DOCSLIB.ORG

Constitutional Chromosome 16Q Mosaicism: Inheritance and Phenotypic Effects 16

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Constitutional Chromosome 16Q Mosaicism: Inheritance and Phenotypic Effects 16 Cukurova Medical Journal Cukurova Med J 2018;43(4):1023-1027 ÇUKUROVA ÜNİVERSİTESİ TIP FAKÜLTESİ DOI: 10.17826/cumj.372388 OLGU SUNUMU / CASE REPORT Constitutional chromosome 16q mosaicism: inheritance and phenotypic effects 16. kromozomun q kolunda gözlenen kalıtımsal mozaisizm ve fenotipik etkileri Osman Demirhan1, Erdal Tunç1, Şakir Altınbaşak2 1Çukurova University Faculty of Medicine, Department of Medical Biology and Genetics, 2Department of Pediatric Neurology, Adana,Turkey Cukurova Medical Journal 2018;43(4):1023-1027 Abstract Öz Partial monosomies of chromosome 16q are rare. Here, 16q parsiyel monozomilerine ender olarak rastlanmaktadır. we report a boy showed various aberrations in the Bu çalışmada, 16. kromozomun q22.1→qter bölgesinde q22.1→qter region of chromosome 16 and some değişik düzensizlikler gösteren ve bunlarla birlikte önemli important clinical features. The patient presented low IQ, klinik bulguları bulunan bir erkek çocuğu olgusu delayed speech, delayed psychomotor development, late sunulmaktadır. Hastada; düşük IQ, konuşma güçlüğü, geç walking, clapping hands in case of excitement, deficiency psikomotor gelişme ve yürüme, heyecan durumunda el in social adjustment and incompatibility with peers. çırpma, sosyal uyumda eksiklik ve akranlarıyla uyumlu Standard cytogenetic analysis was performed to patient olamama gibi klinik bulgulara rastlandı. Hastaya ve ailesine and his family. Cytogenetic analysis results showed standart sitogenetik kromozom analizi yapıldı. Sitogenetik deletions, breaks and fragilities in the q22.1 region in one analiz sonucunda, 16. kromozomun q22.1 bölgesinde of chromosome 16. Analyzed cells of patient and his delesyonlara, kırıklara ve frajilitelere rastlandı. Hasta ve father showed 38% and 26% structural aberrations, babasının analiz edilen hücrelerinde, sırasıyla %38 ve %26 respectively. Aberrations were inherited from an oranlarında 16q22.1 bölgesinde yapısal hasarlara rastlandı. apparently normal father. The comparison of the present Kromozom hasarlarının fenotipik olarak normal case to other 16q22.1→qter monosomies contributed to görünümlü babadan aktarıldığı anlaşıldı. Bu vakadan elde narrow down the critical region for delayed speech and full edilen sonuçlar, diğer q22.1→qter monozomisi vakaları ile undeveloped fine motor skills in the 16q22.1→qter karşılaştırmalı olarak değerlendirildiğinde, q22.1→qter deletion syndrome. We showed that 16q deletions are delesyon sendromunda geç konuşma ve motor confined to the phenotypic features such as delayed yeteneklerin gelişememesi ile ilişkili kritik kromozom speech, full undeveloped fine motor skills. bölgesi daha da spesifik olarak ortaya çıkmıştır. Key words: Delayed speech, Full undeveloped fine motor Anahtar kelimeler: Geç konuşma, gelişmemiş motor skills, Monosomy 16q22→qter yetenekler, 16q22→qter monozomisi of DNA, CAs and the spontaneous reversion of INTRODUCTION inherited mutations1. The chromosome 16 deletions are genetic Partial monosomy for an autosomal chromosome is conditions in which part of the genetic material that often associated with a specific pattern of makes up chromosome 16 are missing1. Mosaicism recognizable malformations. Although such as the presence of genetically distinct populations of autosomal monosomy may involve large regions of somatic cells in an organism can result in major DNA which would contain many genes, it is phenotypic changes and reveal the expression of apparent that monosomy syndromes can originate otherwise lethal genetic mutations. Mosaicism can from the effects of abnormal dosage of relatively be caused by DNA mutations, epigenetic alterations few genes. Partial monosomies often originating Yazışma Adresi/Address for Correspondence: Dr. Osman Demirhan, Çukurova University, Faculty of Medicine, Department of Medical Biology and Genetics, Adana, Turkey E-mail: [email protected] Geliş tarihi/Received: 28.12.2017 Kabul tarihi/Accepted: 30.01.2018 Cilt/Volume 43 Yıl/Year 2018 Constitutional chromosome 16q mosaicism from meiotic segregation of parental balanced normal. Eye contact, interest to his surroundings translocations, can be viable and be associated with and speaking about individuals and events in his a specific recognizable pattern of malformations1. near surroundings were present. When he gets excited he shoots one of his hands. IQ was scored Published reports of chromosome 16 abnormalities as 72 (Stanford Binet test). Tyroid functions, blood have been described as rare events. A patient levels of glucose, vitamin B12 and folate were also reported as a del(16q22) was subsequently shown to recorded as normal. In cerebral MRI scanning, a be a balanced t(5;16) translocation1. A malformed small arachnoid cyst which developed in the newborn with a karyotype 46,XX,del( 16q21) was posterior aspect of the vermis and did not have any reported in 19772. There have been confirmed pressing effect was found. EEG test result showed partial monosomies for the distal segment of the biphasic and triphasic sharp waves in the mid- long arm of chromosome 16. The deletions vary in temporal region. Waves sometimes took generalized size with the distal breakpoint between 16q22.1 and form. 16q242. Generally, the more distal the deletion, the patients have been less severely affected3,4. Some of the patients with deleted 16q have similar patterns Cytogenetic analysis of malformations and this has resulted in the Firstly, patient has been seen and diagnosed by the concept of a deletion syndrome involving the long Departments of Pediatrics and then they were arm of chromosome 16. It has been suggested that referred to Department of Medical Biology and there are critical regions within 16q225 which Genetics, Faculty of Medicine, Çukurova University produce a pattern of features including growth for cytogenetic analyses. Peripheral blood was taken retardation, intellectual disability, physical anomalies, from the patient and her parents for culture studies. renal and musculoskeletal malformations and A 0.3 ml sample of blood was incubated at 37°C for congenital heart defects. In addition, deletion of 72 h in 2 media (RPMI-1640). For eliminating chromosome 16q is frequently associated with ethical concerns, informed consent document has diverse tumors. Numerous studies strongly suggest been obtained from patient’s parents. Standard the presence of one or more tumor suppressor techniques used for the cultivation of lymphocytes genes on chromosome 16q22 to 16qter including from peripheral blood. Metaphase spread the widely studied cadherin gene family. However, preparations and GTG-banding was performed the specific tumor suppressor genes residing in this according to standard method. A total of 50 region need better definition and characterization. metaphase cells were analysed. Evaluation of Here, we report a boy showed some important karyotypes was done according to the International clinical features and various paternally inherited CAs System for Human Cytogenetic Nomenclature in the q22.1→qter region of chromosome 16. We (ISCN, 2005). have compared clinical and the various aberrations A total of 3 individuals from the same family in the q22.1→qter region of chromosome 16 in this members were analyzed (the patient and his case with those described in the literature to gain parents). The patient showed structural aberrations more accurate genotype-phenotype correlations. in 38% (19 cells) of 50 cells analyzed but the karyotype results were normal in 62% (31 cells). CASE These CAs were very serious and very important genetic instabilities; 4 deletions (21.1% of CAs), 3 The patient is the first child of healthy parents (non- chromosome breaks (15.8%), 5 chromatid breaks consanguineous). He was born preterm at 39 weeks (26.3%) and 7 gaps (36.8%) in q22.1 region of of gestation with a weight of 3.700 kg, now was 4.5 chromosome 16 (Figure). Chromosome breaks were years old. He applied to the clinic because he was also evaluated as deletion. So the ratio of all delayed in speaking and his fine motor skills were deletions proportion was 18% (4 del, + 5 chrbr) not good. Perinatal anoxia was not observed. Patient (Table). In the father, the distal deletion on started to walk at 18 months. He could compose chromosome 16q was found in 28% (14 cells) of 50 simple sentences but showed difficulties in cells analyzed. These CAs included 4 deletions (8%), understanding. Social adaptation was not good and 5 chromosome breaks (10%), 4 chromatid breaks he was not inclinable to play with his peers. Results (8%) and 1 gap (2%). The proportion of all of physical and neurological examinations were deletions was 18% (4 del, 5 chrbr) (Table). The 1024 Demirhan et al. Cukurova Medical Journal mother showed normal karyotype. Structural published cases with the deletion 16q22→qter chromosome 16 abnormalities in the boy inherited mosaicism. However, 16q22 deletion is a recognized from an apparently normal father. OMIM6 syndrome, associated with the deletion of the whole 16q22 band, presenting failure to thrive in infancy, poor growth, delayed psychomotor development, hypotonia, and dysmorphic features, including large anterior fontanelle, high forehead, diastasis of the cranial sutures, broad nasal bridge, hypertelorism, low-set abnormal ears, and short neck. The phenotypic features and deletion sizes of the affected patients are variable, but deletion of 16q22 appears to be critical for manifestations of the syndrome5. Our case had lost only part of this chromosome material and showed significant impairments. Our case did not
Load more

Recommended publications
  • Human Chromosome‐Specific Aneuploidy Is Influenced by DNA
    Article Human chromosome-specific aneuploidy is influenced by DNA-dependent centromeric features Marie Dumont1,†, Riccardo Gamba1,†, Pierre Gestraud1,2,3, Sjoerd Klaasen4, Joseph T Worrall5, Sippe G De Vries6, Vincent Boudreau7, Catalina Salinas-Luypaert1, Paul S Maddox7, Susanne MA Lens6, Geert JPL Kops4 , Sarah E McClelland5, Karen H Miga8 & Daniele Fachinetti1,* Abstract Introduction Intrinsic genomic features of individual chromosomes can contri- Defects during cell division can lead to loss or gain of chromosomes bute to chromosome-specific aneuploidy. Centromeres are key in the daughter cells, a phenomenon called aneuploidy. This alters elements for the maintenance of chromosome segregation fidelity gene copy number and cell homeostasis, leading to genomic instabil- via a specialized chromatin marked by CENP-A wrapped by repeti- ity and pathological conditions including genetic diseases and various tive DNA. These long stretches of repetitive DNA vary in length types of cancers (Gordon et al, 2012; Santaguida & Amon, 2015). among human chromosomes. Using CENP-A genetic inactivation in While it is known that selection is a key process in maintaining aneu- human cells, we directly interrogate if differences in the centro- ploidy in cancer, a preceding mis-segregation event is required. It was mere length reflect the heterogeneity of centromeric DNA-depen- shown that chromosome-specific aneuploidy occurs under conditions dent features and whether this, in turn, affects the genesis of that compromise genome stability, such as treatments with micro- chromosome-specific aneuploidy. Using three distinct approaches, tubule poisons (Caria et al, 1996; Worrall et al, 2018), heterochro- we show that mis-segregation rates vary among different chromo- matin hypomethylation (Fauth & Scherthan, 1998), or following somes under conditions that compromise centromere function.
    [Show full text]
  • Searching the Genomes of Inbred Mouse Strains for Incompatibilities That Reproductively Isolate Their Wild Relatives
    Journal of Heredity 2007:98(2):115–122 ª The American Genetic Association. 2007. All rights reserved. doi:10.1093/jhered/esl064 For permissions, please email: [email protected]. Advance Access publication January 5, 2007 Searching the Genomes of Inbred Mouse Strains for Incompatibilities That Reproductively Isolate Their Wild Relatives BRET A. PAYSEUR AND MICHAEL PLACE From the Laboratory of Genetics, University of Wisconsin, Madison, WI 53706. Address correspondence to the author at the address above, or e-mail: [email protected]. Abstract Identification of the genes that underlie reproductive isolation provides important insights into the process of speciation. According to the Dobzhansky–Muller model, these genes suffer disrupted interactions in hybrids due to independent di- vergence in separate populations. In hybrid populations, natural selection acts to remove the deleterious heterospecific com- binations that cause these functional disruptions. When selection is strong, this process can maintain multilocus associations, primarily between conspecific alleles, providing a signature that can be used to locate incompatibilities. We applied this logic to populations of house mice that were formed by hybridization involving two species that show partial reproductive isolation, Mus domesticus and Mus musculus. Using molecular markers likely to be informative about species ancestry, we scanned the genomes of 1) classical inbred strains and 2) recombinant inbred lines for pairs of loci that showed extreme linkage disequi- libria. By using the same set of markers, we identified a list of locus pairs that displayed similar patterns in both scans. These genomic regions may contain genes that contribute to reproductive isolation between M. domesticus and M.
    [Show full text]
  • 16P11.2 Deletion Syndrome Guidebook
    16p11.2 Deletion Syndrome Guidebook Page 1 Version 1.0, 12/11/2015 16p11.2 Deletion Syndrome Guidebook This guidebook was developed by the Simons VIP Connect Study Team to help you learn important information about living with the 16p11.2 deletion syndrome. Inside, you will find that we review everything from basic genetics and features of 16p11.2 deletion syndrome, to a description of clinical care and management considerations. - Simons VIP Connect Page 2 Version 1.0, 12/11/2015 Table of Contents How Did We Collect All of this Information? ................................................................................................ 4 What is Simons VIP Connect? ................................................................................................................... 4 What is the Simons Variation in Individuals Project (Simons VIP)? .......................................................... 5 Simons VIP Connect Research................................................................................................................... 5 Definition of 16p11.2 Deletion ..................................................................................................................... 6 What is a Copy Number Variant (CNV)? ................................................................................................... 7 Inheritance ................................................................................................................................................ 8 How is a 16p11.2 Deletion Found? ..........................................................................................................
    [Show full text]
  • Definition of the Landscape of Promoter DNA Hypomethylation in Liver Cancer
    Published OnlineFirst July 11, 2011; DOI: 10.1158/0008-5472.CAN-10-3823 Cancer Therapeutics, Targets, and Chemical Biology Research Definition of the Landscape of Promoter DNA Hypomethylation in Liver Cancer Barbara Stefanska1, Jian Huang4, Bishnu Bhattacharyya1, Matthew Suderman1,2, Michael Hallett3, Ze-Guang Han4, and Moshe Szyf1,2 Abstract We use hepatic cellular carcinoma (HCC), one of the most common human cancers, as a model to delineate the landscape of promoter hypomethylation in cancer. Using a combination of methylated DNA immunopre- cipitation and hybridization with comprehensive promoter arrays, we have identified approximately 3,700 promoters that are hypomethylated in tumor samples. The hypomethylated promoters appeared in clusters across the genome suggesting that a high-level organization underlies the epigenomic changes in cancer. In normal liver, most hypomethylated promoters showed an intermediate level of methylation and expression, however, high-CpG dense promoters showed the most profound increase in gene expression. The demethylated genes are mainly involved in cell growth, cell adhesion and communication, signal transduction, mobility, and invasion; functions that are essential for cancer progression and metastasis. The DNA methylation inhibitor, 5- aza-20-deoxycytidine, activated several of the genes that are demethylated and induced in tumors, supporting a causal role for demethylation in activation of these genes. Previous studies suggested that MBD2 was involved in demethylation of specific human breast and prostate cancer genes. Whereas MBD2 depletion in normal liver cells had little or no effect, we found that its depletion in human HCC and adenocarcinoma cells resulted in suppression of cell growth, anchorage-independent growth and invasiveness as well as an increase in promoter methylation and silencing of several of the genes that are hypomethylated in tumors.
    [Show full text]
  • How Genes Work
    Help Me Understand Genetics How Genes Work Reprinted from MedlinePlus Genetics U.S. National Library of Medicine National Institutes of Health Department of Health & Human Services Table of Contents 1 What are proteins and what do they do? 1 2 How do genes direct the production of proteins? 5 3 Can genes be turned on and off in cells? 7 4 What is epigenetics? 8 5 How do cells divide? 10 6 How do genes control the growth and division of cells? 12 7 How do geneticists indicate the location of a gene? 16 Reprinted from MedlinePlus Genetics (https://medlineplus.gov/genetics/) i How Genes Work 1 What are proteins and what do they do? Proteins are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of thebody’s tissues and organs. Proteins are made up of hundreds or thousands of smaller units called amino acids, which are attached to one another in long chains. There are 20 different types of amino acids that can be combined to make a protein. The sequence of amino acids determineseach protein’s unique 3-dimensional structure and its specific function. Aminoacids are coded by combinations of three DNA building blocks (nucleotides), determined by the sequence of genes. Proteins can be described according to their large range of functions in the body, listed inalphabetical order: Antibody. Antibodies bind to specific foreign particles, such as viruses and bacteria, to help protect the body. Example: Immunoglobulin G (IgG) (Figure 1) Enzyme.
    [Show full text]
  • Gene Mapping and Medical Genetics
    J Med Genet: first published as 10.1136/jmg.24.8.451 on 1 August 1987. Downloaded from Gene mapping and medical genetics Journal of Medical Genetics 1987, 24, 451-456 Molecular genetics of human chromosome 16 GRANT R SUTHERLAND*, STEPHEN REEDERSt, VALENTINE J HYLAND*, DAVID F CALLEN*, ANTONIO FRATINI*, AND JOHN C MULLEY* From *the Cytogenetics Unit, Adelaide Children's Hospital, North Adelaide, South Australia 5006; and tUniversity of Oxford, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DU. SUMMARY The major diseases mapped to chromosome 16 are adult polycystic kidney disease and those resulting from mutations in the a globin complex. There are at least six other less important genetic diseases which map to this chromosome. The adenine phosphoribosyltransferase gene allows for selection of chromosome 16 in somatic cell hybrids and a hybrid panel is available which segments the chromosome into six regions to facilitate gene mapping. Genes which have been mapped to this chromosome or which have had their location redefined since HGM8 include APRT, TAT, MT, HBA, PKDI, CTRB, PGP, HAGH, HP, PKCB, and at least 19 cloned DNA sequences. There are RFLPs at 13 loci which have been regionally mapped and can be used for linkage studies. Chromosome 16 is not one of the more extensively have been cloned and mapped to this chromosome. mapped human autosomes. However, it has a Brief mention will be made of a hybrid cell panel http://jmg.bmj.com/ number of features which make it attractive to the which allows for an efficient regional localisation of gene mapper.
    [Show full text]
  • Rapid Molecular Assays to Study Human Centromere Genomics
    Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Method Rapid molecular assays to study human centromere genomics Rafael Contreras-Galindo,1 Sabrina Fischer,1,2 Anjan K. Saha,1,3,4 John D. Lundy,1 Patrick W. Cervantes,1 Mohamad Mourad,1 Claire Wang,1 Brian Qian,1 Manhong Dai,5 Fan Meng,5,6 Arul Chinnaiyan,7,8 Gilbert S. Omenn,1,9,10 Mark H. Kaplan,1 and David M. Markovitz1,4,11,12 1Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA; 2Laboratory of Molecular Virology, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay 11400; 3Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan 48109, USA; 4Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; 5Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan 48109, USA; 6Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48109, USA; 7Michigan Center for Translational Pathology and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA; 8Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA; 9Department of Human Genetics, 10Departments of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA; 11Program in Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA; 12Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of cen- tromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere genomics in biology are laborious.
    [Show full text]
  • Comparative Mapping of DNA Markers from the Familial Alzheimer Mouse Chromosomes 16 and 17
    Proc. Natl. Acad. Sci. USA Vol. 85, pp. 6032-6036, August 1988 Genetics Comparative mapping of DNA markers from the familial Alzheimer disease and Down syndrome regions of human chromosome 21 to mouse chromosomes 16 and 17 (restriction fragment length polymorphism/genetic linkage analysis/recombinant inbred strains/interspecific backcross) SHIRLEY V. CHENG*, JOSEPH H. NADEAUt, RUDOLPH E. TANZI*, PAUL C. WATKINSt, JAYASHREE JAGADESH*, BENJAMIN A. TAYLORt, JONATHAN L. HAINES*, NICOLETTA SACCHI§, AND JAMES F. GUSELLA* *Neurogenetics Laboratoiy, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114; tThe Jackson Laboratory, Bar Harbor, ME 04609; tIntegrated Genetics, Inc., 31 New York Avenue, Framingham, MA 01701; and §Laboratory of Molecular Oncology, National Cancer Institute, Frederick, MD 21701 Communicated by Elizabeth S. Russell, April 18, 1988 ABSTRACT Mouse trisomy 16 has been proposed as an mouse genome, mouse trisomy 16 has been used as an animal animal model of Down syndrome (DS), since this chromosome model of DS (9, 10). contains homologues of several loci from the q22 band of Interest in human chromosome 21 has increased with the human chromosome 21. The recent mapping of the defect recent localizations of the defect causing familial Alzheimer causing familial Alzheimer disease (FAD) and the locus encod- disease (FAD) and the gene (APP) encoding the precursor for ing the Alzheiner amyloid (3 precursor protein (APP) to human amyloid ,8 protein to the proximal half of 21q (11, 12). FAD chromosome 21 has prompted a more detailed examination of is the autosomal dominantly inherited form of the common the extent ofconservation ofthis linkage group between the two late-onset neurodegenerative disorder that results in the species.
    [Show full text]
  • 16 Chromosome Chapter
    Chromosome 16 ©Chromosome Disorder Outreach Inc. (CDO) Technical genetic content provided by Dr. Iosif Lurie, M.D. Ph.D Medical Geneticist and CDO Medical Consultant/Advisor. Ideogram courtesy of the University of Washington Department of Pathology: ©1994 David Adler.hum_16.gif Introduction The length of chromosome 16 is 90 Mb. It is ~3% of the total human genetic material. The length of the short arm is ~35 Mb; the length of the long arm is 55 Mb. Chromosome 16 is extremely gene rich. It contains at least 1,100–1,150 genes, including more than 150 genes related to genetic diseases in humans. The genetic structure of the short arm of chromosome 16 has two areas (16p11.2 and 16p13.11), which (similar to 15q11.2 and 15q13.3) are predisposed to an unusually frequent origin of microdeletions and microduplications. These microanomalies were completely unknown before the invention of molecular cytogenetics. Several studies over recent years show that these microanomalies should be placed in a special position between completely normal variants and 100%– deleterious abnormalities. These microanomalies should be considered as relatively unspecific “risk factors”. The presence of these microdeletions significantly increases the risk of the development of autism, obesity or attention deficit disorder, but neither of these deletions should be viewed as the sole and only factor leading to these pathologies. Numerous reports show a considerable prevalence (frequency) of these microanomalies among control patients as well as among unaffected parents of affected individuals. The distal part of 16p (16p13.3) contains several genes responsible for well–known and relatively frequent genetic disorders.
    [Show full text]
  • 1 SUPPLEMENTARY RESULTS Hypomethylated Promoters Are
    SUPPLEMENTARY RESULTS Hypomethylated promoters are neither mutated nor deleted in HCC samples To rule out the possibility that the demethylation observed in gene promoters in our pyrosequencing assays (conversion of a C to T following bisulfite conversion) indicates a mutation of C to T rather than demethylation, we sequenced the unconverted DNA of AKR1B10, CENPH, MMP2, MMP9, MMP12, NUPR1, PAGE4, PLAU, and S100A5 promoter regions using the pyrosequencing SNP assay (Supplementary Fig. S2). We show that in all cases the fraction of cytosines in the unconverted sequence is similar in normal liver and in HCC. Therefore, the increase in the fraction of cytosines that were converted to thymidine in the tumor samples occurred only after bisulfite treatment and it was not due to mutations of Cs to Ts. Loss of signal for methylated DNA in hypomethylated promoters in HCC did not result from loss of DNA by deletions since our method internally controls for loss of DNA. Our MeDIP arrays are hybridized with both DNA immunoprecipitated with anti-5-methylcytosine antibody as well as total DNA. Thus, our assays measure both DNA methylation and DNA integrity. The DNA methylation signal reflects the ratio of signal for methylated DNA immunoprecipitation with the anti-5-methylcytosine antibody over total DNA in the sample at the indicated genome position. Loss of DNA by deletion would have increased the ratio of methylated DNA to total DNA to infinity and would have presented itself as hypermethylation rather than hypomethylation. Careful examination of the promoters that were demethylated in HCC provides evidence for the absence of deletions/amplifications in the genes that are hypomethylated in HCC patients.
    [Show full text]
  • Quantitative Trait Loci Mapping of Macrophage Atherogenic Phenotypes
    QUANTITATIVE TRAIT LOCI MAPPING OF MACROPHAGE ATHEROGENIC PHENOTYPES BRIAN RITCHEY Bachelor of Science Biochemistry John Carroll University May 2009 submitted in partial fulfillment of requirements for the degree DOCTOR OF PHILOSOPHY IN CLINICAL AND BIOANALYTICAL CHEMISTRY at the CLEVELAND STATE UNIVERSITY December 2017 We hereby approve this thesis/dissertation for Brian Ritchey Candidate for the Doctor of Philosophy in Clinical-Bioanalytical Chemistry degree for the Department of Chemistry and the CLEVELAND STATE UNIVERSITY College of Graduate Studies by ______________________________ Date: _________ Dissertation Chairperson, Johnathan D. Smith, PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, David J. Anderson, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Baochuan Guo, PhD Department of Chemistry, Cleveland State University ______________________________ Date: _________ Dissertation Committee member, Stanley L. Hazen, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Renliang Zhang, MD PhD Department of Cellular and Molecular Medicine, Cleveland Clinic ______________________________ Date: _________ Dissertation Committee member, Aimin Zhou, PhD Department of Chemistry, Cleveland State University Date of Defense: October 23, 2017 DEDICATION I dedicate this work to my entire family. In particular, my brother Greg Ritchey, and most especially my father Dr. Michael Ritchey, without whose support none of this work would be possible. I am forever grateful to you for your devotion to me and our family. You are an eternal inspiration that will fuel me for the remainder of my life. I am extraordinarily lucky to have grown up in the family I did, which I will never forget.
    [Show full text]
  • The Mapping of Chromosome 16
    The M:apping of Chrolnosome, A Norman A. 16Carl E. Hil( u The Mapping of Chromosome 16 Setting the Stage mapping techniques had been developed of lambda-phage clones, each containing and were being applied to the genomes DNA from one of the twenty-four hu- Bc}th the molecular and the physical of some of the favorite organisms of man chromosomes (see “Libraries from technology for constructing physical molecular biologists. Flow-sorted Chromosomes”), Those maps of complex genomes have devel- Cassandra Smith and Charles Cantor chromosome-specific libraries were oped at a blistering pace over the past had used pulsed-field gel electrophoresis designed as a source of probes to five years, due largely to the initiation to order the very large restriction frag- find polymorphic DNA markers for of the Human Genome Project. These ments produced by cutting the E. coli constructing genetic-linkage maps (see technologies include thecloning of very genome with two rare-cutting restriction “Modern Linkage Mapping”) and as large DNA fragments, electrophoretic enzymes. The resulting long-range a source of clones’ for rapid isolation separation of million-base-sized DNA restriction map of E. coli demonstrated of genes using cDNAs, or coding-region fragments, and sequence-based mapping that pulsed-field gel electrophoresis is probes, to pick out the appropriate clones using the polymerase chain reaction a way to study the long-range order from the libraries. Deaven and his group (PCFL) to identify unique sequences of landmarks on the DNA of human were also constructing larger-insert along the genome. The latter provides a chromosomes.
    [Show full text]