DOCSLIB.ORG

University of Alberta Application of Genetic Markers for Evaluation Of

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Alberta Application of Genetic Markers for Evaluation Of University of Alberta Application of genetic markers for evaluation of residual feed intake in beef cattle by Fidalis Denis Nagwalla Mujibi A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Animal Science Department of Agricultural, Food and Nutritional Science ©Fidalis Denis Nagwalla Mujibi Fall 2010 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. Library and Archives Bibliothèque et Canada Archives Canada Published Heritage Direction du Branch Patrimoine de l’édition 395 Wellington Street 395, rue Wellington Ottawa ON K1A 0N4 Ottawa ON K1A 0N4 Canada Canada Your file Votre référence ISBN: 978-0-494-67576-2 Our file Notre référence ISBN: 978-0-494-67576-2 NOTICE: AVIS: The author has granted a non- L’auteur a accordé une licence non exclusive exclusive license allowing Library and permettant à la Bibliothèque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par télécommunication ou par l’Internet, prêter, telecommunication or on the Internet, distribuer et vendre des thèses partout dans le loan, distribute and sell theses monde, à des fins commerciales ou autres, sur worldwide, for commercial or non- support microforme, papier, électronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L’auteur conserve la propriété du droit d’auteur ownership and moral rights in this et des droits moraux qui protège cette thèse. Ni thesis. Neither the thesis nor la thèse ni des extraits substantiels de celle-ci substantial extracts from it may be ne doivent être imprimés ou autrement printed or otherwise reproduced reproduits sans son autorisation. without the author’s permission. In compliance with the Canadian Conformément à la loi canadienne sur la Privacy Act some supporting forms protection de la vie privée, quelques may have been removed from this formulaires secondaires ont été enlevés de thesis. cette thèse. While these forms may be included Bien que ces formulaires aient inclus dans in the document page count, their la pagination, il n’y aura aucun contenu removal does not represent any loss manquant. of content from the thesis. Examining Committee Dr Stephen Moore, Agricultural Food and Nutritional Sciences Dr Zhiquan Wang, Agricultural Food and Nutritional Sciences Dr Guohui Lin, Computing Science Dr Denny Crews, Animal Science, Colorado State University Dr John Basarab, Alberta Agriculture and Rural Development, Government of Alberta Dr Jack Dekkers, Animal Science, Iowa State University Dedicated to the Nagwalla family ABSTRACT Improving feed efficiency has become a top priority in beef cattle production because of the rapidly increasing cost of feed provision. However, because of the expense associated with collecting individual animal feed intake data, only a relatively small number of animals have been tested, leading to low accuracies of estimated breeding values (EBV). Three studies were conducted to demonstrate the usefulness of including DNA marker information in RFI genetic evaluations. In the first study, the effect of period of testing on RFI was assessed. Beef cattle steers were tested for feed intake, with different cohorts tested in the fall-winter and winter-spring seasons. Seasonal differences were detected although these were confounded by differences in age and weight among the seasons. Additionally, mean EBV accuracy obtained was low, ranging between 0.47 and 0.51, implying that strategies to increase this accuracy are necessary. In the 2nd study, a suite of genetic markers predictive of RFI, DMI and ADG were pre-selected using single marker regression analysis and the top 100 SNPs analyzed further in 5 replicates of the training data to provide prediction equations for RFI, DMI and ADG. Cumulative marker phenotypes (CMP) were used to predict trait phenotypes and accuracy of prediction ranged between 0.007 and 0.414. Given that this prediction accuracy was lower than the polygenic EBV accuracy, the CMP would need to be combined with EBV for effective marker assisted selection. In study 3, genomic selection (GS) theory and methodology were used to derive genomic breeding values (GEBV) for RFI, DMI and ADG. The accuracy of prediction obtained with GEBV was low, ranging from 0.223 to 0.479 for marker panel with 200 SNPs, and 0.114 to 0.246 for a marker panel with 37,959 SNPs, depending on the GS method used. The results from these studies demonstrate that the utility of genetic markers for genomic prediction of RFI in beef cattle may be possible, but will likely be more effective if a tool that combines GEBV with traditional BLUP EBV is used for selection. ACKNOWLEDGEMENTS To him that giveth life, knowledge and understanding, I bow in gratitude and reverence. To my family, my biggest fans, thank you very much. My deepest gratitude goes to my supervisor Dr Stephen Moore, who saw to it that I got every opportunity possible to explore and grow in my academic experience. You have been more than a friend and mentor. Special thanks to Dr Denny Crews for introducing me to the world of quantitative genetic and genetic evaluation. You have been my greatest mentor and I owe so much to your guidance. Dr John Basarab accept my sincere gratitude for schooling me about RFI, and the many discussions, insights and directions you have provided,. Thank you Dr Donald Nkrumah for the many heated arguments, the lively conversations, and many suggestions you’ve provided. To Dr Graham Plastow, for critical appraisal of my manuscripts, I appreciate. Thank you Dr Zhiquan Wang for the many discussions we held about emerging issues in quantitative genetics and animal breeding. Dr Laki Goonewardene, thank you for help with statistical analyses. To Drs Paul Stothard and Jason Grant for help with Perl programming; to my wonderful colleagues at the University of Alberta’s Bovine Genomic program, thanks for your support and friendship. Lastly, to my friends who made my experience in Edmonton bearable and fun-filled. Patrick Asante, Michael Mbogga, Eric and Pam Amulaku, Muasya Musau, Kenya Kondo, Aparna Prasad, Katayoon Navabi, Monica Leon-Quintero, Lucianne Almeida, Hinako Ishikawa, plus many more (don’t feel left out), you guys are precious and I will always cherish you. TABLE OF CONTENTS ABSTRACT ........................................................................................................... iv ACKNOWLEDGEMENTS ................................................................................... vi TABLE OF CONTENTS ...................................................................................... vii LIST OF TABLES ................................................................................................. xi LIST OF FIGURES .............................................................................................. xv LIST OF ABBREVIATIONS ............................................................................. xvii CHAPTER 1 : Literature review .................................................................. 1 1.1 INTRODUCTION .......................................................................... 1 1.1.1 Measuring feed efficiency ......................................................... 3 1.1.2 Estimation of phenotypic (RFI) and genetic (RFIG) residual feed intake ................................................................................. 4 1.1.3 Economic implications of residual feed intake (RFI) estimation ................................................................................................... 7 1.1.4 Genetic evaluation of residual feed intake (RFI) ...................... 9 1.1.5 Prospects for genetic selection of residual feed intake (RFI) . 12 1.1.6 Indicator traits for residual feed intake (RFI) ........................ 14 1.1.7 The molecular basis for residual feed intake (RFI) ................ 16 1.2 OVERALL OBJECTIVES ........................................................... 18 1.3 LITERATURE CITED ................................................................. 21 CHAPTER 2 : Season of testing and its effect on feed intake and efficiency in growing beef cattle....................................................... 31 2.1 INTRODUCTION ........................................................................ 31 2.2 MATERIALS AND METHODS ................................................. 32 2.2.1 Animal resource and data collection ...................................... 32 2.2.2 Trait derivations...................................................................... 34 2.2.3 Statistical analysis .................................................................. 35 2.3 RESULTS ...................................................................................
Load more

Recommended publications
  • Role of Glypican-6 and Ng2 As Metastasis Promoting Factors
    UNIVERSITA’ DEGLI STUDI DI PARMA Dottorato di ricerca in Fisiopatologia Sistemica Ciclo XX ROLE OF GLYPICAN-6 AND NG2 AS METASTASIS PROMOTING FACTORS Coordinatore: Chiar.mo Prof. Ezio Musso Tutor: Chiar.mo Prof.Roberto Perris Dottoranda: Katia Lacrima Anni Accademici 2005-2008 To Indy L'anima libera e' rara, ma quando la vedi la riconosci: soprattutto perché provi un senso di benessere, quando gli sei vicino. (Charles Bukowski ) Index Summary ……………………………………………………..................................................... 3 1. Introduction …………………………………………………………………………………… 5 1.1. Proteoglycans (PGs)………………………………………………………………......... 6 1.2. Membrane associated proteoglycans……………………………………………..…... 8 1.3. Syndecans……………………………………………………………………………..…. 9 1.4. Glypicans……………………………………………………………………………...….. 11 1.5. GPC6……………………………………………………………………………….…….. 13 1.6. NG2/CSPG4……………………………………………………………………….…….. 14 1.7. Metastasis………………………………………………………………………….….…. 16 1.8. Soft Tissue Sarcoma (STS)…………………………………………………………….. 17 1.9. Membrane PGs and tumour……………………………………………………………. 18 1.10. Membrane PGs in sarcoma…………………………………………………………….. 24 2. Material and Methods ……………………………………………………………………… 26 2.1. Cell Culture……………………………………………………………………….………. 27 2.2. RNA extraction……………………………………………………………………….…. 28 2.3. Real Time quantitative PCR……………………………………………….………….. 28 2.4. DNA extraction…………………………………………….……………………………. 30 2.5. Plasmids and Transfection………………………………………….………………… 30 2.6. Western Blotting………………………………………………………………………... 31 2.7. Preparation of ECM substrates………………………………………….……………
    [Show full text]
  • Supplementary Table 1: Adhesion Genes Data Set
    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
    [Show full text]
  • 1 Mutational Heterogeneity in Cancer Akash Kumar a Dissertation
    Mutational Heterogeneity in Cancer Akash Kumar A dissertation Submitted in partial fulfillment of requirements for the degree of Doctor of Philosophy University of Washington 2014 June 5 Reading Committee: Jay Shendure Pete Nelson Mary Claire King Program Authorized to Offer Degree: Genome Sciences 1 University of Washington ABSTRACT Mutational Heterogeneity in Cancer Akash Kumar Chair of the Supervisory Committee: Associate Professor Jay Shendure Department of Genome Sciences Somatic mutation plays a key role in the formation and progression of cancer. Differences in mutation patterns likely explain much of the heterogeneity seen in prognosis and treatment response among patients. Recent advances in massively parallel sequencing have greatly expanded our capability to investigate somatic mutation. Genomic profiling of tumor biopsies could guide the administration of targeted therapeutics on the basis of the tumor’s collection of mutations. Central to the success of this approach is the general applicability of targeted therapies to a patient’s entire tumor burden. This requires a better understanding of the genomic heterogeneity present both within individual tumors (intratumoral) and amongst tumors from the same patient (intrapatient). My dissertation is broadly organized around investigating mutational heterogeneity in cancer. Three projects are discussed in detail: analysis of (1) interpatient and (2) intrapatient heterogeneity in men with disseminated prostate cancer, and (3) investigation of regional intratumoral heterogeneity in
    [Show full text]
  • Identification of 526 Conserved Metazoan Genetic Innovations Exposes a New Role for Cofactor E-Like in Neuronal Microtubule Homeostasis
    Identification of 526 Conserved Metazoan Genetic Innovations Exposes a New Role for Cofactor E-like in Neuronal Microtubule Homeostasis Melissa Y. Fre´de´ric1., Victor F. Lundin1,2., Matthew D. Whiteside1, Juan G. Cueva2, Domena K. Tu1, S. Y. Catherine Kang1,3, Hansmeet Singh2, David L. Baillie1, Harald Hutter4, Miriam B. Goodman2, Fiona S. L. Brinkman1, Michel R. Leroux1* 1 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada, 2 Department of Molecular and Cellular Physiology, Stanford University, Stanford, California, United States of America, 3 Department of Cancer Control Research, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada, 4 Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada Abstract The evolution of metazoans from their choanoflagellate-like unicellular ancestor coincided with the acquisition of novel biological functions to support a multicellular lifestyle, and eventually, the unique cellular and physiological demands of differentiated cell types such as those forming the nervous, muscle and immune systems. In an effort to understand the molecular underpinnings of such metazoan innovations, we carried out a comparative genomics analysis for genes found exclusively in, and widely conserved across, metazoans. Using this approach, we identified a set of 526 core metazoan- specific genes (the ‘metazoanome’), approximately 10% of which are largely uncharacterized, 16% of which are associated with known human disease, and 66% of which are conserved in Trichoplax adhaerens, a basal metazoan lacking neurons and other specialized cell types. Global analyses of previously-characterized core metazoan genes suggest a prevalent property, namely that they act as partially redundant modifiers of ancient eukaryotic pathways.
    [Show full text]
  • The Expression of Cell Surface Heparan Sulfate Proteoglycans and Their Roles in Turkey Skeletal Muscle Formation
    THE EXPRESSION OF CELL SURFACE HEPARAN SULFATE PROTEOGLYCANS AND THEIR ROLES IN TURKEY SKELETAL MUSCLE FORMATION DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Xiaosong Liu, M.S. ***** The Ohio State University 2003 Dissertation Committee: Approved by Dr. Sandra G. Velleman, Advisor Dr. Karl E. Nestor Dr. Joy L. Pate _______________________ Advisor Dr. Wayne L. Bacon Department of Animal Sciences ABSTRACT Skeletal muscle myogenesis is a series of highly organized processes including cell migration, adhesion, proliferation, and differentiation that are precisely regulated by the extrinsic environment of muscle cells. Fibroblast growth factor 2 (FGF2) is one of the key growth factors involved in the regulation of skeletal muscle myogenesis. Since FGF2 is a potent stimulator of skeletal muscle cell proliferation but an intense inhibitor of cell differentiation, changes in FGF2 signaling to muscle cells will influence cell behavior and result in differences in cell proliferation and differentiation. As the cell surface heparan sulfate proteoglycans (HSPG), syndecans and glypicans, are the low- affinity receptors of FGF2 and function to regulate the binding of FGF2 to the high- affinity fibroblast growth factor receptors (FGFR) and affect the activity of FGF2, differences in the expression of these molecules may cause alterations in cell responsiveness to FGF2 stimulation, which can lead to changes in skeletal muscle development and growth. However, the precise functional differences of syndecans and glypicans in FGF2 signaling are unknown to date. Our hypothesis is that syndecans and glypicans may play different roles in regulating the FGF2-FGFR interaction, and the relative expression of these molecules is critical for determining the cell status in proliferation and differentiation.
    [Show full text]
  • Evolution of Gene Expression Between Closely Related Taxa of Mus
    Evolution of gene expression between closely related taxa of Mus I n a u g u r a l – D i s s e r t a t i o n zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Universität zu Köln vorgelegt von Christian Voolstra aus Offenbach am Main Köln, 2006 Berichterstatter: Prof. Dr. Diethard Tautz Prof. Dr. Thomas Wiehe Tag der letzten mündlichen Prüfung: 29.05.2006 Table of Contents Table of Contents Table of Contents ........................................................................................................................i Danksagung................................................................................................................................ v Zusammenfassung.....................................................................................................................vi Abstract ...................................................................................................................................viii 1 Introduction ........................................................................................................................ 1 1.1 Microarrays as a tool to study evolution of gene expression ..................................... 1 1.2 Intra-specific transcriptome variation ........................................................................ 2 1.3 Inter-specific transcriptome variation - tempo and mode of transcriptome evolution3 1.4 Transcriptome divergence and speciation.................................................................. 4 1.5 The genetic
    [Show full text]
  • Diagnostic and Prognostic Significance of Glypican 5 and Glypican 6 Gene Expression Levels in Gastric Adenocarcinoma
    584 MOLECULAR AND CLINICAL ONCOLOGY 3: 584-590, 2015 Diagnostic and prognostic significance of glypican 5 and glypican 6 gene expression levels in gastric adenocarcinoma MELIKE DINCCELIK-ASLAN1, GUVEM GUMUS-AKAY2, ATILLA HALIL ELHAN3, EKREM UNAL4 and AJLAN TUKUN5 1Biotechnology Institute, Ankara University, Golbasi, Ankara 06830; 2Brain Research Centre, Ankara University, Mamak, Ankara 06900; 3Department of Biostatistics, Faculty of Medicine, Ankara University, Sihhiye, Ankara 06100; 4Department of Surgical Oncology, Research and Training Hospital, Faculty of Medicine, Ankara University, Cebeci, Ankara 06580; 5Department of Medical Genetics, Faculty of Medicine, Ankara University, Sihhiye, Ankara 06100, Turkey Received May 16, 2014; Accepted December 9, 2014 DOI: 10.3892/mco.2015.486 Abstract. Gastric cancer is one of the most common malig- demonstrated that multiple genetic alterations are responsible nancies worldwide and the second most common cause of for the development and progression of gastric cancer (2,3). cancer-related mortality. Previous studies revealed several Genomic amplification is one of the most common types genetic alterations specific to gastric cancer. In this study, we of genetic abnormalities encountered in gastric cancer and aimed to investigate the diagnostic and prognostic significance frequently leads to the overexpression of genes that may of the expression levels of the glypican 5 and glypican 6 affect cellular behavior. Therefore, the identification of the genes (GPC5 and GPC6, respectively) in gastric cancer. For genes residing at the genomic amplification regions may help this purpose, GPC5 and GPC6 expression was quantitatively researchers elucidate the details of the tumorigenic processes determined by quantitative polymerase chain reaction method in gastric cancer and identify diagnostic and/or prognostic in normal gastric mucosa and intestinal type gastric adeno- markers, which may also serve as novel target molecules for carcinoma samples from 35 patients.
    [Show full text]
  • Mutations in the Heparan-Sulfate Proteoglycan Glypican 6 (GPC6) Impair Endochondral Ossification and Cause Recessive Omodysplasia
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector ARTICLE Mutations in the Heparan-Sulfate Proteoglycan Glypican 6 (GPC6) Impair Endochondral Ossification and Cause Recessive Omodysplasia Ana Belinda Campos-Xavier,1 Danielle Martinet,2 John Bateman,3 Dan Belluoccio,3 Lynn Rowley,3 Tiong Yang Tan,4 Alica Baxova´,5 Karl-Henrik Gustavson,6 Zvi U. Borochowitz,7 A. Micheil Innes,8 Sheila Unger,9,11 Jacques S. Beckmann,2,10 Laure´ane Mittaz,1 Diana Ballhausen,1 Andrea Superti-Furga,11 Ravi Savarirayan,4 and Luisa Bonafe´1,* Glypicans are a family of glycosylphosphatidylinositol (GPI)-anchored, membrane-bound heparan sulfate (HS) proteoglycans. Their bio- logical roles are only partly understood, although it is assumed that they modulate the activity of HS-binding growth factors. The involvement of glypicans in developmental morphogenesis and growth regulation has been highlighted by Drosophila mutants and by a human overgrowth syndrome with multiple malformations caused by glypican 3 mutations (Simpson-Golabi-Behmel syndrome). We now report that autosomal-recessive omodysplasia, a genetic condition characterized by short-limbed short stature, craniofacial dys- morphism, and variable developmental delay, maps to chromosome 13 (13q31.1-q32.2) and is caused by point mutations or by larger genomic rearrangements in glypican 6 (GPC6). All mutations cause truncation of the GPC6 protein and abolish both the HS-binding site and the GPI-bearing membrane-associated domain, and thus loss of function is predicted. Expression studies in microdissected mouse growth plate revealed expression of Gpc6 in proliferative chondrocytes. Thus, GPC6 seems to have a previously unsuspected role in endo- chondral ossification and skeletal growth, and its functional abrogation results in a short-limb phenotype.
    [Show full text]
  • Genomic Structure and Marker-Derived Gene Networks for Growth and Meat Quality Traits of Brazilian Nelore Beef Cattle Maurício A
    Mudadu et al. BMC Genomics (2016) 17:235 DOI 10.1186/s12864-016-2535-3 RESEARCH ARTICLE Open Access Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle Maurício A. Mudadu1,2*† , Laercio R. Porto-Neto3†, Fabiana B. Mokry4†, Polyana C. Tizioto4, Priscila S. N. Oliveira4, Rymer R. Tullio2, Renata T. Nassu2, Simone C. M. Niciura2, Patrícia Tholon2, Maurício M. Alencar2, Roberto H. Higa1, Antônio N. Rosa5, Gélson L. D. Feijó5, André L. J. Ferraz6, Luiz O. C. Silva5, Sérgio R. Medeiros5, Dante P. Lanna7, Michele L. Nascimento7, Amália S. Chaves7, Andrea R. D. L. Souza8, Irineu U. Packer7ˆ, Roberto A. A. Torres Jr.5, Fabiane Siqueira5, Gerson B. Mourão7, Luiz L. Coutinho7, Antonio Reverter3 and Luciana C. A. Regitano2 Abstract Background: Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.
    [Show full text]
  • Molecular Sciences High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorder
    Int. J. Mol. Sci. 2015, 16, 6464-6495; doi:10.3390/ijms16036464 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorders Merlin G. Butler *, Syed K. Rafi † and Ann M. Manzardo † Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA; E-Mails: [email protected] (S.K.R.); [email protected] (A.M.M.) † These authors contributed to this work equally. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-913-588-1873; Fax: +1-913-588-1305. Academic Editor: William Chi-shing Cho Received: 23 January 2015 / Accepted: 16 March 2015 / Published: 20 March 2015 Abstract: Recently, autism-related research has focused on the identification of various genes and disturbed pathways causing the genetically heterogeneous group of autism spectrum disorders (ASD). The list of autism-related genes has significantly increased due to better awareness with advances in genetic technology and expanding searchable genomic databases. We compiled a master list of known and clinically relevant autism spectrum disorder genes identified with supporting evidence from peer-reviewed medical literature sources by searching key words related to autism and genetics and from authoritative autism-related public access websites, such as the Simons Foundation Autism Research Institute autism genomic database dedicated to gene discovery and characterization. Our list consists of 792 genes arranged in alphabetical order in tabular form with gene symbols placed on high-resolution human chromosome ideograms, thereby enabling clinical and laboratory geneticists and genetic counsellors to access convenient visual images of the location and distribution of ASD genes.
    [Show full text]
  • The Analysis of the Mcf7 Cancer Model System And
    THE ANALYSIS OF THE MCF7 CANCER MODEL SYSTEM AND THE EFFECTS OF 5-AZA-2’-DEOXYCYTIDINE TREATMENT ON THE CHROMATIN STATE USING A NOVEL MICROARRAY-BASED TECHNOLOGY FOR HIGH RESOLUTION GLOBAL CHROMATIN STATE MEASUREMENT APPROVED BY SUPERVISORY COMMITTEE Harold Garner, Ph.D. Elliott Ross, Ph.D. Thomas Kodadek, Ph.D. John Minna, M.D. Keith Wharton, M.D., Ph.D. DEDICATION Omnibus qui adiuverunt THE ANALYSIS OF THE MCF7 CANCER MODEL SYSTEM AND THE EFFECTS OF 5-AZA-2’-DEOXYCYTIDINE TREATMENT ON THE CHROMATIN STATE USING A NOVEL MICROARRAY-BASED TECHNOLOGY FOR HIGH RESOLUTION GLOBAL CHROMATIN STATE MEASUREMENT by MICHAEL RYAN WEIL DISSERTATION Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY The University of Texas Southwestern Medical Center at Dallas Dallas, Texas March, 2006 Copyright by Michael Ryan Weil All Rights Reserved THE ANALYSIS OF THE MCF7 CANCER MODEL SYSTEM AND THE EFFECTS OF 5-AZA-2’-DEOXYCYTIDINE TREATMENT ON THE CHROMATIN STATE USING A NOVEL MICROARRAY-BASED TECHNOLOGY FOR HIGH RESOLUTION GLOBAL CHROMATIN STATE MEASUREMENT Publication No. MICHAEL RYAN WEIL, B.S. The University of Texas Southwestern Medical Center at Dallas, 2006 Supervising Professor: Harold Ray (Skip) Garner, Ph.D. A microarray method to measure the global chromatin state of the human genome was developed in order to provide a novel view of gene regulation. The 'chromatin array' employs traditional methods of chromatin isolation, microarray technology, and advanced data analysis, and was applied to a cancer model system.
    [Show full text]
  • Full-Text PDF (Accepted Author Manuscript)
    Kemp, J. P., Medina-Gomez, C., Forgetta, V., Warrington, N. M., Youlten, S. E., Zheng, J., Gregson, C. L., Grundberg, E., Trajanoska, K., Logan, J. G., Pollard, A. S., Sparkes, P. C., Ghirardello, E. J., Leitch, V. D., Butterfield, N. C., Komla-Ebri, D., Adoum, A-T., Curry, K. F., White, J. K., ... Evans, D. M. (2017). Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis. Nature Genetics, 49, 1468–1475. https://doi.org/10.1038/ng.3949 Peer reviewed version Link to published version (if available): 10.1038/ng.3949 Link to publication record in Explore Bristol Research PDF-document This is the author accepted manuscript (AAM). The final published version (version of record) is available online via Nature at http://www.nature.com/doifinder/10.1038/ng.3949. Please refer to any applicable terms of use of the publisher. University of Bristol - Explore Bristol Research General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above. Full terms of use are available: http://www.bristol.ac.uk/red/research-policy/pure/user-guides/ebr-terms/ TITLE: Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis 1 AUTHOR LIST AND AFFILIATIONS John P Kemp1,2§, John A Morris3,4§, Carolina Medina-Gomez5,6§, Vincenzo Forgetta3, Nicole M Warrington1,7, Scott E Youlten8,9, Jie Zheng2, Celia L Gregson10, Elin Grundberg4, Katerina Trajanoska5,6,
    [Show full text]