Notes for an Undergraduate Course on Behavioral Genetics and Evolution
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Genotype, Phenotype and Cancer: Role of Low Penetrance Genes and Environment in Tumour Susceptibility
Genotype, phenotype and cancer: Role of low penetrance genes and environment in tumour susceptibility † ASHWIN KOTNIS, RAJIV SARIN and RITA MULHERKAR* Genetic Engineering, ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai 410 208, India †Tata Memorial Hospital, Parel, Mumbai 400 012, India *Corresponding author (Fax, 91-22-27412892; Email, [email protected]) Role of heredity and lifestyle in sporadic cancers is well documented. Here we focus on the influence of low penetrance genes and habits, with emphasis on tobacco habit in causing head and neck cancers. Role of such gene-environment interaction can be well studied in individuals with multiple primary cancers. Thus such a bio- logical model may elucidate that cancer causation is not solely due to genetic determinism but also significantly relies on lifestyle of the individual. [Kotnis A, Sarin R and Mulherkar R 2005 Genotype, phenotype and cancer: Role of low penetrance genes and environment in tumour sus- ceptibility; J. Biosci. 30 93–102] 1. Introduction are chromosomal translocations which result in fusion proteins (e.g. bcr-abl fusion protein due to translocation Cancer has been a scourge on the human population for of abl gene to bcr locus in Chronic Myeloid Leukemia) many years. Although numerous advances have been made or apposition of one gene to the regulatory region of an- in prevention, diagnosis and treatment of the disease, it other gene (e.g. RET and NTRK1 in thyroid papillary carci- still continues to torment mankind. As is widely believed, noma), resulting in giving the cell a growth advantage. cancer is the result of many genetic and epigenetic changes These chromosomal translocations are common in lym- in a population of cells as well as in the surrounding phomas, leukemias and mesenchymal tumours (Futreal stroma and blood vessels. -
Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings
G C A T T A C G G C A T genes Article Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings Jasleen Dhaliwal 1 , Ying Qiao 1,2, Kristina Calli 1,2, Sally Martell 1,2, Simone Race 3,4,5, Chieko Chijiwa 1,5, Armansa Glodjo 3,5, Steven Jones 1,6 , Evica Rajcan-Separovic 2,7, Stephen W. Scherer 4 and Suzanne Lewis 1,2,5,* 1 Department of Medical Genetics, University of British Columbia (UBC), Vancouver, BC V6H 3N1, Canada; [email protected] (J.D.); [email protected] (Y.Q.); [email protected] (K.C.); [email protected] (S.M.); [email protected] (C.C.); [email protected] (S.J.) 2 BC Children’s Hospital, Vancouver, BC V5Z 4H4, Canada; [email protected] 3 Department of Pediatrics, University of British Columbia (UBC), Vancouver, BC V6T 1Z7, Canada; [email protected] (S.R.); [email protected] (A.G.) 4 The Centre for Applied Genomics and McLaughlin Centre, Hospital for Sick Children and University of Toronto, Toronto, ON M5G 0A4, Canada; [email protected] 5 BC Children’s and Women’s Health Center, Vancouver, BC V6H 3N1, Canada 6 Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada 7 Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, BC V6T 1Z7, Canada * Correspondence: [email protected] Abstract: Autism Spectrum Disorder (ASD) is the most common neurodevelopmental disorder in Citation: Dhaliwal, J.; Qiao, Y.; Calli, children and shows high heritability. -
Bibliography.Pdf
Bibliography AAAAI 2000 Allergy Report vols. I–III. The American meta-analysis.” Annals of Epidemiology 8:64–74. Academy of Allergy, Asthma and Immunology, ACS 1999 Cancer Facts and Figures – 1999. Atlanta, GA: in partnership with the National Institute of American Cancer Society. Allergy and Infectious Diseases (NIAID). 2000 “How has the occurrence of breast cancer http://www.theallergyreport.org/. changed over time?” Atlanta, GA: American Abdulaziz, Abuzinda and Fridhelm Krupp 1997 Cancer Society. http://www.cancer.org/ “What happened to the Gulf: two years after statistics/99bcff/occurrence.html. the world’s greatest oil-slick.” Arabian Wildlife Acsadi, George and J. Nemeskeri 1970 History of 2:1. http://www.arabianwildlife.com/past_arw/ Human Life Span and Mortality. Budapest: vol2.1/oilglf.htm. Akademiai Kiado. Abell, Annette, Erik Ernst and Jens Peter Bonde Adams, John 1995 Risk. London: University College 1994 “High sperm density among members of London Press. organic farmers’ association.” The Lancet Adams, W. C. 1986 “Whose lives count? TV coverage 343:1,498. of natural disasters.” Journal of Communication Abelson, Philip H. 1994 “Editorial: adequate 36(2):113–22. supplies of fruits and vegetables.” Science Adleman, Morris A. 1995 “Trends in the price and 266:1,303. supply of oil.” In Simon 1995b:287–93. Abrahamsen, Gunnar, Arne O. Stuames and Bjørn AEA 1999 Economic Evaluation of Air Quality Targets Tveite 1994a “Discussion and synthesis.” In for CO and Benzene. By AEA Technology Abrahamsen et al. 1994c:297–331. for European Commission DGXI. 1994b: “Summary and conclusions.” In http://europa.eu.int/comm/environment/ Abrahamsen et al. -
A Curated Gene List for Reporting Results of Newborn Genomic Sequencing
© American College of Medical Genetics and Genomics ORIGINAL RESEARCH ARTICLE A curated gene list for reporting results of newborn genomic sequencing Ozge Ceyhan-Birsoy, PhD1,2,3, Kalotina Machini, PhD1,2,3, Matthew S. Lebo, PhD1,2,3, Tim W. Yu, MD3,4,5, Pankaj B. Agrawal, MD, MMSC3,4,6, Richard B. Parad, MD, MPH3,7, Ingrid A. Holm, MD, MPH3,4, Amy McGuire, PhD8, Robert C. Green, MD, MPH3,9,10, Alan H. Beggs, PhD3,4, Heidi L. Rehm, PhD1,2,3,10; for the BabySeq Project Purpose: Genomic sequencing (GS) for newborns may enable detec- of newborn GS (nGS), and used our curated list for the first 15 new- tion of conditions for which early knowledge can improve health out- borns sequenced in this project. comes. One of the major challenges hindering its broader application Results: Here, we present our curated list for 1,514 gene–disease is the time it takes to assess the clinical relevance of detected variants associations. Overall, 954 genes met our criteria for return in nGS. and the genes they impact so that disease risk is reported appropri- This reference list eliminated manual assessment for 41% of rare vari- ately. ants identified in 15 newborns. Methods: To facilitate rapid interpretation of GS results in new- Conclusion: Our list provides a resource that can assist in guiding borns, we curated a catalog of genes with putative pediatric relevance the interpretive scope of clinical GS for newborns and potentially for their validity based on the ClinGen clinical validity classification other populations. framework criteria, age of onset, penetrance, and mode of inheri- tance through systematic evaluation of published evidence. -
Genetic Risk Assessment and BRCA Mutation Testing for Breast and Ovarian Cancer Susceptibility: Evidence Synthesis
Evidence Synthesis Number 37 Genetic Risk Assessment and BRCA Mutation Testing for Breast and Ovarian Cancer Susceptibility: Evidence Synthesis Prepared for: Agency for Healthcare Research and Quality U.S. Department of Health and Human Services 540 Gaither Road Rockville, MD 20850 www.ahrq.gov Contract No. 290-02-0024 Task Order No. 2 Technical Support of the U.S. Preventive Services Task Force Prepared by: Oregon Evidence-based Practice Center Portland, Oregon Investigators Heidi D. Nelson, MD, MPH Laurie Hoyt Huffman, MS Rongwei Fu, PhD Emily L. Harris, PhD, MPH Miranda Walker, BA Christina Bougatsos, BS September 2005 This report may be used, in whole or in part, as the basis of the development of clinical practice guidelines and other quality enhancement tools, or a basis for reimbursement and coverage policies. AHRQ or U.S. Department of Health and Human Services endorsement of such derivative products may not be stated or implied. AHRQ is the lead Federal agency charged with supporting research designed to improve the quality of health care, reduce its cost, address patient safety and medical errors, and broaden access to essential services. AHRQ sponsors and conducts research that provides evidence-based information on health care outcomes; quality; and cost, use, and access. The information helps health care decisionmakers—patients and clinicians, health system leaders, and policymakers—make more informed decisions and improve the quality of health care services. Preface The Agency for Healthcare Research and Quality (AHRQ) sponsors the development of Systematic Evidence Reviews (SERs) and Evidence Syntheses through its Evidence-based Practice Program. With guidance from the U.S. -
The Nature and Significance of Behavioural Genetic Information
Postprint This is a pre-copyedited, author-produced PDF of an article accepted for publication in Theoretical Medicine and Bioethics following peer review. The definitive publisher-authenticated version [Newson, A.J. (2004) “The nature and significance of behavioural genetic information.” Theoretical Medicine and Bioethics, 25: 89–111.] is available online at http://link.springer.com/article/10.1023/B:META.0000033764.50604.85 The nature and significance of behavioural genetic information Ainsley Newson BSc (Hons) PhD, 2004 Abstract In light of the human genome project, establishing the genetic aetiology of complex human diseases has become a research priority within Western medicine. However, in addition to the identification of disease genes, numerous research projects are also being undertaken to identify genes contributing to the development of human behavioural characteristics, such as cognitive ability and criminal tendency. The permissibility of this research is obviously controversial: will society benefit from this research, or will it adversely affect our conceptions of ourselves and each other? When assessing the permissibility of this research, it is important to consider the nature and deterministic significance of behavioural genetic information. Whilst to date there has been much discussion and debate about the properties of genetic information per se and genetic determinism, this has not been applied to behavioural genetic research and its ethical implications. Therefore, this paper elucidates how behavioural genetic information can be distinguished from different from other types of genetic and non-genetic information and also synthesises the determinative significance of genetic factors for the development of human behavioural traits. Undertaking this analysis enables the ethical issues raised by this research to be debated in an appropriate context and indicates that separate policy considerations are warranted. -
NARRATIVE Directions in Econarratology
ENVIRONMENT New NARRATIVE Directions in Econarratology edited by ERIN JAMES AND ERIC MOREL ENVIRONMENT AND NARRATIVE THEORY AND INTERPRETATION OF NARRATIVE James Phelan and Katra Byram, Series Editors ENVIRONMENT AND NARRATIVE NEW DIRECTIONS IN ECONARRATOLOGY EDITED BY Erin James AND Eric Morel THE OHIO STATE UNIVERSITY PRESS COLUMBUS Copyright © 2020 by The Ohio State University. This edition licensed under a Creative Commons Attribution-NonCommercial-NoDerivs License. Library of Congress Cataloging-in-Publication Data Names: James, Erin, editor. | Morel, Eric, editor. Title: Environment and narrative : new directions in econarratology / edited by Erin James and Eric Morel. Other titles: Theory and interpretation of narrative series. Description: Columbus : The Ohio State University Press, [2020] | Series: Theory and interpretation of narrative | Includes bibliographical references and index. | Summary: “Collection of essays connecting ecocriticism and narrative theory to encourage constructive discourse on narrative’s influence of real-world environmental perspectives and the challenges that necessitate revision to current narrative models”—Provided by publisher. Identifiers: LCCN 2019034865 | ISBN 9780814214206 (cloth) | ISBN 0814214207 (cloth) | ISBN 9780814277546 (ebook) | ISBN 0814277543 (ebook) Subjects: LCSH: Ecocriticism. | Environmental literature. | Narration (Rhetoric) Classification: LCC PN98.E36 E55 2020 | DDC 809/.93355—dc23 LC record available at https://lccn.loc.gov/2019034865 Cover design by Andrew Brozyna Text design by Juliet Williams Type set in Adobe Minion Pro for Ben and Freddie, my favorites From Erin for Grandmaman, an avid reader and early recommender of books From Eric CONTENTS Acknowledgments ix INTRODUCTION Notes Toward New Econarratologies ERIN JAMES AND ERIC MOREL 1 I. NARRATOLOGY AND THE NONHUMAN CHAPTER 1 Unnatural Narratology and Weird Realism in Jeff VanderMeer’s Annihilation JON HEGGLUND 27 CHAPTER 2 Object-Oriented Plotting and Nonhuman Realities in DeLillo’s Underworld and Iñárritu’s Babel MARCO CARACCIOLO 45 II. -
Guide to Interpreting Genomic Reports: a Genomics Toolkit
Guide to Interpreting Genomic Reports: A Genomics Toolkit A guide to genomic test results for non-genetics providers Created by the Practitioner Education Working Group of the Clinical Sequencing Exploratory Research (CSER) Consortium Genomic Report Toolkit Authors Kelly East, MS, CGC, Wendy Chung MD, PhD, Kate Foreman, MS, CGC, Mari Gilmore, MS, CGC, Michele Gornick, PhD, Lucia Hindorff, PhD, Tia Kauffman, MPH, Donna Messersmith , PhD, Cindy Prows, MSN, APRN, CNS, Elena Stoffel, MD, Joon-Ho Yu, MPh, PhD and Sharon Plon, MD, PhD About this resource This resource was created by a team of genomic testing experts. It is designed to help non-geneticist healthcare providers to understand genomic medicine and genome sequencing. The CSER Consortium1 is an NIH-funded group exploring genomic testing in clinical settings. Acknowledgements This work was conducted as part of the Clinical Sequencing Exploratory Research (CSER) Consortium, grants U01 HG006485, U01 HG006485, U01 HG006546, U01 HG006492, UM1 HG007301, UM1 HG007292, UM1 HG006508, U01 HG006487, U01 HG006507, R01 HG006618, and U01 HG007307. Special thanks to Alexandria Wyatt and Hugo O’Campo for graphic design and layout, Jill Pope for technical editing, and the entire CSER Practitioner Education Working Group for their time, energy, and support in developing this resource. Contents 1 Introduction and Overview ................................................................ 3 2 Diagnostic Results Related to Patient Symptoms: Pathogenic and Likely Pathogenic Variants . 8 3 Uncertain Results -
Autism Spectrum Disorders: an Updated Guide for Genetic Counseling Transtornos Do Espectro Autista: Um Guia Atualizado Para Aconselhamento Genético
REVIEWING BASIC SCIENCES Autism spectrum disorders: an updated guide for genetic counseling Transtornos do espectro autista: um guia atualizado para aconselhamento genético Karina Griesi-Oliveira1, Andréa Laurato Sertié1 ABSTRACT desenvolvimento de novas ferramentas de diagnóstico molecular, Autism spectrum disorder is a complex and genetically heterogeneous tem mudado este cenário de forma substancial. Atualmente, estima- disorder, which has hampered the identification of the etiological se que, por meio de testes moleculares, é possível detectar uma factors in each patient and, consequently, the genetic counseling alteração genética potencialmente causal em cerca de 25% dos for families at risk. However, in the last decades, the remarkable casos. Considerando-se também a avaliação clínica, a história advances in the knowledge of genetic aspects of autism based on pré-natal e a investigação de outros aspectos fisiológicos, pode- genetic and molecular research, as well as the development of new se atribuir uma etiologia para aproximadamente 30 a 40% dos molecular diagnostic tools, have substantially changed this scenario. pacientes. Assim, em vista do conhecimento atual sobre a arquitetura Nowadays, it is estimated that using the currently available molecular genética do transtorno do espectro autista, que tem tornado o tests, a potential underlying genetic cause can be identified in nearly aconselhamento genético cada vez mais preciso, e dos potenciais 25% of cases. Combined with clinical assessment, prenatal history benefícios que a investigação etiológica pode trazer aos pacientes e evaluation and investigation of other physiological aspects, an familiares, tornam-se cada vez mais importantes os testes genéticos etiological explanation for the disease can be found for approximately moleculares. -
Estimating Penetrance from Multiple Case Families with Predisposing Mutations: Extension of the ‘Genotype-Restricted Likelihood’ (GRL) Method
European Journal of Human Genetics (2011) 19, 173–179 & 2011 Macmillan Publishers Limited All rights reserved 1018-4813/11 www.nature.com/ejhg ARTICLE Estimating penetrance from multiple case families with predisposing mutations: extension of the ‘genotype-restricted likelihood’ (GRL) method Bernard Bonaı¨ti1,2, Vale´rie Bonadona3,4, Herve´ Perdry2,5, Nadine Andrieu6,7,8 and Catherine Bonaı¨ti-Pellie´*,2,5 Some diseases are due to germline mutations in predisposing genes, such as cancer family syndromes. Precise estimation of the age-specific cumulative risk (penetrance) for mutation carriers is essential for defining prevention strategies. The genotype- restricted likelihood (GRL) method is aimed at estimating penetrance from multiple case families with such a mutation. In this paper, we proposed an extension of the GRL to account for multiple trait disease and to allow for a parent-of-origin effect. Using simulations of pedigrees, we studied the properties of this method and the effect of departures from underlying hypotheses, misspecification of disease incidence in the general population or misspecification of the index case, and penetrance heterogeneity. In contrast with the previous version of the GRL, accounting for multiple trait disease allowed unbiased estimation of penetrance. We also showed that accounting for a parent-of-origin effect allowed a powerful test for detecting this effect. We found that the GRL method was robust to misspecification of disease incidence in the population, but that misspecification of the index case induced a bias in some situations for which we proposed efficient corrections. When ignoring heterogeneity, the penetrance estimate was biased toward that of the highest risk individuals. -
Evolution and the Origins of Disease by Randolph M
The principles of evolution by natural selection are finally beginning to inform medicine Evolution and the Origins of Disease by Randolph M. Nesse and George C. Williams houghtful contemplation of the human body elicits awe—in equal measure with perplexity. The eye, for instance, has long been an object of wonder, T with the clear, living tissue of the cornea curving just the right amount, the iris adjusting to brightness and the lens to distance, so that the optimal quantity of light focuses exactly on the surface of the retina. Admiration of such apparent perfection soon gives way, however, to consternation. Contrary to any sensible design, blood vessels and nerves traverse the inside of the retina, creating a blind spot at their point of exit. The body is a bundle of such jarring contradictions. For each exquisite heart valve, we have a wisdom tooth. Strands of DNA direct the development of the 10 trillion cells that make up a human adult but then permit his or her steady deterioration and eventual death. Our immune system can identify and destroy a million kinds of foreign matter, yet many bacteria can still kill us. These contradictions make it appear as if the body was de- signed by a team of superb engineers with occasional interventions by Rube Goldberg. In fact, such seeming incongruities make sense but only when we investigate the origins of the body’s vulnerabilities while keeping in mind the wise words of distinguished geneti- cist Theodosius Dobzhansky: “Nothing in biology makes sense except in the light of evo- lution.” Evolutionary biology is, of course, the scientific foundation for all biology, and bi- ology is the foundation for all medicine. -
Association Between Genetic Polymorphisms and Ovarian Cancer Risk
ANTICANCER RESEARCH 28 : 3079-3082 (2008) Association Between Genetic Polymorphisms and Ovarian Cancer Risk LAETITIA DELORT 1,2,3 , NASSÉRA CHALABI 1,2,3 , SAMIR SATIH 1,2,3 , NADÈGE RABIAU 1,2,3 , FABRICE KWIATKOWSKI 1, YVES-JEAN BIGNON 1,2,3,4 and DOMINIQUE J BERNARD-GALLON 1,2,3 1Département d’Oncogénétique du Centre Jean Perrin, CBRV, 3EA 2416, Université d’Auvergne-CJP and 4Univ-Clermont 1, 63001 Clermont-Ferrand; 2CRNH, 63009 Clermont-Ferrand; France Abstract. Background: The etiology of ovarian cancer is and estrone at ovulation. These compounds could in turn not fully understood. Polymorphisms in low penetrance genes stimulate the proliferation of ovarian cells (3). Indeed, estrogen involved in carcinogen and estrogen metabolism are metabolism produces reactive estrogen metabolites hypothesized to play a role in the initiation of (catecholestrogens, CE) by phase I enzymes which are then carcinogenesis. Patients and Methods: A case –control study metabolized to semi-quinones and quinones. Two phase I was conducted to investigate the role of these polymorphisms enzymes are involved in this pathway: cytochrome P450 1A1 in ovarian cancer risk. The participants were genotyped for (CYP1A1) produces 2-OH-E2, a CE which can form stable eleven polymorphisms in seven genes involved in estrogen adducts; cytochrome P450 1B1 (CYP1B1) produces 4-OH-E2, and xenobiotic metabolism (CYP1A1, CYP1B1, COMT, which forms depurinating agents which may lead to the GSTP1, NAT2, estrogen receptor ESR, and progesterone initiation of a carcinogenic process. Phase II enzymes such as receptor PGR). Results and Conclusion: The odds ratios for catechol- O-methyl transferase (COMT) and glutathione-S- ovarian cancer risk were 2.02 (95% confidence interval [CI] transferase (GSTP1) intervene by inactivating CE and quinones = 1.14-3.56) in the NAT2 intermediate acetylators and 4.07 respectively.