6Cognitive and Behavioral Characteristics of Children With
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(Lcrs) in 22Q11 Mediate Deletions, Duplications, Translocations, and Genomic Instability: an Update and Literature Review Tamim H
review January/February 2001 ⅐ Vol. 3 ⅐ No. 1 Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: An update and literature review Tamim H. Shaikh, PhD1, Hiroki Kurahashi, MD, PhD1, and Beverly S. Emanuel, PhD1,2 Several constitutional rearrangements, including deletions, duplications, and translocations, are associated with 22q11.2. These rearrangements give rise to a variety of genomic disorders, including DiGeorge, velocardiofacial, and conotruncal anomaly face syndromes (DGS/VCFS/CAFS), cat eye syndrome (CES), and the supernumerary der(22)t(11;22) syndrome associated with the recurrent t(11;22). Chromosome 22-specific duplications or low copy repeats (LCRs) have been directly implicated in the chromosomal rearrangements associated with 22q11.2. Extensive sequence analysis of the different copies of 22q11 LCRs suggests a complex organization. Examination of their evolutionary origin suggests that the duplications in 22q11.2 may predate the divergence of New World monkeys 40 million years ago. Based on the current data, a number of models are proposed to explain the LCR-mediated constitutional rearrangements of 22q11.2. Genetics in Medicine, 2001:3(1):6–13. Key Words: duplication, evolution, 22q11, deletion and translocation Although chromosome 22 represents only 2% of the haploid The 22q11.2 deletion syndrome, which includes DGS/ human genome,1 recurrent, clinically significant, acquired, VCFS/CAFS, is the most common microdeletion syndrome. and somatic -
An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial Chromosome
The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 133-151 Article 7 2018 An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial chromosome Robert W. Carter Stephen Lee University of Idaho John C. Sanford Cornell University, Cornell University College of Agriculture and Life Sciences School of Integrative Plant Science,Follow this Plant and Biology additional Section works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y- chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. -
Organization, Evolution and Function of Alpha Satellite Dna
ORGANIZATION, EVOLUTION AND FUNCTION OF ALPHA SATELLITE DNA AT HUMAN CENTROMERES by M. KATHARINE RUDD Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Advisor: Dr. Huntington F. Willard Department of Genetics CASE WESTERN RESERVE UNIVERSITY January, 2005 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of ______________________________________________________ candidate for the Ph.D. degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. 1 Table of Contents Table of contents.................................................................................................1 List of Tables........................................................................................................2 List of Figures......................................................................................................3 Acknowledgements.............................................................................................5 Abstract................................................................................................................6 -
Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories
Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002) -
DGCR6 at the Proximal Part of the Digeorge Critical Region Is Involved in Conotruncal Heart Defects
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Institutional Repository : the EHIME area OPEN Citation: Human Genome Variation (2015) 2, 15004; doi:10.1038/hgv.2015.4 © 2015 The Japan Society of Human Genetics All rights reserved 2054-345X/15 www.nature.com/hgv ARTICLE DGCR6 at the proximal part of the DiGeorge critical region is involved in conotruncal heart defects Wenming Gao1, Takashi Higaki1, Minenori Eguchi-Ishimae1, Hidehiko Iwabuki1, Zhouying Wu1, Eiichi Yamamoto2, Hidemi Takata1, Masaaki Ohta1, Issei Imoto3, Eiichi Ishii1 and Mariko Eguchi1 Cardiac anomaly is one of the hallmarks of DiGeorge syndrome (DGS), observed in approximately 80% of patients. It often shows a characteristic morphology, termed as conotruncal heart defects. In many cases showing only the conotruncal heart defect, deletion of 22q11.2 region cannot be detected by fluorescence in situ hybridization (FISH), which is used to detect deletion in DGS. We investigated the presence of genomic aberrations in six patients with congenital conotruncal heart defects, who show no deletion at 22q11.2 in an initial screening by FISH. In these patients, no abnormalities were identified in the coding region of the TBX1 gene, one of the key genes responsible for the phenotype of DGS. However, when copy number alteration was analyzed by high-resolution array analysis, a small deletion or duplication in the proximal end of DiGeorge critical region was detected in two patients. The affected region contains the DGCR6 and PRODH genes. DGCR6 has been reported to affect the expression of the TBX1 gene. Our results suggest that altered dosage of gene(s) other than TBX1, possibly DGCR6, may also be responsible for the development of conotruncal heart defects observed in patients with DGS and, in particular, in those with stand-alone conotruncal heart defects. -
Network Effects of the Neuropsychiatric 15Q13.3 Microdeletion on the Transcriptome and Epigenome in Human Induced Neurons
bioRxiv preprint doi: https://doi.org/10.1101/772541; this version posted September 19, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Network effects of the neuropsychiatric 15q13.3 microdeletion on the transcriptome and epigenome in human induced neurons Siming Zhang (B.S., Stanford University), Xianglong Zhang (Ph.D., Stanford University), Shining Ma (Ph.D., Stanford University), Carolin Purmann (Ph.D., Stanford University), Kasey Davis (Ph.D., Stanford University), Wing Hung Wong (Ph.D., Stanford University), Jonathan Bernstein (MD, Ph.D., Stanford University), Joachim Hallmayer (MD, Stanford University), Alexander E Urban (Ph.D., Stanford University) Corresponding author: Alexander E Urban Address: 3165 Porter Drive, Stanford CA 94304 Phone: (650) 736-9528, Fax: (650) 725-4913 email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/772541; this version posted September 19, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Heterozygous deletions in the 15q13.3 region are associated with several neuropsychiatric disorders including autism, schizophrenia, and attention deficit hyperactivity disorder. Several genes within the 15q13.3 deletion region may play a role in neuronal dysfunction, based on association studies in humans and functional studies in mice, but the intermediate molecular mechanisms remain unknown. -
Basic Genetic Mechanisms— the Ways in Which the Cell Maintains, Replicates, Expresses, and Occasionally Improves the Genetic Information Carried in Its DNA
BASIC GENETIC PART MECHANISMS II 4 DNA AND CHROMOSOMES 5 DNA REPLICATION, REPAIR, AND RECOMBINATION 6 HOW CELLS READ THE GENOME: FROM DNA TO PROTEIN 7 CONTROL OF GENE EXPRESSION The ribosome. The large subunit of the bacterial ribosome is shown here with the ribosomal RNA shown in gray and the ribosomal proteins in gold.The ribosome is the complex catalytic machine at the heart of protein synthesis. (From N. Ban et al., Science 289:905–920, 2000. © AAAS.) The nucleosome. The basic structural unit of all eucaryotic chromosomes is the nucleosome.The DNA double helix (gray) is wrapped around a core particle of histone proteins (colored) to create the nucleosome. Nucleosomes are spaced roughly 200 nucleotide pairs apart along the chromosomal DNA. (Reprinted by permission from K. Luger et al., Nature 389:251–260, 1997. © Macmillan Magazines Ltd.) 4 THE STRUCTURE AND FUNCTION DNA AND OF DNA CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN CHROMOSOMES FIBER THE GLOBAL STRUCTURE OF CHROMOSOMES Life depends on the ability of cells to store, retrieve, and translate the genetic instructions required to make and maintain a living organism. This hereditary information is passed on from a cell to its daughter cells at cell division, and from one generation of an organism to the next through the organism’s repro- ductive cells. These instructions are stored within every living cell as its genes, the information-containing elements that determine the characteristics of a species as a whole and of the individuals within it. As soon as genetics emerged as a science at the beginning of the twentieth century, scientists became intrigued by the chemical structure of genes. -
Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications
Stem Cell Rev and Rep DOI 10.1007/s12015-016-9662-8 Detailed Characterization of Human Induced Pluripotent Stem Cells Manufactured for Therapeutic Applications Behnam Ahmadian Baghbaderani 1 & Adhikarla Syama2 & Renuka Sivapatham3 & Ying Pei4 & Odity Mukherjee2 & Thomas Fellner1 & Xianmin Zeng3,4 & Mahendra S. Rao5,6 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract We have recently described manufacturing of hu- help determine which set of tests will be most useful in mon- man induced pluripotent stem cells (iPSC) master cell banks itoring the cells and establishing criteria for discarding a line. (MCB) generated by a clinically compliant process using cord blood as a starting material (Baghbaderani et al. in Stem Cell Keywords Induced pluripotent stem cells . Embryonic stem Reports, 5(4), 647–659, 2015). In this manuscript, we de- cells . Manufacturing . cGMP . Consent . Markers scribe the detailed characterization of the two iPSC clones generated using this process, including whole genome se- quencing (WGS), microarray, and comparative genomic hy- Introduction bridization (aCGH) single nucleotide polymorphism (SNP) analysis. We compare their profiles with a proposed calibra- Induced pluripotent stem cells (iPSCs) are akin to embryonic tion material and with a reporter subclone and lines made by a stem cells (ESC) [2] in their developmental potential, but dif- similar process from different donors. We believe that iPSCs fer from ESC in the starting cell used and the requirement of a are likely to be used to make multiple clinical products. We set of proteins to induce pluripotency [3]. Although function- further believe that the lines used as input material will be used ally identical, iPSCs may differ from ESC in subtle ways, at different sites and, given their immortal status, will be used including in their epigenetic profile, exposure to the environ- for many years or even decades. -
The Symptom Profile and Experience of Children with Rare Life-Limiting Conditions
The symptom profile and experience of children with rare life-limiting conditions: Perspectives of their families and key health professionals Document Title The symptom profile and experience of children with rare life-limiting conditions: Perspectives of their families and key health professionals Authors Cari Malcolm, Sally Adams, Gillian Anderson, Faith Gibson, Richard Hain, Anthea Morley, Liz Forbat. Publisher Cancer Care Research Centre, University of Stirling Publication Date 2011 Target Audience Paediatric palliative care staff, paediatric clinicians, policy-makers, service developers, families supporting children with life-limiting conditions. Funded By Children’s Hospice Association Scotland Key Words Advance care planning, Batten disease, expertise, extended family, family, Morquio disease, progressive life-limiting, relationships, Sanfilippo disease, siblings, symptoms. Contact Details www.cancercare.stir.ac.uk Tel: 01786 849260 Email: [email protected] Copyright This publication is copyright CCRC and may be reproduced free of charge in any format or medium. Any material used must be fully acknowledged, and the title of the publication, authors and date of publication specified. The symptom profile and experience of children with rare life- limiting conditions: Perspectives of their families and key health professionals Executive Summary Background Many non-malignant life-limiting conditions are individually extremely rare and little is known, even by professionals in the field, about the actual day-to-day symptomatology or the impact of these symptoms on the child and family. With little recorded in the literature regarding the symptoms that children with rare life-limiting conditions experience, and the associated impact of managing these symptoms on the wider family, an opportunity exists to widen the knowledge base in this area. -
22Q12 and 22Q13 Duplications
22q12 and 22q13 duplications rarechromo.org Duplications of 22q12 and 22q13 A duplication of 22q12 and/or 22q13 is a very rare genetic condition in which the cells of the body have a small but variable amount of extra genetic material from one of the body’s 46 chromosomes – chromosome 22. For healthy development, chromosomes should contain just the right amount of genetic material (DNA) – not too much and not too little. Like most other chromosome disorders, having an extra part of chromosome 22 may increase the risk of birth defects, developmental delay and intellectual disability. However, there is individual variation. Background on Chromosomes Chromosomes are structures which contain our DNA and are found in almost every cell of the body. Every chromosome contains thousands of genes which may be thought of as individual instruction booklets (or recipes) that contain all the genetic information telling the body how to develop, grow and function. Chromosomes (and genes) usually come in pairs with one member of each chromosome pair being inherited from each parent. Most cells of the human body have a total of 46 (23 pairs of) chromosomes. The egg and the sperm cells, however have 23 unpaired chromosomes, so that when the egg and sperm join together at conception, the chromosomes pair up and the number is restored to 46. Of these 46 chromosomes, two are the sex chromosomes that determine gender. Females have two X chromosomes and males have one X chromosome and one Y chromosome. The remaining 44 chromosomes are grouped in 22 pairs, numbered 1 to 22 approximately from the largest to the smallest. -
Constitutional 9P22q Translocation in a Patient with Melanoma, Deafness and DNA Repair Deficiency Disrupts P14arf and Down-Regulates TBX1
Constitutional 9p22q translocation in a patient with melanoma, deafness and DNA repair deficiency disrupts p14arf and down-regulates TBX1 Xiaohui Tan1, Sarah Anzick2, Sikandar G. Khan1, Takahiro Ueda1,3, Gary Stone2, John J. DiGiovanna1,4, Deborah Tamura1, Daniel Wattendorf5, Carmen Brewer6, Chris Zalewski6, Robert Walker2, John A Butman7, Andrew Griffith6, Paul Meltzer2, Paul Bergstresser8 and Kenneth H. Kraemer1 1DNA Repair Section, Dermatology Branch, CCR, NCI 2Genetics Branch, NCI 3Pharm/ Medical Device Agency, Tokyo, Japan 4 Derm, Brown Med School, Providence, RI 5Office of the Air Force Surgeon General 6Otolaryngology Br, NIDCD 7Radiology, CC 8Derm, Univ of Texas SW, Dallas, TX DNA REPAIR DEFICIENCY, MELANOMA, DEAFNESS, AND CHROMOSOME 9p22q TRANSLOCATION – A NEW SYNDROME? Low set ears Contractures Posterior fifth toes 12 y/o Patient DD129BE Sensorineural deafness, DiGeorge Syndrome / Velo-cardio-facial Syndrome like features Melanoma 0.25 mm 14 y/o CLINICAL EXAMINATION • Audiologic assessment No measureable hearing bilaterally and absent vestibular reactivity • CT and MRI Bilaterally symmetric cochlear hypoplasia and vestibular dysplasia with absence of the cochlear nerve. KARYOTYPE ANALYSIS t(9;22)(p21;q11.2) Reciprocal translocation between the short arm of chromosome 9 and the long arm of chromosome 22 THE AIM 1. To map the chromosome breakpoints in cells from patient DD129BE 2. To develop a detailed molecular characterization of the candidate genes for his clinical syndrome of melanoma, defective DNA repair and deafness. FISH -
Chromosome 22Q11.2 Deletion Syndrome (Digeorge and Velocardiofacial Syndromes) Elena Perez, MD, Phd, and Kathleen E
Chromosome 22q11.2 deletion syndrome (DiGeorge and velocardiofacial syndromes) Elena Perez, MD, PhD, and Kathleen E. Sullivan, MD, PhD Chromosome 22q11.2 deletion syndrome occurs in Overview approximately 1 of 3000 children. Clinicians have defined the Chromosome 22q11.2 deletion syndrome is the name phenotypic features associated with the syndrome and the given to a heterogeneous group of disorders that share a past 5 years have seen significant progress in determining the common genetic basis. Most patients with DiGeorge frequency of the deletion in specific populations. As a result, syndrome and velocardiofacial syndrome have monoso- caregivers now have a better appreciation of which patients mic deletions of chromosome 22q11.2 [1,2]. Other syn- are at risk for having the deletion. Once identified, patients dromes in which a substantial fraction of patients have with the deletion can receive appropriate multidisciplinary care. been determined to have the deletion are conotruncal We describe recent advances in understanding the genetic anomaly face syndrome,Caylor cardiofacial syndrome, basis for the syndrome, the clinical manifestations of the and autosomal dominant Opitz-G/BBB syndrome. Com- syndrome, and new information on autoimmune diseases in plicating the situation further is the fact that not all pa- this syndrome. Curr Opin Pediatr 2002, 14:678–683 © 2002 Lippincott tients with hemizygous deletions of chromosome Williams & Wilkins, Inc. 22q11.2 have identical deletions. Despite the heteroge- neity of both the clinical manifestations and the chromo- somal deletions,much progress has been made in the last year in understanding the genetic basis of the chromo- some 22q11.2 deletion syndromes.