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Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
Distinctive Regulatory Architectures of Germline-Active and Somatic Genes in C
Downloaded from genome.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press Research Distinctive regulatory architectures of germline-active and somatic genes in C. elegans Jacques Serizay, Yan Dong, Jürgen Jänes, Michael Chesney, Chiara Cerrato, and Julie Ahringer The Gurdon Institute and Department of Genetics, University of Cambridge, CB2 1QN Cambridge, United Kingdom RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory ar- chitectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regu- latory element activities across five tissues of Caenorhabditis elegans, covering ∼90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue–specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well-positioned +1 and −1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue–specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue–specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies. [Supplemental material is available for this article.] Cell type–specific transcription regulation underlies production tissues are achieved and whether expression is governed by dis- of the myriad of different cells generated during development. -
Personal and Population Genomics of Human Regulatory Variation
Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Research Personal and population genomics of human regulatory variation Benjamin Vernot, Andrew B. Stergachis, Matthew T. Maurano, Jeff Vierstra, Shane Neph, Robert E. Thurman, John A. Stamatoyannopoulos,1 and Joshua M. Akey1 Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA The characteristics and evolutionary forces acting on regulatory variation in humans remains elusive because of the difficulty in defining functionally important noncoding DNA. Here, we combine genome-scale maps of regulatory DNA marked by DNase I hypersensitive sites (DHSs) from 138 cell and tissue types with whole-genome sequences of 53 geo- graphically diverse individuals in order to better delimit the patterns of regulatory variation in humans. We estimate that individuals likely harbor many more functionally important variants in regulatory DNA compared with protein-coding regions, although they are likely to have, on average, smaller effect sizes. Moreover, we demonstrate that there is sig- nificant heterogeneity in the level of functional constraint in regulatory DNA among different cell types. We also find marked variability in functional constraint among transcription factor motifs in regulatory DNA, with sequence motifs for major developmental regulators, such as HOX proteins, exhibiting levels of constraint comparable to protein-coding regions. Finally, we perform a genome-wide scan of recent positive selection and identify hundreds of novel substrates of adaptive regulatory evolution that are enriched for biologically interesting pathways such as melanogenesis and adipo- cytokine signaling. These data and results provide new insights into patterns of regulatory variation in individuals and populations and demonstrate that a large proportion of functionally important variation lies beyond the exome. -
Genomic Approaches for Understanding the Genetics of Complex Disease
Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Perspective Genomic approaches for understanding the genetics of complex disease William L. Lowe Jr.1 and Timothy E. Reddy2,3 1Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA; 2Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, North Carolina 27708, USA; 3Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27708, USA There are thousands of known associations between genetic variants and complex human phenotypes, and the rate of novel discoveries is rapidly increasing. Translating those associations into knowledge of disease mechanisms remains a fundamental challenge because the associated variants are overwhelmingly in noncoding regions of the genome where we have few guiding principles to predict their function. Intersecting the compendium of identified genetic associations with maps of regulatory activity across the human genome has revealed that phenotype-associated variants are highly enriched in candidate regula- tory elements. Allele-specific analyses of gene regulation can further prioritize variants that likely have a functional effect on disease mechanisms; and emerging high-throughput assays to quantify the activity of candidate regulatory elements are a promising next step in that direction. Together, these technologies have created the ability to systematically and empirically test hypotheses about the function of noncoding variants and haplotypes at the scale needed for comprehensive and system- atic follow-up of genetic association studies. Major coordinated efforts to quantify regulatory mechanisms across genetically diverse populations in increasingly realistic cell models would be highly beneficial to realize that potential. -
The Economic Impact and Functional Applications of Human Genetics and Genomics
The Economic Impact and Functional Applications of Human Genetics and Genomics Commissioned by the American Society of Human Genetics Produced by TEConomy Partners, LLC. Report Authors: Simon Tripp and Martin Grueber May 2021 TEConomy Partners, LLC (TEConomy) endeavors at all times to produce work of the highest quality, consistent with our contract commitments. However, because of the research and/or experimental nature of this work, the client undertakes the sole responsibility for the consequence of any use or misuse of, or inability to use, any information or result obtained from TEConomy, and TEConomy, its partners, or employees have no legal liability for the accuracy, adequacy, or efficacy thereof. Acknowledgements ASHG and the project authors wish to thank the following organizations for their generous support of this study. Invitae Corporation, San Francisco, CA Regeneron Pharmaceuticals, Inc., Tarrytown, NY The project authors express their sincere appreciation to the following indi- viduals who provided their advice and input to this project. ASHG Government and Public Advocacy Committee Lynn B. Jorde, PhD ASHG Government and Public Advocacy Committee (GPAC) Chair, President (2011) Professor and Chair of Human Genetics George and Dolores Eccles Institute of Human Genetics University of Utah School of Medicine Katrina Goddard, PhD ASHG GPAC Incoming Chair, Board of Directors (2018-2020) Distinguished Investigator, Associate Director, Science Programs Kaiser Permanente Northwest Melinda Aldrich, PhD, MPH Associate Professor, Department of Medicine, Division of Genetic Medicine Vanderbilt University Medical Center Wendy Chung, MD, PhD Professor of Pediatrics in Medicine and Director, Clinical Cancer Genetics Columbia University Mira Irons, MD Chief Health and Science Officer American Medical Association Peng Jin, PhD Professor and Chair, Department of Human Genetics Emory University Allison McCague, PhD Science Policy Analyst, Policy and Program Analysis Branch National Human Genome Research Institute Rebecca Meyer-Schuman, MS Human Genetics Ph.D. -
Molecular Biology and Applied Genetics
MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included. -
Micropropagation, Genetic Engineering, and Molecular Biology Expression Vectors Containing the Gene(S) and Promoter(S) of Populus
This file was created by scanning the printed publication. Errors identified by the software have been corrected; however, some errors may remain. Chapter 11 Growth and Development Alteration in Transgenic Populus: Status and Potential Applications1 Bjorn Sundberg, Hannele Tuominen, Ove Nilsson, Thomas Moritz, c. H. Anthony Little, Goran Sandberg, and Olof Olsson Introduction Using Transgenic Populus to Study Growth and Development With the development of gene-transfer techniques appli cable to forest tree species, genetic engineering is becoming in Woody Species an alternative to traditional tree breeding. To date, routine transformation methods for several hardwood species, par The best model system for understanding the genetic ticularly Populus and Eucalyptus, have been established and and physiological control of tree growth and wood for promising advances have occurred in the development ~f mation is a perennial species containing a vascular cam transformation protocols for conifers (Olarest et al. 1996; Ellis bium, which is the meristem that produces secondary et al. 1996; Jouanin et al. 1993; Walters et al. 1995). Rapid xylem and phloem. Presently, Populus is the preferred tree progress in transformation technology makes it possible to model system because it has several useful fea.tures. develop genetic engineering tools that modify economically Populus has a small genome, approximately 5 x lOS base tractable parameters related to growth and yield in tree spe pairs (bp ), which encourages molecular mapping, library cies. Such work will also increase our understanding of ge screening, and rescue cloning. Saturated genetic maps are netic and physiological regulation of growth and already constructed for several Populus spp. (Bradshaw et development in woody species. -
Retrospective Evaluation of Whole Exome and Genome Mutation Calls in 746 Cancer Samples
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2020 Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples Matthew H. Bailey Washington University School of Medicine in St. Louis William U. Meyerson Yale University Lewis Jonathan Dursi Ontario Institute for Cancer Research Liang-Bo Wang Washington University School of Medicine in St. Louis Guanlan Dong Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Bailey, Matthew H.; Meyerson, William U.; Dursi, Lewis Jonathan; Wang, Liang-Bo; Dong, Guanlan; Liang, Wen-Wei; Weerasinghe, Amila; Li, Shantao; Kelso, Sean; MC3 Working Group; PCAWG novel somatic mutation calling methods working group; Saksena, Gordon; Ellrott, Kyle; Wendl, Michael C.; Wheeler, David A.; Getz, Gad; Simpson, Jared T.; Gerstein, Mark B.; Ding, Li; and PCAWG Consortium, ,"Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples." Nature Communications.,. (2020). https://digitalcommons.wustl.edu/open_access_pubs/9548 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Matthew H. Bailey, William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C. Wendl, David A. Wheeler, Gad Getz, Jared T. -
Glossary/Index
Glossary 03/08/2004 9:58 AM Page 119 GLOSSARY/INDEX The numbers after each term represent the chapter in which it first appears. additive 2 allele 2 When an allele’s contribution to the variation in a One of two or more alternative forms of a gene; a single phenotype is separately measurable; the independent allele for each gene is inherited separately from each effects of alleles “add up.” Antonym of nonadditive. parent. ADHD/ADD 6 Alzheimer’s disease 5 Attention Deficit Hyperactivity Disorder/Attention A medical disorder causing the loss of memory, rea- Deficit Disorder. Neurobehavioral disorders character- soning, and language abilities. Protein residues called ized by an attention span or ability to concentrate that is plaques and tangles build up and interfere with brain less than expected for a person's age. With ADHD, there function. This disorder usually first appears in persons also is age-inappropriate hyperactivity, impulsive over age sixty-five. Compare to early-onset Alzheimer’s. behavior or lack of inhibition. There are several types of ADHD: a predominantly inattentive subtype, a predomi- amino acids 2 nantly hyperactive-impulsive subtype, and a combined Molecules that are combined to form proteins. subtype. The condition can be cognitive alone or both The sequence of amino acids in a protein, and hence pro- cognitive and behavioral. tein function, is determined by the genetic code. adoption study 4 amnesia 5 A type of research focused on families that include one Loss of memory, temporary or permanent, that can result or more children raised by persons other than their from brain injury, illness, or trauma. -
On the Origin of Darwinism
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Preface On the origin of Darwinism Charles Darwin was almost scooped. A quintessential thinker, af- and W. Ford Doolittle and Olga Zhaxybayeva take a Darwinist ter five years voyaging around the globe on the HMS Beagle and view in demonstrating there’s no universally applicable pro- filling notebooks upon notebooks with his careful observations, karyotic ‘‘species’’ concept, but argue that, in the absence of spe- he did not rush to widely disseminate the conclusions of his field cies definitions, progress in metagenomics will surely guide us study. Almost 20 years passed during which he further reflected on toward a deeper understanding of evolution in these populations what he called ‘‘his theory’’ before he was urged to publish si- (Doolittle and Zhaxybayeva 2009). These reviews emphasize the multaneously with Alfred Russell Wallace, another naturalist and advances in our understanding of evolutionary concepts made great thinker, who had independently formulated similar con- possible by progress in genomic research, outline the current clusions on variation within species and survival of the fittest challenges we face, and offer likely paths ahead over the next few (Darwin and Wallace 1858). These first extracts from Darwin’s years. memoir were short and merely outlined what Darwin termed Primary research reports in this special issue all reflect Dar- ‘‘natural selection,’’ but they established that he was the father of winian themes. They include detailed analyses of fine-scale pop- what we now know to be one of the greatest conceptual con- ulation structure, human genetic variation, and recent positive tributions to science and society. -
Handbook of Epigenetics: the New Molecular and Medical Genetics
CHAPTER 21 Epigenetics, Stem Cells, Cellular Differentiation, and Associated Hereditary Neurological Disorders Bhairavi Srinageshwar*, Panchanan Maiti*,**, Gary L. Dunbar*,**, Julien Rossignol* *Central Michigan University, Mt. Pleasant, MI, United States; **Field Neurosciences Institute, Saginaw, MI, United States OUTLINE Introduction to Epigenetics 323 Histones and Their Structure 325 Epigenetics and Neurological Disorders 326 Epigenetics and the Human Brain 324 Stem Cells 324 Conclusions 335 Eukaryotic Chromosomal Organization 325 References 336 INTRODUCTION TO EPIGENETICS changes are discussed in detail elsewhere [3,4], but are briefly described later as an overview for this chapter. Epigenetics is defined as structural and functional DNA methylation. DNA methylation and some of the changes occurring in histones and DNA, in the absence histone modifications are interdependent and play an of alterations of the DNA sequence, which, in turn, has important role in gene activation and repression during a significant impact on how gene expression is altered development [5]. DNA methylation reactions are cata- in a cell [1]. The term “epigenetics” was coined by the lyzed by a family of enzymes called DNA methyl trans- famous developmental biologist, Cornard Hal Wad- ferases (DNMTs), which add methyl groups to a cytosine dington, as “the branch of biology that studies the causal base of the DNA at the 5’-end, giving rise to the 5’-methyl interactions between genes and their products, which cytosine. This reaction can either activate or repress gene bring the phenotype into being”[2]. Epigenetics bridge expression, depending on the site of methylation and it the gap between the environment and gene expression, can also determine how well the enzymes for gene tran- which was once believed to function independently [3]. -
Computational Proteomics for Genome Annotation
A thesis submitted to The University of Manchester for the Degree of PhD in the Faculty of Life Sciences Computational Proteomics for Genome Annotation Paul David Blakeley January 2013 1 List of Contents List of Figures ....................................................................................................................... 5 List of Tables ........................................................................................................................ 6 Abstract ................................................................................................................................. 7 Declaration ............................................................................................................................ 8 Copyright .............................................................................................................................. 9 Acknowledgements ............................................................................................................. 10 The Author .......................................................................................................................... 11 Rationale for an Alternative Format Thesis .................................................................... 12 Abbreviations ..................................................................................................................... 13 Chapter 1: Introduction .................................................................................................... 14 1.1. Genome annotation