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Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

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Nature communications 2018年第1期9卷 3493页

作者： Seyedeh M Zekavat Sanni Ruotsalainen Robert E Handsaker Maris Alver Jonathan Bloom Timothy Poterba Cotton Seed Jason Ernst Mark Chaffin Jesse Engreitz Gina M Peloso Ani Manichaikul Chaojie Yang Kathleen A Ryan Mao Fu W Craig Johnson Michael Tsai Matthew Budoff Ramachandran S Vasan L Adrienne Cupples Jerome I Rotter Stephen S Rich Wendy Post Braxton D Mitchell Adolfo Correa Andres Metspalu James G Wilson Veikko Salomaa Manolis Kellis Mark J Daly Benjamin M Neale Steven McCarroll Ida Surakka Tonu Esko Andrea Ganna Samuli Ripatti Sekar Kathiresan Pradeep Natarajan Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA 02142 USA. Yale School of Medicine New Haven CT 06510 USA. Department of Computational Biology & Bioinformatics Yale University New Haven CT 06510 USA. Institute for Molecular Medicine University of Helsinki Helsinki Finland. Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA 02142 USA. Department of Genetics Harvard Medical School Boston MA 02115 USA. Department of Biotechnology Institute of Molecular and Cell Biology University of Tartu Tartu Estonia. Estonian Genome Center Tallinn Estonia. Analytic and Translational Genetics Unit Boston MA 02142 USA. Department of Biological Chemistry University of California Los Angeles Los Angeles CA 90095 USA. Department of Biostatistics Boston University School of Public Health Boston MA 02118 USA. Center for Public Health Genomics University of Virginia Charlottesville VA 22904 USA. Program in Personalized and Genomic Medicine Division of Endocrinology Diabetes & Nutrition Department of Medicine University of Maryland School of Medicine Baltimore MD 21201 USA. Department of Biostatistics School of Public Health and Community Medicine University of Washington Seattle WA 98195 USA. Department of Laboratory Medicine and Pathology University of Minnesota Minneapolis MN 55455 USA. Division of Cardiology Harbor-UCLA Medical Center Los Angeles Biomedical Research Institute Los Angeles CA 90509 USA. NHLBI Framingham Heart Study Framingham MA 20892 USA. Sections of Preventive medicine and Epidemiology and cardiovascular medicine Departments of Medicine and Epidemiology Boston university Schools of Medicine and Public health Boston MA 02118 USA. Departments of Pediatrics and Medicine The Institute for Translational Genomics and Population Sciences Los Angeles Biomedical Research Institute Harbor-UCLA Medical Center Torrance CA 90509 USA. Division of Cardiology

The original version of this article contained an error in the name of the author Ramachandran S. Vasan, which was incorrectly given as Vasan S. Ramachandran. This has now been corrected in both the PDF and HTML versi...

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Methods for Evaluating Medical Tests and Biomarkers

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Diagnostic and Prognostic Research 2017年第1期1卷 1-34页

作者： Gowri Gopalakrishna Miranda Langendam Patrick Bossuyt Mariska Leeflang Rob Scholten Anna Noel-Storr James Thomas Iain Marshall Byron Wallace Penny Whiting Clare Davenport Gowri GopalaKrishna Isabel de Salis Sue Mallett Robert Wolff Marie Westwood Jos Kleinen Richard Riley Gary Collins Hans Reitsma Karel Moons Antonia Zapf Katharina Kramer Annika Hoyer Oliver Kuss J. Ensor R. D. Riley J. J. Deeks E. C. Martin Gerta Rücker Martin Schumacher Susanne Steinhauser Joie Ensor Kym Snell Brian Willis Jon Deeks Thomas Debray Lavinia Ferrante di Ruffano Sian Taylor-Phillips Chris Hyde Stuart A. Taylor Gauraang Batnagar Lavinia Ferrante Di Ruffano Farah Seedat Aileen Clarke Sarah Byron Frances Nixon Rebecca Albrow Thomas Walker Carla Deakin Zhivko Zhelev Harriet Hunt Yaling Yang Lucy Abel James Buchanan Thomas Fanshawe Bethany Shinkins Laure Wynants Sabine Van Huffel Jan Verbakel Dirk Timmerman Ben Van Calster Aeliko Zwinderman Jason Oke Jack O’Sullivan Rafael Perera Brian Nicholson Hannah L. Bromley Tracy E. Roberts Adele Francis Denniis Petrie G. Bruce Mann Kinga Malottki Holly Smith Lucinda Billingham Alice Sitch Oke Gerke Mie Holm-Vilstrup Eivind Antonsen Segtnan Ulrich Halekoh Poul Flemming Høilund-Carlsen Bernard G. Francq Jac Dinnes Julie Parkes Walter Gregory Jenny Hewison Peter Selby Doug Altman William Rosenberg Julien Asselineau Paul Perez Aïssatou Paye Emilie Bessede Cécile Proust-Lima Christiana Naaktgeboren Joris de Groot Johannes Reitsma Anne Rutjes Emmanuel Ogundimu Jonathan Cook Yannick Le Manach Yvonne Vergouwe Romin Pajouheshnia Rolf Groenwold Karen Moons Linda Peelen Bavo De Cock Daan Nieboer Ewout W. Steyerberg Micael J. Pencina Jennifer Cooper Nick Parsons Chris Stinton Steve Smith Andy Dickens Rachel Jordan Alexandra Enocson David Fitzmaurice Peymane Adab Charles Boachie Gaj Vidmar Karoline Freeman Martin Connock Rachel Court Carl Moons Jessica Harris Zoe Plummer Barnaby Reeves Chris Rogers Andrew Mumford Kurtis Lee Veerle Verheyden Gianni D. Angelini Gavin J. Murphy Jeremy Huddy Melody Ni George Hanna Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands Department of Clinical Epidemiology and Biostatistics Academic Medical Center University of Amsterdam Amsterdam Netherlands Cochrane Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht Netherlands Cochrane Dementia and Cognitive Improvement Group University of Oxford Oxford UK EPPI-Centre Department of Social Science University College London London UK Division of Health and Social Care Research King’s College London London UK College of Computer and Information Science Northeastern University Boston USA University Hospitals Bristol NHS Foundation Trust School of Social and Community Medicine Bristol UK Institute of Applied Health Research University of Birmingham Birmingham UK School of Social and Community Medicine University of Bristol Bristol UK Kleijnen Systematic Reviews Ltd York UK Research Institute for Primary Care and Health Sciences Keele University Keele UK Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Cochrane Netherlands University Medical Center Utrecht Utrecht The Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands Department of Medical Statistics University Medical Center Göttingen Göttingen Germany Institute for Biometry and Epidemiology German Diabetes Center Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf Germany Manchester Pharmacy School University of Manchester Manchester UK Institute for Medical Biometry and Statistics Faculty of Medicine and Medical Center – University of Freiburg Stefan-Meier-Str. 26 79104 Freiburg Germany

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Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

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Genome biology 2016年第1期17卷 78页

作者： Paul Muir Shantao Li Shaoke Lou Daifeng Wang Daniel J Spakowicz Leonidas Salichos Jing Zhang George M Weinstock Farren Isaacs Joel Rozowsky Mark Gerstein Department of Molecular Cellular and Developmental Biology Yale University New Haven CT 06520 USA. Systems Biology Institute Yale University West Haven CT 06516 USA. Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven CT 06520 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. The Jackson Laboratory for Genomic Medicine Farmington CT 06032 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. mark@***. Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06520 USA. mark@***. Department of Computer Science Yale University New Haven CT 06520 USA. mark@***.

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Proceedings of the 15th Annual UT-KBRIN bioinformatics Summit 2016 : Cadiz, KY, USA. 8-10 April 2016

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BMC bioinformatics 2016年第SUPPL 10期17卷 297页

作者： Eric C. Rouchka Julia H. Chariker Benjamin J. Harrison Juw Won Park Xueyuan Cao Stanley Pounds Susana Raimondi James Downing Raul Ribeiro Jeffery Rubnitz Jatinder Lamba Bernie J. Daigle Deborah Burgess Stephanie Gehrlich John C. Carmen Nicholas Johnson Chandrakanth Emani Kalpani De Silva Michael P. Heaton Theodore S. Kalbfleisch Teeradache Viangteeravat Rahul Mudunuri Oluwaseun Ajayi Fatih Şen Eunice Y. Huang Mohammad Mohebbi Luaire Florian Douglas J. Jackson John F. Naber AKM Sabbir Sally R. Ellingson Yuping Lu Charles A Phillips Michael A. Langston Rahul K. Sevakula Raghuveer Thirukovalluru Nishchal K. Verma Yan Cui Mohammed Sayed Jing Wang Qi Liu Yu Shyr Xiaofei Zhang Naresh Prodduturi Gavin R. Oliver Diane Grill Jie Na Jeanette Eckel-Passow Eric W. Klee Michael M. Goodin Mark Farman Harrison Inocencio Chanyong Jang Jerzy W. Jaromczyk Neil Moore Kelly Sovacool Leon Dent Mike Izban Sammed Mandape Shruti Sakhare Siddharth Pratap Dana Marshall M Scotty DePriest James N. MacLeod Hanady Adam Ethan Blandford Joel Campbell Joshua Castlen Brittany Dixon Ginger Gilbert Aaron Hall Philip Kreisle Jessica Lasher Bethany Oakes Allison Speer Maximilian Valentine Naga Satya V. Rao Nagisetty Rony Jose Robert Rooney David Hains Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core Louisville USA Department of Psychological and Brain Sciences University of Louisville Louisville USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville USA Department of Biostatistics St. Jude Children’s Research Hospital Memphis USA Department of Pathology St. Jude Children’s Research Hospital Memphis USA Department of Oncology St. Jude Children’s Research Hospital Memphis USA Department of Pharmacotherapy and Translational Research College of Pharmacy University of Florida Gainesville USA Department of Biological Sciences University of Memphis Memphis USA Department of Computer Science University of Memphis Memphis USA Department of Computer Science Northern Kentucky University Highland Heights USA Department of Biological Sciences Northern Kentucky University Highland Heights USA Department of Biology Western Kentucky University Bowling Green USA Interdisciplinary Studies Program: Specialization in Bioinformatics University of Louisville Louisville USA United States Department of Agriculture Agricultural Research Service United States Meat Animal Research Center Clay Center USA Department of Biochemistry and Molecular Genetics School of Medicine University of Louisville Louisville USA Biomedical Informatics Core Children’s Foundation Research Institute Memphis USA Department of Pediatrics University of Tennessee Health Science Center Memphis USA Department of Electrical and Computer Engineering University of Louisville Louisville USA Department of Computer Science University of Kentucky Lexington USA Division of Biomedical Informatics College of Medicine University of Kentucky Lexington USA Department of Electrical Engineering and Computer Science University of Tennessee Knoxville USA Department of Electrical E

I1 Proceedings of the Fifteenth Annual UT- KBRIN bioinformatics Summit 2016 Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park P1 CC-PROMISE: Projection onto the Most Interesting Statistical Evidence (PROMISE) with Canonical Correlation to integrate gene expression and methylation data with multiple pharmacologic and clinical endpoints Xueyuan Cao, Stanley Pounds, Susana Raimondi, James Downing, Raul Ribeiro, Jeffery Rubnitz, Jatinder Lamba P2 Integration of microRNA-mRNA interaction networks with gene expression data to increase experimental power Bernie J Daigle, Jr. P3 Designing and writing software for in silico subtractive hybridization of large eukaryotic genomes Deborah Burgess, Stephanie Gehrlich, John C Carmen P4 Tracking the molecular evolution of Pax gene Nicholas Johnson; Chandrakanth Emani P5 Identifying genetic differences in thermally dimorphic and state specific fungi using in silico genomic comparison Stephanie Gehrlich, Deborah Burgess, John C Carmen P6 Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing Kalpani De Silva, Michael P Heaton, Theodore S Kalbfleisch P7 Mining physiological data to identify patients with similar medical events and phenotypes Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun Ajayi, Fatih Şen, Eunice Y Huang P8 Smart brief for home health monitoring Mohammad Mohebbi, Luaire Florian, Douglas J Jackson, John F Naber P9 Side-effect term matching for computational adverse drug reaction predictions AKM Sabbir, Sally R Ellingson P10 Enrichment vs robustness: A comparison of transcriptomic data clustering metrics Yuping Lu, Charles A Phillips, Michael A Langston P11 Deep neural networks for transcriptome-based cancer classification Rahul K Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui P12 Motif discovery using K-means clustering Mohammed Sayed, Juw Won Park P13 Large scale discovery of active enhancers from nasce

关键词： True Negative Differential Expression UCSC Genome Browser Laboratory Information Management System Biomedical Informatics

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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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The upregulation of Myb and Peg3 may mediate EGCG inhibition effect on mouse lung adenocarcinoma

The upregulation of Myb and Peg3 may mediate EGCG inhibition...

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IEEE International Conference on bioinformatics and Biomedicine

作者： Hong Zhou Joseph Manthey Ekaterina Lioutikova William Yang Kenji Yoshigoe Mary Qu Yang Hong Wang Department of Mathematical Sciences School of Health and Natural Sciences University of Saint Joseph Department of Computer Science George Washington Donaghey College of Engineering and Information Technology University of Arkansas at Little Rock and University of Arkansas for Medical Sciences Middle South Bioinformatics Center and Joint Bioinformatics Ph.D. Program George Washington Donaghey College of Engineering and Information Technology University of Arkansas at Little Rock and University of Arkansas for Medical Sciences Susan L. Cullman Laboratory for Cancer Research Department of Chemical Biology and Center for Cancer Prevention Research Ernest Mario School of Pharmacy Rutgers The State University of New Jersey

ISBN: (纸本)9781467368001

The antioxidant activity of green tea polyphenol epigallocatechin-3-gallate (EGCG) has been found to be critical in inhibiting carcinogenesis. In our previous study, we identified a set of protein coding genes and microRNAs whose expressions were significantly modulated in response to the EGCG treatment in tobacco carcinogen-induced lung adenocarcinoma in A/J mice. In this study, we further conducted some statistical analysis on our microarray data and employed The Cancer Genome Atlas (TCGA) lung adenocarcinoma datasets as additional control. We postulated that if a gene mediates EGCG's cancer inhibition, its expression level change caused by EGCG should be opposite to what occurred in the carcinogenesis. With this assumption, we identified Myb and Peg3 as the primary genes involved in the cancer inhibitory activities of EGCG.

关键词： EGCG Myb Peg3 Lung adenocarcinoma

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Forecasting a moving target: Ensemble models for ILI case count predictions 14

Forecasting a moving target: Ensemble models for ILI case co...

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14th SIAM International Conference on Data Mining, SDM 2014

作者： Chakraborty, Prithwish Khadivi, Pejman Lewis, Bryan Mahendiran, Aravindan Chen, Jiangzhuo Butler, Patrick Nsoesie, Elaine O. Mekaru, Sumiko R. Brownstein, John S. Marathe, Madhav V. Ramakrishnan, Naren Dept. of Computer Science Virginia Tech BlacksburgVA United States Discovery Analytics Center Virginia Tech BlacksburgVA United States Network Dynamics and Simulation Science Laboratory Virginia Bioinformatics Institute Virginia Tech BlacksburgVA United States Childrens Hospital Informatics Program Boston Childrens Hospital BostonMA United States Department of Pediatrics Harvard Medical School BostonMA United States

ISBN: (纸本)9781510811515

Modern epidemiological forecasts of common illnesses, such as the flu, rely on both traditional surveillance sources as well as digital surveillance data. However, most published studies have been retrospective. Concurrently, the reports about flu activity generally lags by several weeks and even when published are revised for several weeks more. We posit that effectively handling this uncertainty is one of the key challenges for a real-time prediction system in this sphere. In this paper, we present a detailed prospective analysis on the generation of robust quantitative predictions about temporal trends of flu activity, using several surrogate data sources for 15 Latin American countries. We present our findings about the limitations and possible advantages of correcting the uncertainty associated with official flu estimates. We also compare the prediction accuracy between model-level fusion of different surrogate data sources against data-level fusion. Finally, we present a novel matrix factorization approach using neighborhood embedding to predict flu case counts. Comparing our proposed ensemble method against several baseline methods helps us demarcate the importance of different data sources for the countries under consideration. Copyriqht © SIAM.

关键词： Forecasting

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A web-based, hospital-wide health care-associated bloodstream infection surveillance and classification system: Development and evaluation

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JMIR Medical Informatics 2015年第3期3卷 e31页

作者： Tseng, Yi-Ju Wu, Jung-Hsuan Lin, Hui-Chi Chen, Ming-Yuan Ping, Xiao-Ou Sun, Chun-Chuan Shang, Rung-Ji Sheng, Wang-Huei Chen, Yee-Chun Lai, Feipei Chang, Shan-Chwen Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Computational Health Informatics Program Boston Children's Hospital Boston MA United States Department of Electrical Engineering National Taiwan University Taipei Taiwan Center for Infection Control National Taiwan University Hospital Taipei Taiwan National Taiwan University Hospital Information Systems Office Taipei Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei Taiwan Department of Internal Medicine National Taiwan University Hospital and College of Medicine Taipei Taiwan National Health Research Institutes National Institute of Infectious Diseases and Vaccinology Miaoli Taiwan

Background: Surveillance of health care-associated infections is an essential component of infection prevention programs, but conventional systems are labor intensive and performance dependent. Objective: To develop an automatic surveillance and classification system for health care-associated bloodstream infection (HABSI), and to evaluate its performance by comparing it with a conventional infection control personnel (ICP)-based surveillance system. Methods: We developed a Web-based system that was integrated into the medical information system of a 2200-bed teaching hospital in Taiwan. The system automatically detects and classifies HABSIs. Results: In this study, the number of computer-detected HABSIs correlated closely with the number of HABSIs detected by ICP by department (n=20;r=.999 P<.001) and by time (n=14;r=.941;P<.001). Compared with reference standards, this system performed excellently with regard to sensitivity (98.16%), specificity (99.96%), positive predictive value (95.81%), and negative predictive value (99.98%). The system enabled decreasing the delay in confirmation of HABSI cases, on average, by 29 days. Conclusions: This system provides reliable and objective HABSI data for quality indicators, improving the delay caused by a conventional surveillance system. © 2020 JMIR Publications Inc. All rights reserved.

关键词： Health care-associated infection Infection control Information systems Surveillance Web-based services

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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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A randomized algorithm for aligning DNA sequences to reference genomes

A randomized algorithm for aligning DNA sequences to referen...

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2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical sciences, ICCABS 2013

作者： Vo, Nam S. Tran, Quang Niraula, Nobal Phan, Vinhthuy Department of Computer Science United States Bioinformatics Program University of Memphis Memphis TN 38152 United States

ISBN: (纸本)9781479907144

The alignment of reads generated by nextgeneration sequencers is an important problem in many biomedical applications. Although many methods have been proposed, we introduce a new randomized algorithm with the distinction of having high performance across a wide range of read lengths and base error rates. We utilize two FM indices to facilitate efficient bidirectional searching. Randomization allows us to estimate effectively key parameters, which ultimately account for the consistency in performance of the method. Our method by and large outperformed some of the recent and popular methods over a wide range of read lengths and base error rates. © 2013 IEEE.

关键词： DNA sequences

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