarcoma and signaling pathways and is part of a family of Rho GTPases myxoid liposarcoma, as well as spindle cell lipomas with that act as guanine nucleotide exchange factors [7]. -
95 Birth Defects Exec Summ
Executive Summary In 1995, 865 cases of birth defects were detected among live born infants and fetuses of 20 or more weeks gestation delivered to mothers residing in Texas Public Health Regions 6 and 11 (Houston/Galveston region and Lower Rio Grande Valley). In this first full year of the Registry, surveillance was limited to approximately 23 major categories of birth defects, comprising 30 to 40 percent of all known structural malformations. Down syndrome, oral clefts, and spina bifida were the most common birth defects, although some major structural malformations were not yet monitored in 1995. Age Patterns: Both trisomy 21 (Down syndrome) and trisomy 18 (Edwards syndrome) demonstrated an age-specific rate pattern that was J-shaped, with the highest birth prevalence (“rates”) observed among mothers 35 years of age and older. Gastroschisis, a malformation of the abdominal wall, exhibited highest rates among the youngest mothers and decreased with each older age group. Racial/Ethnic Patterns: Anencephaly and spina bifida were lowest among African Americans; however, rates were similar in whites and Hispanics. Among the heart defects, relatively high rates of tetralogy of Fallot were observed among African Americans, although they exhibited relatively low rates of hypoplastic left heart. Cleft palate alone was more likely to occur among whites and Hispanics. Rates of trisomy 18 (Edwards syndrome) were highest among African Americans and whites. Gender Patterns: With regard to sex, higher rates were documented among females for anencephaly, and to a lesser extent, spina bifida. Females experienced two-fold higher rates of trisomy 18 (Edwards syndrome). Males had higher rates of cleft lip with or without cleft palate. -
Pathology and Genetics of Tumours of Soft Tissue and Bone
bb5_1.qxd 13.9.2006 14:05 Page 3 World Health Organization Classification of Tumours WHO OMS International Agency for Research on Cancer (IARC) Pathology and Genetics of Tumours of Soft Tissue and Bone Edited by Christopher D.M. Fletcher K. Krishnan Unni Fredrik Mertens IARCPress Lyon, 2002 bb5_1.qxd 13.9.2006 14:05 Page 4 World Health Organization Classification of Tumours Series Editors Paul Kleihues, M.D. Leslie H. Sobin, M.D. Pathology and Genetics of Tumours of Soft Tissue and Bone Editors Christopher D.M. Fletcher, M.D. K. Krishnan Unni, M.D. Fredrik Mertens, M.D. Coordinating Editor Wojciech Biernat, M.D. Layout Lauren A. Hunter Illustrations Lauren A. Hunter Georges Mollon Printed by LIPS 69009 Lyon, France Publisher IARCPress International Agency for Research on Cancer (IARC) 69008 Lyon, France bb5_1.qxd 13.9.2006 14:05 Page 5 This volume was produced in collaboration with the International Academy of Pathology (IAP) The WHO Classification of Tumours of Soft Tissue and Bone presented in this book reflects the views of a Working Group that convened for an Editorial and Consensus Conference in Lyon, France, April 24-28, 2002. Members of the Working Group are indicated in the List of Contributors on page 369. bb5_1.qxd 22.9.2006 9:03 Page 6 Published by IARC Press, International Agency for Research on Cancer, 150 cours Albert Thomas, F-69008 Lyon, France © International Agency for Research on Cancer, 2002, reprinted 2006 Publications of the World Health Organization enjoy copyright protection in accordance with the provisions of Protocol 2 of the Universal Copyright Convention. -
Application of Neural Networks for Classification of Patau, Edwards
Catic et al. BMC Medical Genomics (2018) 11:19 DOI 10.1186/s12920-018-0333-2 RESEARCHARTICLE Open Access Application of Neural Networks for classification of Patau, Edwards, Down, Turner and Klinefelter Syndrome based on first trimester maternal serum screening data, ultrasonographic findings and patient demographics Aida Catic1,2* , Lejla Gurbeta1,4, Amina Kurtovic-Kozaric1,3, Senad Mehmedbasic2 and Almir Badnjevic1,4,5,6 Abstract Background: The usage of Artificial Neural Networks (ANNs) for genome-enabled classifications and establishing genome-phenotype correlations have been investigated more extensively over the past few years. The reason for this is that ANNs are good approximates of complex functions, so classification can be performed without the need for explicitly defined input-output model. This engineering tool can be applied for optimization of existing methods for disease/syndrome classification. Cytogenetic and molecular analyses are the most frequent tests used in prenatal diagnostic for the early detection of Turner, Klinefelter, Patau, Edwards and Down syndrome. These procedures can be lengthy, repetitive; and often employ invasive techniques so a robust automated method for classifying and reporting prenatal diagnostics would greatly help the clinicians with their routine work. Methods: The database consisted of data collected from 2500 pregnant woman that came to the Institute of Gynecology, Infertility and Perinatology “Mehmedbasic” for routine antenatal care between January 2000 and December 2016. During first trimester all women were subject to screening test where values of maternal serum pregnancy- associated plasma protein A (PAPP-A) and free beta human chorionic gonadotropin (β-hCG) were measured. Also, fetal nuchal translucency thickness and the presence or absence of the nasal bone was observed using ultrasound. -
SUPPORTING FAMILIES, CELEBRATING LIVES a WORD from 2 Our Chair
SUMMER 2019 Soft UK SUPPORTING FAMILIES, CELEBRATING LIVES A WORD FROM 2 Our Chair Welcome to a packed newsletter, full to participate of family stories, information and in some work updates. We hope you enjoy reading being carried and finding out what is going on in out by the University of Leeds, into the world of SOFT UK! the delivery of challenging news There is so much in these pages but after ultrasound scan. They are I would just like to highlight one focusing on identifying the specific article – the blog that Alison Pearson words, phrases and behaviours that (mum to Isabel) has written, with sonographers should use to deliver another mum of a little girl with different types of unexpected or Down’s syndrome, for Public Health challenging news that they identify England on the use of language. during ultrasound. Interestingly, there is no widespread agreement on We know that the words we speak how this should be done. The result can leave a huge impact and create is that sonographers often decide a lasting memory - either good or for themselves what works best, and bad; for those who hear them. Joel their conclusions are not always in Osteen said: "Be careful what you line with parent preferences. say. You can say something hurtful One, small step, but hopefully we in ten seconds, but ten years later, can get your views and experiences the wounds are still there." We hear across and make a difference for that from many families when they families in the future. talk of how they were told of a high Enjoy the rest of the newsletter risk or diagnosis of Trisomy, or when and do keep letting us know your medical professionals talk about the feedback, contributions and ideas for future for their child with Edwards’ or future editions. -
Double Aneuploidy in Down Syndrome
Chapter 6 Double Aneuploidy in Down Syndrome Fatma Soylemez Additional information is available at the end of the chapter http://dx.doi.org/10.5772/60438 Abstract Aneuploidy is the second most important category of chromosome mutations relat‐ ing to abnormal chromosome number. It generally arises by nondisjunction at ei‐ ther the first or second meiotic division. However, the existence of two chromosomal abnormalities involving both autosomal and sex chromosomes in the same individual is relatively a rare phenomenon. The underlying mechanism in‐ volved in the formation of double aneuploidy is not well understood. Parental ori‐ gin is studied only in a small number of cases and both nondisjunctions occurring in a single parent is an extremely rare event. This chapter reviews the characteristics of double aneuploidies in Down syndrome have been discussed in the light of the published reports. Keywords: Double aneuploidy, Down Syndrome, Klinefelter Syndrome, Chromo‐ some abnormalities 1. Introduction With the discovery in 1956 that the correct chromosome number in humans is 46, the new area of clinical cytogenetic began its rapid growth. Several major chromosomal syndromes with altered numbers of chromosomes were reported, such as Down syndrome (trisomy 21), Turner syndrome (45,X) and Klinefelter syndrome (47,XXY). Since then it has been well established that chromosome abnormalities contribute significantly to genetic disease resulting in reproductive loss, infertility, stillbirths, congenital anomalies, abnormal sexual development, mental retardation and pathogenesis of malignancy [1]. Clinical features of patients with common autosomal or sex chromosome aneuploidy is shown in Table 1. © 2015 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -
The Combined Test
Antenatal Screening Antenatal Screening for Down's syndrome, Edwards syndrome and Patau syndrome The Combined Test Questions and Answers for women considering the test The Wolfson Institute of Preventive Medicine Barts and The London School of Medicine and Dentistry Antenatal Screening This leaflet answers some of the common questions women ask about their screening test – we hope you find it helpful. You are welcome to discuss the test with your midwife or consultant before you decide whether you would like to be screened. If you have any further questions screening staff at the Wolfson Institute are available to talk to you on 020 7882 6293. What is Down's syndrome? What are Edwards and Patau syndrome? Down's syndrome (trisomy 21) is Edwards syndrome (trisomy 18) is defined by the presence of an extra defined by the presence of an extra chromosome number 21 in the cells chromosome number 18 in the cells of the fetus or affected individual. In of the fetus or affected individual an unscreened population about 1 in while Patau syndrome (trisomy 13) every 500 babies is born with Down's is defined by an extra chromosome syndrome. Usually it is not inherited number 13 in the cells of the fetus or and so a baby can be affected affected individual. Both syndromes even if there is no history of Down's affect multiple organs with a high risk syndrome in the family. of fetal death. Down's syndrome is the most At 12 weeks of pregnancy Edwards common cause of severe learning syndrome has a prevalence of about disability and is often associated 1 in 1,500 and Patau syndrome has a with physical problems such as heart prevalence of about 1 in 3,500 in an defects and difficulties with sight and unscreened population.