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Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

Nature communications 2017年第1期8卷 1414页

作者： M Carola Zillikens Serkalem Demissie Yi-Hsiang Hsu Laura M Yerges-Armstrong Wen-Chi Chou Lisette Stolk Gregory Livshits Linda Broer Toby Johnson Daniel L Koller Zoltán Kutalik Jian'an Luan Ida Malkin Janina S Ried Albert V Smith Gudmar Thorleifsson Liesbeth Vandenput Jing Hua Zhao Weihua Zhang Ali Aghdassi Kristina Åkesson Najaf Amin Leslie J Baier Inês Barroso David A Bennett Lars Bertram Rainer Biffar Murielle Bochud Michael Boehnke Ingrid B Borecki Aron S Buchman Liisa Byberg Harry Campbell Natalia Campos Obanda Jane A Cauley Peggy M Cawthon Henna Cederberg Zhao Chen Nam H Cho Hyung Jin Choi Melina Claussnitzer Francis Collins Steven R Cummings Philip L De Jager Ilja Demuth Rosalie A M Dhonukshe-Rutten Luda Diatchenko Gudny Eiriksdottir Anke W Enneman Mike Erdos Johan G Eriksson Joel Eriksson Karol Estrada Daniel S Evans Mary F Feitosa Mao Fu Melissa Garcia Christian Gieger Thomas Girke Nicole L Glazer Harald Grallert Jagvir Grewal Bok-Ghee Han Robert L Hanson Caroline Hayward Albert Hofman Eric P Hoffman Georg Homuth Wen-Chi Hsueh Monica J Hubal Alan Hubbard Kim M Huffman Lise B Husted Thomas Illig Erik Ingelsson Till Ittermann John-Olov Jansson Joanne M Jordan Antti Jula Magnus Karlsson Kay-Tee Khaw Tuomas O Kilpeläinen Norman Klopp Jacqueline S L Kloth Heikki A Koistinen William E Kraus Stephen Kritchevsky Teemu Kuulasmaa Johanna Kuusisto Markku Laakso Jari Lahti Thomas Lang Bente L Langdahl Lenore J Launer Jong-Young Lee Markus M Lerch Joshua R Lewis Lars Lind Cecilia Lindgren Yongmei Liu Tian Liu Youfang Liu Östen Ljunggren Mattias Lorentzon Robert N Luben William Maixner Fiona E McGuigan Carolina Medina-Gomez Thomas Meitinger Håkan Melhus Dan Mellström Simon Melov Karl Michaëlsson Braxton D Mitchell Andrew P Morris Leif Mosekilde Anne Newman Carrie M Nielson Jeffrey R O'Connell Ben A Oostra Eric S Orwoll Aarno Palotie Stephen C J Parker Munro Peacock Markus Perola Annette Peters Ozren Polasek Richard L Prince Katri Räikkönen Stuart H Ralston Samuli Ripatti John A Robbins Jerome I Rotter Igor Rudan Veikko Department of Internal Medicine Erasmus MC Rotterdam 3000 The Netherlands. Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA) Leiden 2593 The Netherlands. Department of Biostatistics Boston University School of Public Health Boston MA 02118 USA. Hebrew SeniorLife Institute for Aging Research Roslindale MA 02131 USA. Harvard Medical School Boston MA 02115 USA. Molecular and Integrative Physiological Sciences Program Harvard School of Public Health Boston MA 02115 USA. Program in Personalized and Genomic Medicine and Department of Medicine Division of Endocrinology Diabetes and Nutrition University of Maryland School of Medicine Baltimore MD 21201 USA. Broad Institute Cambridge MA 02142 USA. Sackler Faculty of Medicine Department of Anatomy and Anthropology Tel Aviv University Tel Aviv 6997801 Israel. Department of Twin Research and Genetic Epidemiology King's College London St Thomas' Campus London WC2R 2LS UK. Department of Epidemiology Erasmus MC Rotterdam 3000 The Netherlands. Department of Medical Genetics University of Lausanne Lausanne 1011 Switzerland. Swiss Institute of Bioinformatics Lausanne 1015 Switzerland. Centre Hospitalier Universitaire (CHUV) University Institute for Social and Preventive Medicine Lausanne 1010 Switzerland. Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN 46202 USA. MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge Biomedical Campus Cambridge CB2 OQQ UK. Institute of Epidemiology II Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg 85764 Germany. Icelandic Heart Association Kopavogur 201 Iceland. Faculty of Medicine University of Iceland Reykjavik 101 Iceland. deCODE Genetics Reykjavik 101 Iceland. Department of Internal Medicine Institute of Medicine Sahlgrenska Academy University of Gothenburg Gothenburg SE-405 30 Sweden. Dep

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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

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Scientific data 2017年第1期4卷 170179页

作者： Jason Flannick Christian Fuchsberger Anubha Mahajan Tanya M Teslovich Vineeta Agarwala Kyle J Gaulton Lizz Caulkins Ryan Koesterer Clement Ma Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Dennis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmu Department of Molecular Biology Massachusetts General Hospital Boston Massachusetts USA. Program in Medical and Population Genetics Broad Institute Cambridge Massachusetts USA. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor Michigan USA. Wellcome Trust Centre for Human Genetics Nuffield Department of Medicine University of Oxford Oxford UK. Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge Massachusetts USA. Department of Statistics University of Oxford Oxford UK. Genetics of Complex Traits University of Exeter Medical School University of Exeter Exeter UK. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Department of Twin Research and Genetic Epidemiology King's College London London UK. Oxford Centre for Diabetes Endocrinology and Metabolism Radcliffe Department of Medicine University of Oxford Oxford UK. Department of Human Genetics Wellcome Trust Sanger Institute Hinxton Cambridgeshire UK. School of Computer Science McGill University Montreal Quebec Canada. McGill University and Génome Québec Innovation Centre Montreal Quebec Canada. Human Genetics Center The University of Texas Graduate School of Biomedical Sciences at Houston The University of Texas Health Science Center at Houston Houston Texas USA. Department of Biostatistics Boston University School of Public Health Boston Massachusetts USA. National Heart Lung and Blood Institute's Framingham Heart Study Framingham Massachusetts USA. Medical Genomics and Metabolic Genetics Branch National Human Genome Research Institute National Institutes of Health Bethesda Maryland USA. Department of Biostatistics Harvard School of Public Health Boston Massachusetts USA. Chronic Disease Epidemiology Swiss Tropical and Public Health Institute University of Basel Basel Switzerland. Institute of Genetic Epidemiology Helmholtz Zentrum München German R

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

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GxG-Viztool: A program for visualizing gene-gene interactions in genetic association analysis

GxG-Viztool: A program for visualizing gene-gene interaction...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Kyunga Kim Min-Seok Kwon Sung Young Lee Junghyun Namkung Ming D. Li Taesung Park Department of Statistics Sookmyung Womens University Seoul South Korea Interdisciplinary Program in Bioinformatics Seoul National University Seoul South Korea Department of Psychiatry and Neurobehavioral Sciences University of Virginia Charlottesville VA USA Interdisciplinary Program in Bioinformatics Department of Statistics Seoul National University Seoul South Korea

ISBN: (纸本)9781467327466

Gene-gene interactions are important factors underlying a common complex trait that is mostly polygenic. While many methods have been proposed to analyze gene-gene interactions in genetic association studies, the interpretation of the identified gene-gene interactions is not straightforward. In order to aid the interpretation of gene-gene interactions, we developed the GxG-Viztool, an executable program for visualizing gene-gene interactions in genetic association analysis. The GxG-Viztool provides an effective way to recognize genotype combinations that enhance/repress a trait and to display polygenic structure of interactions. The GxG-Viztool implements six graphical tools: checkerboard, pairwise checkerboard, forest, funnel, 3D lattice and parallel coordinate plots, which make it effective to recognize certain patterns in gene-gene interactions. It is freely available at http ://bibs. snu. ac. kr/GxG-Viz tool.

关键词： Data visualization Genetics Lattices Visualization Educational institutions Pattern recognition Heating

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Differentially expressed genes in adipose tissues reveals that ECM-receptor interaction affects on the depot-specific adipogenesis in Hanwoo

Differentially expressed genes in adipose tissues reveals th...

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第11届世界畜产大会(WCAP2013)

作者： Mi Jang Hyun-Jeong Lee Hyeongmin Kim Woori Kwak WonCheoul Park Jae-Yeon Hwang Chang-Kyu Lee Gul Won Jang Mi Na Park Hyeong-Cheol Kim Jin Young Jeong Kang Seok Seo Heebal Kim Seoae Cho Bo-Young Lee C&K Genomics Seoul National University NakSeoungDaeGwanakguSeoulKorea Department of Agricultural Biotechnology and Research Institute for Agriculture and Life ScienceSeoul National UniversitySeoulKorea Department of Animal Science and TechnologyCollege of Life Science and Natural ResourcesSunchon National UniversitySeoulRepublic of Korea C&K GenomicsSeoul National University NakSeoungDaeGwanakguSeoulKorea C&K Genomics Seoul National University NakSeoungDaeGwanakguSeoulKorea Department of Agricultural Biotechnology and Research Institute of Population GenomicsSeoul National UniversitySeoulRepublic of Korea Department of Animal Science and Technology College of Life Science and Natural ResourcesSunchon National UniversitySeoulRepublic of Korea Division of Animal Genomics and BioinformaticsNational Institute of Animal scienceRural Development AdministrationSuwonRepublic of Korea Department of Agricultural Biotechnology and Research Institute of Population GenomicsSeoul National UniversitySeoulRepublic of Korea Interdisciplinary Program in BioinformaticsSeoul National UniversityKorea Division of Animal Genomics and Bioinformatics National Institute of Animal scienceRural Development AdministrationSuwonRepublic of Korea

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Proceedings of the 8th Annual Conference on the Science of Dissemination and Implementation : Washington, DC, USA. 14-15 December 2015

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Implementation science : IS 2016年第2期11 Suppl 2卷 100页

作者： Chambers, David Simpson, Lisa Hill-Briggs, Felicia Neta, Gila Vinson, Cynthia Beidas, Rinad Marcus, Steven Aarons, Gregory Hoagwood, Kimberly Schoenwald, Sonja Evans, Arthur Hurford, Matthew Rubin, Ronnie Hadley, Trevor Barg, Frances Walsh, Lucia Adams, Danielle Mandell, David Martin, Lindsey Mignogna, Joseph Mott, Juliette Hundt, Natalie Kauth, Michael Kunik, Mark Naik, Aanand Cully, Jeffrey McGuire, Alan White, Dominique Bartholomew, Tom McGrew, John Luther, Lauren Rollins, Angie Salyers, Michelle Cooper, Brittany Funaiole, Angie Richards, Julie Lee, Amy Lapham, Gwen Caldeiro, Ryan Lozano, Paula Gildred, Tory Achtmeyer, Carol Ludman, Evette Addis, Megan Marx, Larry Bradley, Katharine VanDeinse, Tonya Wilson, Amy Blank Stacey, Burgin Powell, Byron Bunger, Alicia Cuddeback, Gary Barnett, Miya Stadnick, Nicole Brookman-Frazee, Lauren Lau, Anna Dorsey, Shannon Pullmann, Michael Mitchell, Shannon Schwartz, Robert Kirk, Arethusa Dusek, Kristi Oros, Marla Hosler, Colleen Gryczynski, Jan Barbosa, Carolina Dunlap, Laura Lounsbury, David O’Grady, Kevin Brown, Barry Damschroder, Laura Waltz, Thomas Ritchie, Mona Atkins, David Imel, Zac E. Xiao, Bo Can, Doğan Georgiou, Panayiotis Narayanan, Shrikanth Berkel, Cady Gallo, Carlos Sandler, Irwin Brown, C. Hendricks Wolchik, Sharlene Mauricio, Anne Marie Mehrotra, Sanjay Chandurkar, Dharmendra Bora, Siddhartha Das, Arup Tripathi, Anand Saggurti, Niranjan Raj, Anita Hughes, Eric Jacobs, Brian Kirkendall, Eric Loeb, Danielle Trinkley, Katy Yang, Michael Sprowell, Andrew Nease, Donald Lyon, Aaron Lewis, Cara Boyd, Meredith Melvin, Abigail Nicodimos, Semret Liu, Freda Jungbluth, Nathanial Flynn, Allen Landis-Lewis, Zach Sales, Anne Baloh, Jure Ward, Marcia Zhu, Xi Bennett, Ian Unutzer, Jurgen Mao, Johnny Proctor, Enola Vredevoogd, Mindy Chan, Ya-Fen Williams, Nathaniel Green, Phillip Bernstein, Steven Rosner, June-Marie DeWitt, Michelle Tetrault, Jeanette Dziura, James Hsiao, Allen Sussman, Scott O’Connor, Patrick Toll, Benjamin Jones, Michael Gassaway, Julie Tobin, Jonathan Zatzic Division of Cancer Control and Population Sciences National Cancer Institute National Institutes of Health Rockville USA AcademyHealth Washington USA Department of Medicine and Welch Center for Prevention Epidemiology and Clinical Research Johns Hopkins Medical Institutions Baltimore USA Psychiatry University of Pennsylvania Philadelphia USA Family Medicine and Community Health University of Pennsylvania Philadelphia USA School of Social Policy and Practice University of Pennsylvania Philadelphia USA Psychiatry UC San Diego La Jolla USA Child & Adolescent Psychiatry The Child Study Center at NYU Langone Medical Center New York NY New York USA Psychiatry and Behavioral Sciences MUSC Charleston USA DBHIDS City of Philadelphia Philadelphia USA CBH City of Philadelphia Philadelphia USA Psychiatry University of Pennsylvania Perelman School of Medicine Philadelphia USA Health Services Research & Development Department of Veterans Affairs & Baylor College of Medicine Houston USA Treatment Core Department of Veterans Affairs Waco USA National Center for PTSD Executive Division Department of Veterans Affairs White River Junction USA HSR&D HSR&D Center for Health Information and Communication Roudebush VA Medical Center Indianapolis USA Psychology Indiana University Purdue University Indianapolis Indianapolis USA Department of Psychiatric Rehabilitation and Counseling Rutgers University Newark USA Health Services Research & Development Richard L. Roudebush VAMC Indianapolis USA IUPUI Department of Psychology ACT Center of Indiana Indianapolis USA Human Development Washington State University Pullman USA Prevention Science Washington State University Pullman USA Group Health Research Institute Group Health Seattle USA Behavioral Health Services Group Health Seattle USA Preventive Care Group Health Seattle USA Health Services Research & Development Primary and Specialty Medical Care Service VA Puget Sound Seattle USA School of Social Work Un

A1 Introduction to the 8th Annual Conference on the Science of Dissemination and Implementation: Optimizing Personal and Population Health David Chambers, Lisa Simpson D1 Discussion forum: Population health D&I research Felicia Hill-Briggs D2 Discussion forum: Global health D&I research Gila Neta, Cynthia Vinson D3 Discussion forum: Precision medicine and D&I research David Chambers S1 Predictors of community therapists’ use of therapy techniques in a large public mental health system Rinad Beidas, Steven Marcus, Gregory Aarons, Kimberly Hoagwood, Sonja Schoenwald, Arthur Evans, Matthew Hurford, Ronnie Rubin, Trevor Hadley, Frances Barg, Lucia Walsh, Danielle Adams, David Mandell S2 Implementing brief cognitive behavioral therapy (CBT) in primary care: Clinicians' experiences from the field Lindsey Martin, Joseph Mignogna, Juliette Mott, Natalie Hundt, Michael Kauth, Mark Kunik, Aanand Naik, Jeffrey Cully S3 Clinician competence: Natural variation, factors affecting, and effect on patient outcomes Alan McGuire, Dominique White, Tom Bartholomew, John McGrew, Lauren Luther, Angie Rollins, Michelle Salyers S4 Exploring the multifaceted nature of sustainability in community-based prevention: A mixed-method approach Brittany Cooper, Angie Funaiole S5 Theory informed behavioral health integration in primary care: Mixed methods evaluation of the implementation of routine depression and alcohol screening and assessment Julie Richards, Amy Lee, Gwen Lapham, Ryan Caldeiro, Paula Lozano, Tory Gildred, Carol Achtmeyer, Evette Ludman, Megan Addis, Larry Marx, Katharine Bradley S6 Enhancing the evidence for specialty mental health probation through a hybrid efficacy and implementation study Tonya VanDeinse, Amy Blank Wilson, Burgin Stacey, Byron Powell, Alicia Bunger, Gary Cuddeback S7 Personalizing evidence-based child mental health care within a fiscally mandated policy reform Miya Barnett, Nicole Stadnick, Lauren Brookman-Frazee, Anna Lau S8 Leveraging an existing

关键词： Veteran Affair Motivational Interview Qualitative Comparative Analysis Community That Care Supplemental Nutrition Assistance program

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Proceedings of the 3rd IPLeiria's International Health Congress Abstracts

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BMC HEALTH SERVICES RESEARCH 2016年第3期16卷 111-242页

作者： [Anonymous] Health Sciences Research Unit: Nursing Collegue of College of Health Technology of Coimbra Coimbra Portugal Sisters Hospitallers of the Sacred Heart of Jesus Casa de Saúde Rainha Santa Isabel Coimbra Portugal Research Unit for Sport and Physical Activity Faculty of Sport Sciences and Physical Education University of Coimbra Coimbra Portugal Complementary Sciences- INESCC Coimbra Portugal CUF Hospitals Lisbon Portugal Breast Unit Champalimaud Clinical Center Lisbon Portugal Swiss Centre for Medical Simulation & Swiss Association of Simulation in Healthcare Basel Switzerland Basel University Hospital Basel Switzerland HELPO Association Cascais Portugal Centro de Linguística Universidade de Lisboa Lisboa Portugal Centro Superior de Estudios Universitarios La Salle Madrid Spain Universidade da Madeira Funchal Portugal Serviço de Saúde da Região Autónoma da Madeira E.P.E. Funchal Portugal Escola Superior de Enfermagem de Lisboa Lisboa Portugal Instituto Superior Miguel Torga Coimbra Portugal Centro de Investigação do Núcleo de Estudos e Intervenção Cognitivo Comportamental Universidade de Coimbra Coimbra Portugal Escola Superior de Saúde de Leiria & Unidade de Investigação em Saúde Instituto Politécnico de Leiria Leiria Portugal National School of Public Health & Centro de Investigação em Saúde Pública Universidade Nova de Lisboa Lisboa Portugal Agrarian Superior School Polytechnic Institute of Viseu Viseu Portugal Laboratory of Microbiology Department of Biological Sciences Faculty of Pharmacy University of Porto Porto Portugal Unit for Multidisciplinary Biomedical Research Institute of Biomedical Sciences Abel Salazar University of Porto Porto Portugal Agrupamento de Centros de Saúde (ACES) Baixo Mondego Figueira da Foz Portugal Universidade de Trás-os-Montes e Alto Douro Vila Real Portugal Centro de Salud La Paz Badajoz España Centro de Salud San Fernando Badajoz España Complejo Hospitalario Universitario de Badajoz Badajoz España Hospital Don Beni

S1 Health literacy and health education in adolescence Catarina Cardoso Tomás S2 The effect of a walking program on the quality of life and well-being of people with schizophrenia Emanuel Oliveira, D. Sousa, M. Uba-Chupel, G. Furtado, C. Rocha, A. Teixeira, P. Ferreira S3 Diagnosis and innovative treatments - the way to a better medical practice Celeste Alves S4 Simulation-based learning and how it is a high contribution Stefan Gisin S5 Formative research about acceptability, utilization and promotion of a home fortification programme with micronutrient powders (MNP) in the Autonomous Region of Príncipe, São Tomé and Príncipe Elisabete Catarino, Nelma Carvalho, Tiago Coucelo, Luís Bonfim, Carina Silva S6 Safety culture of the patient: a reflexion about the therapeutic approach on the patient with vocal pathology Débora Franco S7 About wine, fortune cookies and patient experience Jesús Alcoba González O1 The psychological impact on the emergency crews after the disaster event on February 20, 2010 Helena G. Jardim, Rita Silva O2 Musculoskeletal disorders in midwives Cristina L. Baixinho, Mª Helena Presado, Mª Fátima Marques, Mário E. Cardoso O3 Negative childhood experiences and fears of compassion: Implications for psychological difficulties in adolescence Marina Cunha, Joana Mendes, Ana Xavier, Ana Galhardo, Margarida Couto O4 Optimal age to give the first dose of measles vaccine in Portugal João G. Frade, Carla Nunes, João R. Mesquita, Maria S. Nascimento, Guilherme Gonçalves O5 Functional assessment of elderly in primary care Conceição Castro, Alice Mártires, Mª João Monteiro, Conceição Rainho O6 Smoking and coronary events in a population of Spanish health-care centre: An observational study Francisco P. Caballero, Fatima M. Monago, Jose T. Guerrero, Rocio M. Monago, Africa P. Trigo, Milagros L. Gutierrez, Gemma M. Milanés, Mercedes G. Reina, Ana G. Villanueva, Ana S. Piñero, Isabel R. Aliseda, Francisco B. Ramirez O7 Prevalence of musculoskeletal injuries in Por

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GWAS-GMDR: A program package for genome-wide scan of gene-gene interactions with covariate adjustment based on multifactor dimensionality reduction

GWAS-GMDR: A program package for genome-wide scan of gene-ge...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Min-Seok Kwon Kyunga Kim Sungyoung Lee Wonil Chung Sung-Gon Yi Junghyun Namkung Taesung Park Interdisciplinary program in Bioinformatics Seoul National University South Korea Department of Statistics Seoul National University South Korea

Multifactor dimensionality reduction (MDR) has been successfully applied to identification of gene-gene interactions for the complex traits. Generalized MDR (GMDR) was its extension that allows adjustment for covariates. The current GMDR software mainly focuses on candidate gene association studies with a relatively small number of genetic markers and has some limitations to be extended to genome-wide association studies (GWAS) with a large number of genetic markers. We develop GWAS-GMDR, an effective parallel computing program package with special features for GWAS with a large number of genetic markers by using distributed job scheduling method and/or CUDA-enabled high-performance graphic processing units (GPU). First, GWAS-GMDR implements an effective memory handling algorithm and efficient procedures for GMDR to make joint analysis of multiple genes feasible for GWAS. Second, a weighted version of cross-validation consistency based on `top-K selection' (WCVC K ) is proposed to report multiple candidates for causal gene-gene interactions. Third, various performance measures are implemented to evaluate MDR classifiers, including balanced accuracy, tau-b, likelihood ratio and normalized mutual information. Fourth, some popular methods for handling missing genotypes are implemented. Finally, our applications support both CPU-based and GPU-based parallel computing system. We applied our applications using a real genome wide data set from WTCCC Crohn's disease dataset to identify two-way interaction models in genome-wide scale. The GWAS-GMDR package is a powerful tool for the gene-gene interaction analysis in a genome-wide scale. High-performance implementations are provided as native binaries for Linux, Mac OS X and Windows systems.

关键词： bioinformatics Graphics processing unit Genomics Diseases Parallel processing

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Gene-gene interaction analysis for the survival phenotype based on the standardized residuals from parametric regression models

Gene-gene interaction analysis for the survival phenotype ba...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Seungyeoun Lee Jinseok Oh Min-Seok Kwon Taesung Park Department of Mathematics and Statistics Sejong University South Korea Interdisciplinary Program in Bioinformatics Seoul National University Seoul South Korea

Most of statistical methods in genome-wide association studies (GWAS) have been developed to identify SNP-SNP interactions using a binary phenotype for case-control studies. However, there is an interest in identifying SNPs and combinations of SNPs that relate to the survival phenotype in many cancer studies. Recently, Gui et al. (2011) proposed a novel method, called Surv-MDR, for detecting gene-gene interactions associated with survival time by modifying the multifactor dimensionality reduction (MDR) method based on the log-rank test. However, the Surv-MDR method needs more-intensive computations and does not allow for a covariate adjustment. Lee et al. (2011) proposed an alternative approach, called Cox-MDR, for detecting gene-gene interactions based on a Cox model by extending generalized multifactor dimensionality reduction (GMDR) to the survival time phenotype. The main idea of Cox-MDR is to use a martingale residual as a score to classify multi-level genotypes as high and low risk groups. Cox-MDR also allows the effects of discrete and quantitative covariates to be easily adjusted in the Cox model and requires much less computation than Surv-MDR. In this paper, we propose to extend the idea of a Cox-MDR to the parametric regression model, called PRM-MDR for identifying gene-gene interactions associated with the survival phenotype. The main idea of PRM-MDR is to use a standardized residual from a parametric regression model as a score to classify multi-level genotypes as high and low risk groups while keeping the rest of the MDR procedure unchanged. We performed a simulation study to compare PRM-MDR with Cox-MDR as well as the Surv-MDR method in detecting two-way interactions. The simulation setting is constructed as similar as that of Gui et al. (2011), so that three methods are comparable. In addition, we compared the power of PRM-MDR with adjusting the covariates versus without adjusting the covariates in two different scenarios. In the first scenario, we a

关键词： Accuracy Computational modeling Cancer Testing Analytical models Mathematical model Training

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CUDA-LR: CUDA-accelerated logistic regression analysis tool for gene-gene interaction for genome-wide association study

CUDA-LR: CUDA-accelerated logistic regression analysis tool ...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Sungyoung Lee Min-Seok Kwon Ik-Soo Huh Taesung Park Interdisciplinary Program in Bioinformatics Seoul National University Seoul South Korea Department of Statistics Seoul National University Seoul South Korea

In genome-wide association studies (GWAS), logistic regression (LR) has been most commonly used for finding an association between a disease phenotype and genetic variants such as single nucleotide polymorphism (SNP). Since logistic regression model requires iterative algorithms to get the parameter estimates, its application to GWAS has been limited to the identification of the individual SNPs. Thus, there have been limited applications of LR to multiple SNP analysis including gene-gene interaction analysis in large scale GWAS data. To overcome this computational burden, we developed a logistic regression analysis tool named CUDA-LR, based on the new programming architecture using Graphics Processing Unit (GPU). CUDA-LR supports not only the simple model with single SNP but also more complex model with two SNPs including the interaction. In addition, CUDA-LR provides various parameters to gain more acceleration and perform specified analysis. In the comparison between our analysis and the other methods, CUDA-LR showed almost 700-folds of acceleration and highly reliable results by our GPU specified optimization techniques. We believe that the CUDA-LR now is a useful logistic regression analysis tool for interaction analysis of large scale GWAS datasets.

关键词： Graphics processing unit bioinformatics Acceleration Genomics Logistics Mathematical model programming

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Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

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BMC genomics 2016年第6期17 Suppl 6卷 487页

作者： Jerry W. Shay Noriko Homma Ruyun Zhou Muhammad Imran Naseer Adeel G. Chaudhary Mohammed Al-Qahtani Nobutaka Hirokawa Maryam Goudarzi Albert J. Fornace Saleh Baeesa Deema Hussain Mohammed Bangash Fahad Alghamdi Hans-Juergen Schulten Angel Carracedo Ishaq Khan Hanadi Qashqari Nawal Madkhali Mohamad Saka Kulvinder S. Saini Awatif Jamal Jaudah Al-Maghrabi Adel Abuzenadah Adeel Chaudhary Mohammed Al Qahtani Ghazi Damanhouri Heba Alkhatabi Anne Goodeve Laura Crookes Nikolas Niksic Nicholas Beauchamp Adel M. Abuzenadah Jim Vaught Bruce Budowle Mourad Assidi Abdelbaset Buhmeida Leena Merdad Sudhir Kumar Sayaka Miura Karen Gomez Mahmood Rasool Ahmed Rebai Sajjad Karim Hend F. Nour Eldin Heba Abusamra Elham M. Alhathli Nada Salem Mohammed H. Al-Qahtani Hossam Faheem Ashok Agarwa Eberhard Nieschlag Joachim Wistuba Oliver S. Damm Mohd A. Beg Taha A. Abdel-Meguid Hisham A. Mosli Osama S. Bajouh Serdar Coskun Muhammad Abu-Elmagd Ashraf Dallol Sahar Hakamy Wejdan Al-Qahtani Asia Al-Harbi Shireen Hussain Burak Ozkosem Rick DuBois Safia S. Messaoudi Maryam T. Dandana Touhami Mahjoub Wassim Y. Almawi S. Abdalla M. Nabil Al-Aama Asmaa Elzawahry Tsuyoshi Takahashi Sachiyo Mimaki Eisaku Furukawa Rie Nakatsuka Isao Kurosaka Takahiko Nishigaki Hiromi Nakamura Satoshi Serada Tetsuji Naka Seiichi Hirota Tatsuhiro Shibata Katsuya Tsuchihara Toshirou Nishida Mamoru Kato Sajid Mehmood Naeem Mahmood Ashraf Awais Asif Muhammad Bilal Malik Siddique Mehmood Aadil Hussain Qazi Mohammad Sajid Jamal Mughees Uddin Siddiqui Mohammad A. Alzohairy Mohammad A. Al Karaawi Taoufik Nedjadi Heba Al-Khattabi Adel Al-Ammari Ahmed Al-Sayyad Hédia Zitouni Nozha Raguema Marwa Ben Ali Wided Malah Raja Lfalah Wassim Almawi Mohammed Elanbari Andrey Ptitsyn Sana Mahjoub Rabeb El Ghali Bechir Achour Nidhal Ben Amor Brahim N’siri Hamid Morjani Esam Azhar Vera Chayeb Maryam Dendena Hedia Zitouni Khedija Zouari-Limayem Bassem Refaat Ahmed M. Ashshi Sarah A. Batwa Hazem Ramadan Amal Awad Ahmed Ateya Adel Galal Ahmed El-Shemi Ahmad Ashshi Mohammed Basalamah Youjin Na Cha University of Texas Southwestern Medical Center Dallas USA Department of Cell Biology and Anatomy Graduate School of Medicine the University of Tokyo Tokyo Japan Center of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Department of Biochemistry and Molecular & Cellular Biology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Radiation Medicine Lombardi Comprehensive Cancer Center Georgetown University Washington USA Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University Jeddah Kingdom of Saudi Arabia King Fahd Medical Research Centre King Abdulaziz University Jeddah Saudi Arabia Centre of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Sheffield Diagnostic Genetic Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield UK Center of Innovations in Personalized Medicine King Abdulaziz University Jeddah Saudi Arabia President ISBER Editor-in-Chief Biopreservation & Biobanking ᅟ USA Institute of Applied Genetics Department of Molecular and Medical Genetics University of North Texas Health Science Center Fort Worth USA Department of Dental Public Health Faculty of Dentistry King Abdulaziz University Jeddah Saudi Arabia Institute for Genomics and Evolutionary Medicine Temple University Philadelphia USA Center of Excellence in Genomic Medicine King Abdulaziz University Jeddah Kingdom of Saudi Arabia Laboratory of Molecular and Cellular Screening Processes (Bioinformatics Group) Centre of Biotechnology of Sfax Sfax Tunisia Fujitsu Technology Solutions International ᅟ ᅟ Case Western Reserve University School of Medicine and Lerner College of Medicine Cleveland Clinic Foundation Cleveland USA American Center for Reproductive Medicine Andrology Center Cleveland USA Center for Reproductive Medicine and

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic me

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