DOCSLIB.ORG

Common Variation Near ROBO2 Is Associated with Expressive Vocabulary in Infancy Beate St Pourcain1,2,3,*, Rolieke A.M

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Common Variation Near ROBO2 Is Associated with Expressive Vocabulary in Infancy Beate St Pourcain1,2,3,*, Rolieke A.M ARTICLE Received 15 Jan 2014 | Accepted 28 Jul 2014 | Published 16 Sep 2014 DOI: 10.1038/ncomms5831 OPEN Common variation near ROBO2 is associated with expressive vocabulary in infancy Beate St Pourcain1,2,3,*, Rolieke A.M. Cents4,5,*, Andrew J.O. Whitehouse6,*, Claire M.A. Haworth7,8,*, Oliver S.P. Davis8,9,*, Paul F. O’Reilly8,10, Susan Roulstone11, Yvonne Wren11,QiW.Ang12, Fleur P. Velders4,5, David M. Evans1,13,14, John P. Kemp1,13,14, Nicole M. Warrington12,14, Laura Miller13, Nicholas J. Timpson1,13, Susan M. Ring1,13, Frank C. Verhulst5, Albert Hofman15, Fernando Rivadeneira15,16, Emma L. Meaburn17, Thomas S. Price18, Philip S. Dale19, Demetris Pillas10, Anneli Yliherva20, Alina Rodriguez10,21, Jean Golding13, Vincent W.V. Jaddoe4,15,22, Marjo-Riitta Jarvelin10,23,24,25,26, Robert Plomin8, Craig E. Pennell12, Henning Tiemeier5,15,* & George Davey Smith1,13 Twin studies suggest that expressive vocabulary at B24 months is modestly heritable. However, the genes influencing this early linguistic phenotype are unknown. Here we conduct a genome-wide screen and follow-up study of expressive vocabulary in toddlers of European descent from up to four studies of the EArly Genetics and Lifecourse Epidemiology consortium, analysing an early (15–18 months, ‘one-word stage’, NTo ta l ¼ 8,889) and a later (24–30 months, ‘two-word stage’, NTo ta l ¼ 10,819) phase of language acquisition. For the early phase, one single-nucleotide polymorphism (rs7642482) at 3p12.3 near ROBO2, encoding a conserved axon-binding receptor, reaches the genome-wide significance level (P ¼ 1.3 Â 10 À 8) in the combined sample. This association links language-related common genetic variation in the general population to a potential autism susceptibility locus and a linkage region for dyslexia, speech-sound disorder and reading. The contribution of common genetic influences is, although modest, supported by 2 2 genome-wide complex trait analysis (meta-GCTA h 15–18-months ¼ 0.13, meta-GCTA h 24–30-months ¼ 0.14) 2 and in concordance with additional twin analysis (5,733 pairs of European descent, h 24-months ¼ 0.20). 1 Medical Research Council Integrative Epidemiology Unit, University of Bristol, Oakfield House, 15-23 Oakfield Grove, Bristol BS8 2BN, UK. 2 School of Oral and Dental Sciences, University of Bristol, Lower Maudlin Street, Bristol BS1 2LY, UK. 3 School of Experimental Psychology, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK. 4 Generation R Study Group, Erasmus MC-University Medical Centre, Postbus 2040, 3000 CA Rotterdam, The Netherlands. 5 Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC-University Medical Centre, Postbus 2060, 3000 CB Rotterdam, The Netherlands. 6 Telethon Kids Institute, Centre for Child Health Research, University of Western Australia, 100 Roberts Road, Subiaco, Western Australia 6008, Australia. 7 Department of Psychology, University of Warwick, Coventry CV4 7AL, UK. 8 Medical Research Council, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, De Crespigny Park, Denmark Hill, London SE5 8AF, UK. 9 Department of Genetics, Evolution and Environment, UCL, UCL Genetics Institute, Darwin Building, Gower Street, London WC1E 6BT, UK. 10 Department of Epidemiology and Biostatistics, Medical Research Council (MRC) Public Health England (PHE) Centre for Environment and Health, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK. 11 Bristol Speech and Language Therapy Research Unit, University of the West of England, Frenchay Hospital, Frenchay Park Road, BS16 1LE Bristol, UK. 12 School of Women’s and Infants’ Health, University of Western Australia, 374 Bagot Road, Subiaco, Western Australia 6008, Australia. 13 School of Social and Community Medicine, University of Bristol, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, UK. 14 University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, 37 Kent Street Woolloongabba, Queensland 4102, Australia. 15 Department of Epidemiology, Erasmus MC-University Medical Centre, Postbus 2040, 3000 CA Rotterdam, The Netherlands. 16 Department of Internal Medicine, Erasmus MC-University Medical Centre, Postbus 2040, 3000 CA Rotterdam, The Netherlands. 17 Department of Psychological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK. 18 Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, 3400 Civic Center Boulevard, Building 421, Philadelphia, Pennsylvania 19104-5158, USA. 19 Department of Speech and Hearing Sciences, University of New Mexico, 1700 Lomas Boulevard NE Suite 1300, Albuquerque, New Mexico 87131, USA. 20 Faculty of Humanities, Logopedics, Child Language Research Center, University of Oulu, BOX 1000, Oulu 90014, Finland. 21 Mid Sweden University Department for Psychology/Mittuniversitetet Avdelningen fo¨r psykologi, 83125 O¨ stersund, Sweden. 22 Department of Pediatrics, Erasmus MC-University Medical Centre, Postbus 2060, 3000 CB Rotterdam, The Netherlands. 23 Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, PO Box 20, FI-90220, Oulu 90029, Finland. 24 Department of Children and Young People and Families, National Institute for Health and Welfare, Aapistie 1, Box 310, FI-90101 Oulu, Finland. 25 Institute of Health Sciences, University of Oulu, PO Box 5000, Oulu FI-90014, Finland. 26 Biocenter Oulu, University of Oulu, PO Box 5000, Aapistie 5A, OuluFI-90014, Finland. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to B.S.P. (email: [email protected]). NATURE COMMUNICATIONS | 5:4831 | DOI: 10.1038/ncomms5831 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms5831 he number of distinct spoken words is a widely used association signal was observed at rs7642482 on chromosome measure of early language abilities, which manifests during 3p12.3 near ROBO2 (P ¼ 9.5 Â 10 À 7, Supplementary Table 1) Tinfancy1. Word comprehension (known as receptive and for the late phase at rs11742977 on chromosome 5q22.1 language) in typically developing children starts at the age of within CAMK4 (P ¼ 3.5 Â 10 À 7, Supplementary Table 2). All about 6–9 months2, and the spontaneous production of words independent variants from the discovery analysis (associated (known as expressive language) emerges at about 10–15 Pr10 À 4, Supplementary Tables 1 and 2), including these SNPs, months1,3. During the next months the accumulation of words were taken forward to a follow-up study (Methods). This is typically slow, but then followed by an increase in rate, often included 2,038 18-month-old Dutch-speaking children for the quite sharp, around 14–22 months of age (‘vocabulary spurt’)1,4. early phase and 4,520 24–30-month-old Dutch or English- As development progresses, linguistic proficiency becomes more speaking children for the later phase (Supplementary Data 1). advanced, with two-word combinations (18–24 months of age)1,3 For four independent loci from the early phase GWAS and more complex grammatical structures (24–36 months of (rs7642482, rs10734234, rs11176749 and rs1654584), but none age)1,3 arising, accompanied by the steady increase in vocabulary for the later phase analysis, we found evidence for association size. Expressive vocabulary is therefore considered to be a rapidly within the follow-up cohort (Po0.05), assuming the same changing phenotype, especially between 12 and 24 months5, with direction of effect as in the discovery sample (Table 1; zero size at birth, B50 words at 15–18 months1,3, B200 words at Supplementary Tables 1–4). In the combined analysis of all 18–30 months1,3, B14,000 words at 6 years of age3,4 and available samples (Table 1; Fig. 3a–d) rs7642482 on chromosome Z50,000 words in high school graduates6,7. 3p12.3 near ROBO2 (the strongest signal in the discovery cohort) Twin analyses of cross-sectional data suggest that expressive reached the genome-wide significance level (P ¼ 1.3 Â 10 À 8), and vocabulary at B24 months is modestly heritable (h2 ¼ 0.16– the three other signals approached the suggestive level 0.38)8,9, and longitudinal twin analyses have reported an increase (rs10734234 on chromosome 11p15.2 near INSC, P ¼ 1.9 Â in heritability of language-related factors during development 10 À 7; rs11176749 on chromosome 12q15 near CAND1; (h2 ¼ 0.47–0.63, Z7 years of age)10. Large-scale investigations of P ¼ 7.2 Â 10 À 7 and rs1654584 on chromosome 19p13.3 within common genetic variation underlying growth in language skills, DAPK3; P ¼ 3.4 Â 10 À 7). however, are challenging owing to the complexity and varying Each of these four polymorphisms explained only a small nature of the phenotype. This is coupled with a change in proportion of the phenotypic variance (adjusted regression R2: for psychological instruments, which are used to assess these rs7642482 ¼ 0.34–0.35%, rs10734234 ¼ 0.27–0.35%, rs11176749 abilities with progressing age. Current genome-wide association ¼ 0.25–0.27% and rs1654584 ¼ 0.22–0.49%) in both the dis- studies (GWASs) using cross-sectional data on language covery and the follow-up cohort, but together the four SNPs abilities in childhood and adolescence have failed to identify accounted for 41% of the variation in early expressive robust signals of genome-wide association11,12, and genes vocabulary scores (joint adjusted regression R2 ¼ 1.10–1.45%). influencing earlier, less-complex linguistic phenotypes are For the SNP reaching genome-wide significance, rs7642482, each currently unknown. increase in the minor G-allele was associated with lower To attempt to understand genetic factors involved in language expressive vocabulary, although, due to the rank-transformation, development during infancy and early childhood, we perform a an interpretation of the magnitude of the genetic effect is not GWAS and follow-up study of expressive vocabulary scores in informative. An empirical estimate of the genetic effect in the independent children of European descent from the general discovery sample, suggested a decrease of 0.098 s.d.
Load more

Recommended publications
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • A Cell Surface Interaction Network of Neural Leucine-Rich Repeat Receptors Christian Söllner*† and Gavin J Wright*
    Open Access Research2009SöllnerVolume and 10, IssueWright 9, Article R99 A cell surface interaction network of neural leucine-rich repeat receptors Christian Söllner*† and Gavin J Wright* Addresses: *Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK. †Current address: Max Planck Institute for Developmental Biology, Department 3 (Genetics), Spemannstraße 35, 72076 Tübingen, Germany. Correspondence: Christian Söllner. Email: [email protected]. Gavin J Wright. Email: [email protected] Published: 18 September 2009 Received: 9 June 2009 Revised: 18 August 2009 Genome Biology 2009, 10:R99 (doi:10.1186/gb-2009-10-9-r99) Accepted: 18 September 2009 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2009/10/9/R99 © 2009 Söllner and Wright; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. An<p>A extracellular network of neuroreceptor Zebrafish extracellular interaction neuroreceptor network interactions are revealed using AVEXIS, a highly stringent interaction assay.</p> Abstract Background: The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families
    [Show full text]
  • Multivariate Analysis Reveals Genetic Associations of the Resting Default
    Multivariate analysis reveals genetic associations of PNAS PLUS the resting default mode network in psychotic bipolar disorder and schizophrenia Shashwath A. Medaa,1, Gualberto Ruañob,c, Andreas Windemuthb, Kasey O’Neila, Clifton Berwisea, Sabra M. Dunna, Leah E. Boccaccioa, Balaji Narayanana, Mohan Kocherlab, Emma Sprootena, Matcheri S. Keshavand, Carol A. Tammingae, John A. Sweeneye, Brett A. Clementzf, Vince D. Calhoung,h,i, and Godfrey D. Pearlsona,h,j aOlin Neuropsychiatry Research Center, Institute of Living at Hartford Hospital, Hartford, CT 06102; bGenomas Inc., Hartford, CT 06102; cGenetics Research Center, Hartford Hospital, Hartford, CT 06102; dDepartment of Psychiatry, Beth Israel Deaconess Hospital, Harvard Medical School, Boston, MA 02215; eDepartment of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390; fDepartment of Psychology, University of Georgia, Athens, GA 30602; gThe Mind Research Network, Albuquerque, NM 87106; Departments of hPsychiatry and jNeurobiology, Yale University, New Haven, CT 06520; and iDepartment of Electrical and Computer Engineering, The University of New Mexico, Albuquerque, NM 87106 Edited by Robert Desimone, Massachusetts Institute of Technology, Cambridge, MA, and approved April 4, 2014 (received for review July 15, 2013) The brain’s default mode network (DMN) is highly heritable and is Although risk for psychotic illnesses is driven in small part by compromised in a variety of psychiatric disorders. However, ge- highly penetrant, often private mutations such as copy number netic control over the DMN in schizophrenia (SZ) and psychotic variants, substantial risk also is likely conferred by multiple genes bipolar disorder (PBP) is largely unknown. Study subjects (n = of small effect sizes interacting together (7). According to the 1,305) underwent a resting-state functional MRI scan and were “common disease common variant” (CDCV) model, one would analyzed by a two-stage approach.
    [Show full text]
  • 45568 ROBO2 (E4M6D) Rabbit Mab
    Revision 1 C 0 2 - t ROBO2 (E4M6D) Rabbit mAb a e r o t S Orders: 877-616-CELL (2355) [email protected] 8 Support: 877-678-TECH (8324) 6 5 Web: [email protected] 5 www.cellsignal.com 4 # 3 Trask Lane Danvers Massachusetts 01923 USA For Research Use Only. Not For Use In Diagnostic Procedures. Applications: Reactivity: Sensitivity: MW (kDa): Source/Isotype: UniProt ID: Entrez-Gene Id: WB, IP, IF-IC H M R Endogenous 180, 220 Rabbit IgG Q9HCK4 6092 Product Usage Information Application Dilution Western Blotting 1:1000 Immunoprecipitation 1:50 Immunofluorescence (Immunocytochemistry) 1:1600 Storage Supplied in 10 mM sodium HEPES (pH 7.5), 150 mM NaCl, 100 µg/ml BSA, 50% glycerol and less than 0.02% sodium azide. Store at –20°C. Do not aliquot the antibody. Specificity / Sensitivity ROBO2 (E4M6D) Rabbit mAb recognizes endogenous levels of total ROBO2 protein. Species Reactivity: Human, Mouse, Rat Source / Purification Monoclonal antibody is produced by immunizing animals with a synthetic peptide corresponding to residues surrounding Leu1172 of human ROBO2 protein. Background ROBO2 is a member of the roundabout (ROBO) receptor family (1). The activation of ROBO2 by SLIT ligand regulates various biological processes, including promoting stem cell senescence via WNT inhibition, destabilizing podocyte actin polymerization and adhesion, and activation of Ena/VASP to facilitate tumor cell extrusion from epithelia (2- 5). In development, the SLIT-ROBO pathways play important roles in neuronal axon guidance and synapse function, retinal neurovascular formation, and muscle patterning (6- 9). Loss of function mutations of ROBO2 have been associated with urinary tract anomalies and vesicoureteral reflux (10).
    [Show full text]
  • Identification of ROBO2 As a Potential Locus Associated with Inhaled
    Journal of Personalized Medicine Article Identification of ROBO2 as a Potential Locus Associated with Inhaled Corticosteroid Response in Childhood Asthma Natalia Hernandez-Pacheco 1,2,3,*,†, Mario Gorenjak 4 , Jiang Li 5 , Katja Repnik 4,6, Susanne J. Vijverberg 7,8,9, Vojko Berce 4,10 , Andrea Jorgensen 11, Leila Karimi 12 , Maximilian Schieck 13,14, Lesly-Anne Samedy-Bates 15,16, Roger Tavendale 17, Jesús Villar 3,18,19 , Somnath Mukhopadhyay 17,20, Munir Pirmohamed 21 , Katia M. C. Verhamme 12, Michael Kabesch 13, Daniel B. Hawcutt 22,23, Steve Turner 24 , Colin N. Palmer 17, Kelan G. Tantisira 5,25, Esteban G. Burchard 15,16, Anke H. Maitland-van der Zee 7,8,9 , Carlos Flores 1,3,26,27 , Uroš Potoˇcnik 4,6,*,‡ and Maria Pino-Yanes 2,3,27,‡ 1 Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Carretera General del Rosario 145, 38010 Santa Cruz de Tenerife, Spain; cfl[email protected] 2 Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Avenida Astrofísico Francisco Sánchez s/n, Faculty of Science, Apartado 456, 38200 San Cristóbal de La Laguna, Spain; [email protected] 3 CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Avenida de Monforte de Lemos, 5, 28029 Madrid, Spain; [email protected] 4 Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia; [email protected] (M.G.); [email protected] (K.R.); [email protected]
    [Show full text]
  • 'A' in Irish Vesicoureteric Reflux Patients Reveals Marked Cpg Island Variation
    www.nature.com/scientificreports OPEN Investigation of DNA variants specifc to ROBO2 Isoform ‘a’ in Irish vesicoureteric refux patients reveals marked CpG island variation John M. Darlow1,2*, Mark G. Dobson1,2, Andrew J. Green1,3, Prem Puri2,3,4 & David E. Barton 1,3 ROBO2 gene disruption causes vesicoureteric refux (VUR) amongst other congenital anomalies. Several VUR patient cohorts have been screened for variants in the ubiquitously expressed transcript, ROBO2b, but, apart from low levels in a few adult tissues, ROBO2a expression is confned to the embryo, and might be more relevant to VUR, a developmental disorder. ROBO2a has an alternative promoter and two alternative exons which replace the frst exon of ROBO2b. We screened probands from 251 Irish VUR families for DNA variants in these. The CpG island of ROBO2a, which includes the non-coding frst exon, was found to contain a run of six variants abolishing/creating CpG dinucleotides, including a novel variant, present in the VUR cases in one family, that was not present in 592 healthy Irish controls. In three of these positions, the CpG was created by the non-reference allele, and the reference allele was not the nucleotide that would result from spontaneous deamination of methylcytosine to thymine, suggesting that there might have been selection for variability in number of CpGs in this island. This is in marked contrast to the CpG island at the start of ROBO2b, which only contained a single variant that abolishes a CpG. ROBO2 is one of at least twenty genes implicated in non-syndromic vesicoureteric refux (VUR), though the majority of genetic aetiology of VUR is still unknown.
    [Show full text]
  • The Slit-Binding Ig1 Domain Is Required for Multiple Axon Guidance Activities of Drosophila Robo2
    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.07.443153; this version posted May 7, 2021. 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. The Slit-binding Ig1 domain is required for multiple axon guidance activities of Drosophila Robo2 LaFreda J. Howard1,2, Marie C. Reichert1, and Timothy A. Evans1* 1Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701 2 Current Address: City of Houston Health Department, Houston, TX 77054 *Corresponding author ([email protected]) Abstract Drosophila Robo2 is a member of the evolutionarily conserved Roundabout (Robo) family of axon guidance receptors. The canonical role of Robo receptors is to signal midline repulsion in response to their cognate Slit ligands, which bind to the N-terminal Ig1 domain in most Robo family members. In the Drosophila embryonic ventral nerve cord, Robo1 and Robo2 cooperate to signal Slit-dependent midline repulsion, while Robo2 also regulates the medial-lateral position of longitudinal axon pathways and acts non-autonomously to promote midline crossing of commissural axons. Although it is clear that Robo2 signals midline repulsion in response to Slit, it is less clear whether Robo2’s other activities are also Slit-dependent. To determine which of Robo2’s axon guidance roles depend on its Slit-binding Ig1 domain, we have used a CRISPR/Cas9-based strategy replace the endogenous robo2 gene with a robo2 variant from which the Ig1 domain has been deleted (robo2∆Ig1).
    [Show full text]
  • Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep
    animals Article Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep Wilber Hernández-Montiel 1,2, Mario Alberto Martínez-Núñez 3 , Julio Porfirio Ramón-Ugalde 1, Sergio Iván Román-Ponce 4,* , Rene Calderón-Chagoya 4 and Roberto Zamora-Bustillos 1,* 1 TecNM/Instituto Tecnológico de Conkal, Av. Tecnológico S/N, Conkal, Yucatán 97345, Mexico; [email protected] (W.H.-M.); [email protected] (J.P.R.-U.) 2 Departamento de Ciencias Agropecuarias, Universidad del Papaloapan, Loma Bonita Oaxaca 68400, Mexico 3 UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sierra Papacal-Chuburna Km 5, Mérida, Yucatán 97302, Mexico; [email protected] 4 Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, INIFAP, Ajuchitlán Colón, Querétaro 76280, Mexico; [email protected] * Correspondence: [email protected] (S.I.R.-P.); [email protected] (R.Z.-B.); Tel.: +52-5538718700 (ext. 80208) (S.I.R.-P.); +52-999-341-0860 (ext. 7631) (R.Z.-B.) Received: 8 January 2020; Accepted: 29 February 2020; Published: 4 March 2020 Simple Summary: Reproductive traits are economically important in the livestock industry, and this is of greater relevance when it comes to indigenous animals, since their study allows improving their use and management. Through a genome-wide association study (GWAS), the reproductive trait of the litter size (prolificity) was analyzed in the indigenous Pelibuey sheep. Several single-nucleotide polymorphisms (SNPs) and candidate genes potentially associated with litter size trait were found in the multiparous ewe’s group. These findings help to understand the genetic basis of reproductive traits of hairy Pelibuey sheep.
    [Show full text]
  • High-Density Array Comparative Genomic Hybridization Detects Novel Copy Number Alterations in Gastric Adenocarcinoma
    ANTICANCER RESEARCH 34: 6405-6416 (2014) High-density Array Comparative Genomic Hybridization Detects Novel Copy Number Alterations in Gastric Adenocarcinoma ALINE DAMASCENO SEABRA1,2*, TAÍSSA MAÍRA THOMAZ ARAÚJO1,2*, FERNANDO AUGUSTO RODRIGUES MELLO JUNIOR1,2, DIEGO DI FELIPE ÁVILA ALCÂNTARA1,2, AMANDA PAIVA DE BARROS1,2, PAULO PIMENTEL DE ASSUMPÇÃO2, RAQUEL CARVALHO MONTENEGRO1,2, ADRIANA COSTA GUIMARÃES1,2, SAMIA DEMACHKI2, ROMMEL MARIO RODRÍGUEZ BURBANO1,2 and ANDRÉ SALIM KHAYAT1,2 1Human Cytogenetics Laboratory and 2Oncology Research Center, Federal University of Pará, Belém Pará, Brazil Abstract. Aim: To investigate frequent quantitative alterations gastric cancer is the second most frequent cancer in men and of intestinal-type gastric adenocarcinoma. Materials and the third in women (4). The state of Pará has a high Methods: We analyzed genome-wide DNA copy numbers of 22 incidence of gastric adenocarcinoma and this disease is a samples and using CytoScan® HD Array. Results: We identified public health problem, since mortality rates are above the 22 gene alterations that to the best of our knowledge have not Brazilian average (5). been described for gastric cancer, including of v-erb-b2 avian This tumor can be classified into two histological types, erythroblastic leukemia viral oncogene homolog 4 (ERBB4), intestinal and diffuse, according to Laurén (4, 6, 7). The SRY (sex determining region Y)-box 6 (SOX6), regulator of intestinal type predominates in high-risk areas, such as telomere elongation helicase 1 (RTEL1) and UDP- Brazil, and arises from precursor lesions, whereas the diffuse Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5 type has a similar distribution in high- and low-risk areas and (B4GALT5).
    [Show full text]
  • Array-Based Profiling of the Differential Methylation Status of Cpg Islands in Hepatocellular Carcinoma Cell Lines
    ONCOLOGY LETTERS 1: 815-820, 2010 Array-based profiling of the differential methylation status of CpG islands in hepatocellular carcinoma cell lines BIN-BIN LIU, DAN ZHENG, YIN-KUN LIU, XIAO-NAN KANG, LU SUN, KUN GUO, RUI-XIA SUN, JIE CHEN and YAN ZHAO Liver Cancer Institute, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China Received February 8, 2010; Accepted June 26, 2010 DOI: 10.3892/ol_00000143 Abstract. Alterations in the DNA methylation status particularly genes was linked to the pathogenesis of various types of in CpG islands are involved in the initiation and progression of cancer, and tumor-specific methylation changes were estab- many types of human cancer. A number of DNA methylation lished as prognostic markers in numerous tumor entities (3). alterations have been reported in hepatocellular carcinoma Unlike genetic modifications, such as mutations or genomic (HCC). However, a systematic analysis is required to elucidate imbalances, epigenetic changes are potentially reversible, the relationship between differential DNA methylation status making these changes particularly important therapeutic targets and the characteristics and progression of HCC. In the present in cancer and other diseases (4). study, a global analysis of DNA methylation using a human In recent years, different techniques have been developed CpG-island 12K array was performed on a number of HCC for the genome-wide screening of CGI methylation status. cell lines of different origin and metastatic potential. Based on Included is differential methylation hybridization (DMH) a standard methylation alteration ratio of ≥2 or ≤0.5, 58 CpG which is a high-throughput DNA methylation screening tool island sites and 66 tumor-related genes upstream, downstream that utilizes methylation-sensitive restriction enzymes to or within were identified.
    [Show full text]
  • The Functional and Structural Analysis of Drosophila Robo2 in Axon Guidance
    University of Arkansas, Fayetteville ScholarWorks@UARK Theses and Dissertations 8-2019 The Functional and Structural Analysis of Drosophila robo2 in Axon Guidance LaFreda Janae Howard University of Arkansas, Fayetteville Follow this and additional works at: https://scholarworks.uark.edu/etd Part of the Cell Biology Commons, Computational Biology Commons, Genetics Commons, and the Molecular and Cellular Neuroscience Commons Recommended Citation Howard, LaFreda Janae, "The Functional and Structural Analysis of Drosophila robo2 in Axon Guidance" (2019). Theses and Dissertations. 3379. https://scholarworks.uark.edu/etd/3379 This Dissertation is brought to you for free and open access by ScholarWorks@UARK. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ScholarWorks@UARK. For more information, please contact [email protected]. The Functional and Structural Analysis of Drosophila robo2 in Axon Guidance A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Cell and Molecular Biology by LaFreda Janae Howard Fort Valley State University Bachelor of Science in Biology, 2014 August 2019 University of Arkansas This dissertation is approved for recommendation to the Graduate Council. Timothy A. Evans, Ph.D. Dissertation Advisor Jeffrey Lewis, Ph.D. Ines Pinto, Ph.D. Committee Member Committee Member Michael Lehmann, Ph.D. Paul Adams, Ph.D. Committee Member Committee Member ABSTRACT In animals with complex nervous systems such as mammals and insects, signaling pathways are responsible for guiding axons to their appropriate synaptic targets. Importantly, when this process is not successful during the development of an organism, outcomes include catastrophes such as human neurological diseases and disorders.
    [Show full text]
  • Downloaded from Ensembl Biomart Martview Application to Perform the GO Enrichment Analysis
    life Article Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability Leyland Fraser 1,* , Łukasz Paukszto 2 , Anna Ma ´nkowska 1, Paweł Brym 3, Przemysław Gilun 4 , Jan P. Jastrz˛ebski 2 , Chandra S. Pareek 5 , Dibyendu Kumar 6 and Mariusz Pierzchała 7 1 Department of Animal Biochemistry and Biotechnology, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; [email protected] 2 Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; [email protected] (Ł.P.); [email protected] (J.P.J.) 3 Department of Animal Genetics, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; [email protected] 4 Department of Local Physiological Regulations, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Bydgoska 7, 10-243 Olsztyn, Poland; [email protected] 5 Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Toru´n,Poland; [email protected] 6 Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08554, USA; [email protected] 7 Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrz˛ebiec, 05-552 Magdalenka, Poland; [email protected] * Correspondence: [email protected] Received: 27 October 2020; Accepted: 19 November 2020; Published: 21 November 2020 Abstract: Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes.
    [Show full text]