Malformation Variability Associated to Chromosome Trisomies
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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. -
Genetic Causes.Pdf
1 September 2015 Genetic causes of childhood apraxia of speech: Case‐based introduction to DNA, inheritance, and clinical management Beate Peter, Ph.D., CCC‐SLP Assistant Professor Dpt. of Speech & Hearing Science Arizona State University Adjunct Assistant Professor AG Dpt. of Communication Sciences & Disorders ATAGCT Saint Louis University T TAGCT Affiliate Assistant Professor Dpt. of Speech & Hearing Sciences University of Washington 1 Disclosure Statement Disclosure Statement Dr. Peter is co‐editor of a textbook on speech development and disorders (B. Peter & A. MacLeod, Eds., 2013), for which she may receive royalty payments. If she shares information about her ongoing research study, this may result in referrals of potential research participants. She has no financial interest or related personal interest of bias in any organization whose products or services are described, reviewed, evaluated or compared in the presentation. 2 Agenda Topic Concepts Why we should care about genetics. Case 1: A sporadic case of CAS who is missing a • Cell, nucleus, chromosomes, genes gene. Introduction to the language of genetics • From genes to proteins • CAS can result when a piece of DNA is deleted or duplicated Case 2: A multigenerational family with CAS • How the FOXP2 gene was discovered and why research in genetics of speech and language disorders is challenging • Pathways from genes to proteins to brain/muscle to speech disorder Case 3: One family's quest for answers • Interprofessional teams, genetic counselors, medical geneticists, research institutes • Early signs of CAS, parent education, early intervention • What about genetic testing? Q&A 3 “Genetic Causes of CAS: Case-Based Introduction to DNA, Inheritance and Clinical Management,” Presented by: Beate Peter, PhD, CCC-SLP, September 29, 2015, Sponsored by: CASANA 2 Why should you care about genetics? 4 If you are a parent of a child with childhood apraxia of speech … 5 When she was in preschool, He doesn’t have any friends. -
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 -
Chromosome Analysis of Single Cells by High Resolution Comparative Genomic Hybridization After Whole Genome Amplifi Cation Using a Random Fragmentation Approach
Chromosome Analysis of Single Cells by High Resolution Comparative Genomic Hybridization after Whole Genome Amplifi cation Using a Random Fragmentation Approach. Brynn Levy 1, Odelia Nahum 2, Kurt Hirschhorn 2 (1) Department of Pathology, College of Physicians and Surgeons of Columbia University, New York, NY (2) Department of Pediatrics, Mount Sinai School of Medicine, New York, NY Introduction Results The preparation of prometaphase/metaphase spreads is an essential part of WGA followed by CGH was performed on single cells obtained from chromosome analysis. Most samples received for cytogenetic study do not 36 random specimen cultures. The specimens analyzed included normal have a signifi cant number of actively dividing cells that can be arrested in the males, normal females, various trisomies (4, 10, 11, 13, 14, 16 and 21), an prometaphase/metaphase stage of the cell cycle and thus require cell culturing. unbalanced translocation and an iso-22 chromosome (Table 1). There were no Single fetal cells derived from a 2–3 day old embryo or from the maternal false negatives and the correct sex and diagnosis was made in 36/36 cases at circulation can therefore not be karyotyped in the traditional way. Fluorescence 99% confi dence, in 35/36 cases at 99.9% confi dence and in 33/36 cases at in situ hybridization (FISH) with chromosome specifi c probes can enumerate 99.99% confi dence (Table 1). Certain artifactual abnormalities were observed individual chromosomes in an interphase cell and it is now possible through a in addition to the true abnormality in some cases and the impact of these still process of combinatorial labeling to produce 24 differentially colored human needs to be determined in a larger test series. -
Sema4 Noninvasive Prenatal Select
Sema4 Noninvasive Prenatal Select Noninvasive prenatal testing with targeted genome counting 2 Autosomal trisomies 5 Trisomy 21 (Down syndrome) 6 Trisomy 18 (Edwards syndrome) 7 Trisomy 13 (Patau syndrome) 8 Trisomy 16 9 Trisomy 22 9 Trisomy 15 10 Sex chromosome aneuploidies 12 Monosomy X (Turner syndrome) 13 XXX (Trisomy X) 14 XXY (Klinefelter syndrome) 14 XYY 15 Microdeletions 17 22q11.2 deletion 18 1p36 deletion 20 4p16 deletion (Wolf-Hirschhorn syndrome) 20 5p15 deletion (Cri-du-chat syndrome) 22 15q11.2-q13 deletion (Angelman syndrome) 22 15q11.2-q13 deletion (Prader-Willi syndrome) 24 11q23 deletion (Jacobsen Syndrome) 25 8q24 deletion (Langer-Giedion syndrome) 26 Turnaround time 27 Specimen and shipping requirements 27 2 Noninvasive prenatal testing with targeted genome counting Sema4’s Noninvasive Prenatal Testing (NIPT)- Targeted Genome Counting analyzes genetic information of cell-free DNA (cfDNA) through a simple maternal blood draw to determine the risk for common aneuploidies, sex chromosomal abnormalities, and microdeletions, in addition to fetal gender, as early as nine weeks gestation. The test uses paired-end next-generation sequencing technology to provide higher depth across targeted regions. It also uses a laboratory-specific statistical model to help reduce false positive and false negative rates. The test can be offered to all women with singleton, twins and triplet pregnancies, including egg donor. The conditions offered are shown in below tables. For multiple gestation pregnancies, screening of three conditions -
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. -
Maternal Age, History of Miscarriage, and Embryonic/Fetal Size Are Associated with Cytogenetic Results of Spontaneous Early Miscarriages
Journal of Assisted Reproduction and Genetics (2019) 36:749–757 https://doi.org/10.1007/s10815-019-01415-y GENETICS Maternal age, history of miscarriage, and embryonic/fetal size are associated with cytogenetic results of spontaneous early miscarriages Nobuaki Ozawa1 & Kohei Ogawa1 & Aiko Sasaki1 & Mari Mitsui1 & Seiji Wada1 & Haruhiko Sago1 Received: 1 October 2018 /Accepted: 28 January 2019 /Published online: 9 February 2019 # Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Purpose To clarify the associations of the maternal age, history of miscarriage, and embryonic/fetal size at miscarriage with the frequencies and profiles of cytogenetic abnormalities detected in spontaneous early miscarriages. Methods Miscarriages before 12 weeks of gestation, whose karyotypes were evaluated by G-banding between May 1, 2005, and May 31, 2017, were included in this study. The relationships between their karyotypes and clinical findings were assessed using trend or chi-square/Fisher’s exact tests and multivariate logistic analyses. Results Three hundred of 364 miscarriage specimens (82.4%) had abnormal karyotypes. An older maternal age was significantly associated with the frequency of abnormal karyotype (ptrend < 0.001), particularly autosomal non-viable and viable trisomies (ptrend 0.001 and 0.025, respectively). Women with ≥ 2 previous miscarriages had a significantly lower possibility of miscarriages with abnormal karyotype than women with < 2 previous miscarriages (adjusted odds ratio [aOR], 0.48; 95% confidence interval [95% CI], 0.27–0.85). Although viable trisomy was observed more frequently in proportion to the increase in embryonic/fetal size at miscarriage (ptrend < 0.001), non-viable trisomy was observed more frequently in miscarriages with an embryonic/fetal size < 10 mm (aOR, 2.41; 95% CI, 1.27–4.58), but less frequently in miscarriages with an embryonic/fetal size ≥ 20 mm (aOR, 0.01; 95% CI, 0.00–0.07) than in anembryonic miscarriages. -
Inside This Issue
Winter 2014 No. 77 Inside this issue Group News | Fundraising | Members’ Letters | One Family Living with Two Different Chromosome Disorders | Bristol Conference 2014 | Unique Leaflets | Christmas Card Order Form Sophie, Unique’s Chair of Trustees Dear Members, In the past month a few things have reminded me of why it is so important to make connections through Unique but also to draw support from other parents around us. I’ve just returned from Unique’s most recent family conference in Bristol where 150 of us parents and carers had a lovely time in workshops, meals and activities, chatting and watching our children milling around together like one big family since – although we had never met before – we have shared so many experiences in common. However in contrast I have also just met a new mum who has just moved to my area from far away with two toddlers, one with a rare joys of the internet, it is becoming easier to meet others with similar, chromosome disorder, who is starting from scratch with no even very rare, chromosome disorders around the world and to find professional, medical or social support. She reminds me of how yourself talking to them in the middle of the night about some lonely I felt when Max was newly diagnosed, when I knew no one interesting things our children share in common (obsession with with a disabled child let alone anyone with a rare chromosome catalogues, anyone?) And of course we also have an enormous disorder. Elsewhere our latest Unique Facebook group, Unique amount in common with so many parents of children with other Russia, is also just starting up – so far it includes just a small special needs or disabilities around us in our own communities who number of members sharing very different experiences to mine here will often be walking the same path as us. -
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. -
©Ferrata Storti Foundation
Haematologica 2000; 85:1207-1210 Acute Leukemias case of the month Cytogenetic characterization of acute myeloid leukemia in Shwachman's syndrome. A case report FRANCESCA R. SPIRITO, BARBARA CRESCENZI, CATERINA MATTEUCCI, MASSIMO F. MARTELLI, CRISTINA MECUCCI Hematology and Bone Marrow Transplantation Unit, University of Perugia, Italy ABSTRACT We report on a case of acute myeloid leukemia in a tion. A recent analysis of 21 patients with SDS 17-year old boy affected by Shwachman Diamond showed that the incidence of myelodysplasia syndrome (SDS). Conventional cytogenetics at diag- and transformation to acute myeloid leukemia nosis revealed an abnormal clone with complex 4 karyotypic changes including typical myeloid aber- is 33% and 24%, respectively. A few cases of rations, such as monosomy 5, tetrasomy of chro- acute lymphoblastic leukemia have also been 5-7 mosome 8, trisomy 9, and deletion of the short arm described as well as one case of a juvenile form of chromosome 12. The boy was treated with con- of chronic myeloid leukemia.8 When leukemia ventional chemotherapy and reached complete develops, due to the preceding bone marrow remission of leukemia, confirmed by cytogenetics failure, serious complications may be induced and fluorescence in situ hybridization. Nevertheless by chemotherapy and, because of the underly- he failed to regenerate normal marrow cellularity ing organ dysfunctions, these patients should and blood cell count. Cytogenetic information on be managed with extreme caution when treat- hematologic malignancies in SDS patients are dis- cussed. ed with allogeneic bone marrow transplanta- 9-13 ©2000; Ferrata Storti Foundation tion. We describe here the cytogenetic char- acterization and clinical course of an acute Key words: Shwachman’s syndrome, leukemia, cytogenetics myeloid leukemia occurring in a young patient affected by Shwachman's syndrome. -
Genetic and Expression Analysis of HER-2 and EGFR Genes in Salivary Duct Carcinoma: Empirical and Therapeutic Significance
Published OnlineFirst April 14, 2010; DOI: 10.1158/1078-0432.CCR-09-0238 Clinical Human Cancer Biology Cancer Research Genetic and Expression Analysis of HER-2 and EGFR Genes in Salivary Duct Carcinoma: Empirical and Therapeutic Significance Michelle D. Williams1, Dianna B. Roberts2, Merrill S. Kies3, Li Mao3, Randal S. Weber2, and Adel K. El-Naggar1,2 Abstract Purpose: Salivary duct carcinoma overexpresses epidermal growth factor receptor (EGFR) and HER-2, although the underlying mechanisms remain undefined. Because of the potential utilization of these markers as treatment targets, we evaluated protein and gene status by several techniques to determine complementary value. Experimental Design: A tissue microarray of 66 salivary duct carcinomas was used for immunohis- tochemical analysis of HER-2 and EGFR expression (semiquantitatively evaluated into a three-tiered system), and fluorescence in situ hybridization for gene copy number, and chromosomes 7 and 17 ploidy status. Sequencing of exons 18, 19, and 21 of the EGFR gene for mutations was carried out. Result: For EGFR, 46 (69.7%) of the 66 tumors showed some form of EGFR expression (17 at 3+, 17 at 2+, 12 at 1+) but none gene amplification. Five (9.4%) of 53 tumors showed mutations in exon 18 (n = 3) and exon 19 (n = 2). Polysomy of chromosome 7 (average >2.5 copies/cell) was detected in 15 (25.0%) of 60 tumors (6 at 3+, 5 at 2+, 2 at 1+, 2 at 0+ expression) and correlated with poor 3-year survival (P = 0.015). For HER-2, 17 (25.8%) of 66 tumors expressed HER-2 (10 at 3+, 3 at 2+, 4 at 1+). -
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.