Extracting research-quality phenotypes from electronic health records to support precision medicine

Genome Medicine
Wei-Qi Wei, Joshua C Denny

Abstract

The convergence of two rapidly developing technologies - high-throughput genotyping and electronic health records (EHRs) - gives scientists an unprecedented opportunity to utilize routine healthcare data to accelerate genomic discovery. Institutions and healthcare systems have been building EHR-linked DNA biobanks to enable such a vision. However, the precise extraction of detailed disease and drug-response phenotype information hidden in EHRs is not an easy task. EHR-based studies have successfully replicated known associations, made new discoveries for diseases and drug response traits, rapidly contributed cases and controls to large meta-analyses, and demonstrated the potential of EHRs for broad-based phenome-wide association studies. In this review, we summarize the advantages and challenges of repurposing EHR data for genetic research. We also highlight recent notable studies and novel approaches to provide an overview of advanced EHR-based phenotyping.

References

Jan 1, 1995·Journal of Clinical Epidemiology·J C Bailar
May 1, 1996·Journal of the American Medical Informatics Association : JAMIA·M M Wagner, William R Hogan
Aug 12, 1999·Critical Care Clinics·A S Sado
Aug 15, 2001·International Journal of Medical Informatics·V J MikulichD L Schriger
May 19, 1977·Nature·Rosmarie Waldner
May 2, 2002·Gastroenterology Nursing : the Official Journal of the Society of Gastroenterology Nurses and Associates·Karen Laing
Dec 4, 2002·The Journal of Clinical Hypertension·James W KinnVincent J Bufalino
Apr 2, 2003·Journal of the American Medical Informatics Association : JAMIA·Joshua C DennyAnderson Spickard
Aug 2, 2003·Nature Medicine·Robert Triendl
Apr 2, 2004·Nature·Wen-Hung ChungYuan-Tsong Chen
Feb 3, 2005·JAMA : the Journal of the American Medical Association·Peter C SmithWilson D Pace
Mar 12, 2005·Science·Jonathan HainesMargaret A Pericak-Vance
Sep 1, 2005·International Journal of Epidemiology·Zhengming ChenRichard Peto
Sep 24, 2005·Health Services Research·Kimberly J O'MalleyCarol M Ashton
Jul 5, 2007·Proceedings of the National Academy of Sciences of the United States of America·Andrey RzhetskyTian Zheng
Oct 20, 2007·Journal of the American Medical Informatics Association : JAMIA·Ozlem UzunerIsaac S Kohane
Jan 29, 2008·Human Genetics·Brian L Browning, Sharon R Browning
Feb 8, 2008·The New England Journal of Medicine·Simon MallalPREDICT-1 Study Team
May 27, 2008·Clinical Pharmacology and Therapeutics·Dan M RodenDan R Masys
Nov 14, 2008·American Journal of Medical Genetics. Part a·C A McCartyMarshfield Clinic PMRP Community Advisory Group
Dec 17, 2008·Breast Cancer Research and Treatment·Adedayo A OnitiloYan Jin
Feb 10, 2009·Nature Genetics·Daniel F GudbjartssonKari Stefansson
Apr 7, 2009·Lancet
Apr 18, 2009·Nature Reviews. Genetics·John P A IoannidisMark J Daly
Dec 8, 2009·Basic & Clinical Pharmacology & Toxicology·Kari FuruHenrik Toft Sørensen
Dec 10, 2009·Nature Reviews. Genetics·Michael L Metzker
Jan 21, 2010·Molecular Systems Biology·Michael KuhnPeer Bork
Feb 13, 2010·Medical Care Research and Review : MCRR·Kitty S ChanJonathan P Weiner
Mar 2, 2010·Journal of the American Medical Informatics Association : JAMIA·Shawn N MurphyIsaac S Kohane
Mar 18, 2010·Arthritis Care & Research·Katherine P LiaoRobert M Plenge
Mar 31, 2010·Pharmacogenomics·David Gurwitz, Munir Pirmohamed
Apr 7, 2010·American Journal of Human Genetics·Marylyn D RitchieDan M Roden
May 14, 2010·The New England Journal of Medicine·Yunjie SongElliott S Fisher
Jul 22, 2010·The New England Journal of Medicine·T Manolio
Dec 15, 2010·Archives of Internal Medicine·Fabienne C BourgeoisKenneth D Mandl
Jan 21, 2011·Clinical Pharmacology and Therapeutics·Russell A WilkeGuergana Savova
Feb 11, 2011·Nature·Elaine R Mardis
Feb 15, 2011·Computer Methods and Programs in Biomedicine·Thuppahi Sisira De SilvaBonnie Cochrane
May 19, 2011·Nature Reviews. Genetics·Isaac S Kohane
Jun 21, 2011·Journal of the American Medical Informatics Association : JAMIA·Ozlem UzunerScott L DuVall
Jun 28, 2011·American Journal of Human Genetics·Iftikhar J KulloChristopher G Chute
Jul 9, 2011·Human Genetics·Bradley MalinE W Clayton
Aug 19, 2011·Journal of the American Medical Informatics Association : JAMIA·Prakash M NadkarniWendy W Chapman
Oct 11, 2011·Nature Genetics·Patrick SulemKari Stefansson
Nov 22, 2011·Journal of the American Medical Informatics Association : JAMIA·Abel N KhoWilliam L Lowe
Dec 23, 2011·Clinical Pharmacology and Therapeutics·Jessica T DelaneyJoshua C Denny
Jan 17, 2012·American Journal of Human Genetics·Peter M VisscherJian Yang
Mar 1, 2012·Journal of the American Medical Informatics Association : JAMIA·Robert J CarrollJoshua C Denny
Mar 30, 2012·Human Mutation·Raoul C M Hennekam, Leslie G Biesecker
Apr 27, 2012·Clinical Pharmacology and Therapeutics·Dan M RodenRussell A Wilke
Jul 4, 2012·Journal of Biomedical Informatics·Himali SaitwalTodd R Johnson
Sep 8, 2012·Journal of the American Medical Informatics Association : JAMIA·George Hripcsak, David J Albers
Jan 10, 2013·PLoS Computational Biology·Joshua C Denny
Jan 29, 2013·Genome Medicine·Gail E HendersonBryan J Weiner
Feb 9, 2013·Genes and Immunity·Scott J HebbringMurray H Brilliant
Mar 2, 2013·Preventing Chronic Disease·Thomas E Kottke, Courtney Jordan Baechler
Mar 28, 2013·Journal of the American Medical Informatics Association : JAMIA·Katherine M NewtonJoshua C Denny
Apr 9, 2013·Journal of the American Medical Informatics Association : JAMIA·Weiyi SunOzlem Uzuner
Apr 12, 2013·Journal of the American Medical Informatics Association : JAMIA·Wei-Qi WeiJoshua C Denny
Jun 8, 2013·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Omri GottesmaneMERGE Network
Jul 3, 2013·Journal of the American Medical Informatics Association : JAMIA·Sungrim MoonGenevieve B Melton
Jul 11, 2013·Journal of the American Medical Informatics Association : JAMIA·Casey Lynnette OverbyChunhua Weng
Jul 13, 2013·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Keith Marsolo, S Andrew Spooner
Aug 13, 2013·Nature Genetics·Cross-Disorder Group of the Psychiatric Genomics ConsortiumInternational Inflammatory Bowel Disease Genetics Consortium (IIBDGC)
Sep 4, 2013·Nature Reviews. Genetics·Kym M BoycottAlex E MacKenzie
Oct 8, 2013·Clinical Pharmacology and Therapeutics·W-Q WeiJoshua C Denny
Oct 8, 2013·Nature Genetics·Cristen J WillerGlobal Lipids Genetics Consortium
Nov 14, 2013·Nature Communications·Julius GudmundssonKari Stefansson
Nov 26, 2013·Journal of the American Medical Informatics Association : JAMIA·A Rosemary TateAdrian Bleach
Dec 10, 2013·Nucleic Acids Research·Danielle WelterHelen Parkinson
Dec 20, 2013·Nature·Hreinn StefanssonKari Stefansson
Mar 13, 2014·American Journal of Medical Genetics. Part C, Seminars in Medical Genetics·Kristin W WeitzelJulie A Johnson
Mar 19, 2014·Journal of Biomedical Informatics·Tae Youn KimAmy Coenen
Apr 15, 2014·European Heart Journal·Peter E WeekeNational Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project
May 3, 2014·Science Translational Medicine·Erica BowtonJill M Pulley
Jun 21, 2014·Science·H3Africa ConsortiumHeather Zar
Jul 6, 2014·Frontiers in Genetics·Dana C CrawfordMarylyn D Ritchie
Jul 31, 2014·European Journal of Human Genetics : EJHG·Zhan YeScott J Hebbring
Oct 10, 2014·Genes and Immunity·David R CrosslinGail P Jarvik
Oct 23, 2014·Journal of the American Medical Informatics Association : JAMIA·Cosmin Adrian BejanJoshua C Denny
Oct 26, 2014·Annals of Oncology : Official Journal of the European Society for Medical Oncology·F AndreC Swanton
Dec 19, 2014·Pharmacogenomics·Vivian K KawaiC Michael Stein
Jun 19, 2015·Life Sciences, Society and Policy·Mahsa Shabani, Pascal Borry
Jan 1, 2015·Genes and Environment : the Official Journal of the Japanese Environmental Mutagen Society·Rakmetkazhy I Bersimbaev, Olga Bulgakova

Citations

Dec 17, 2015·Clinical Pharmacology and Therapeutics·Dan M Roden, Joshua C Denny
Oct 16, 2015·Journal of Biomedical Informatics·Rimma PivovarovNoémie Elhadad
Mar 31, 2016·Journal of the American Medical Informatics Association : JAMIA·Jacqueline C KirbyJoshua C Denny
Sep 5, 2015·Journal of the American Medical Informatics Association : JAMIA·Wei-Qi WeiJoshua C Denny
Apr 29, 2016·Journal of the American Medical Informatics Association : JAMIA·Ayush SinghalZhiyong Lu
May 14, 2016·Journal of the American Medical Informatics Association : JAMIA·Vibhu AgarwalNigam H Shah
Aug 9, 2016·Journal of the American Medical Informatics Association : JAMIA·Pedro L TeixeiraJoshua C Denny
Sep 2, 2016·Briefings in Bioinformatics·Lucia Bianchi, Pietro Liò
Mar 1, 2017·Statistics in Medicine·Matthew ZawistowskiWyndy L Wiitala
Dec 10, 2016·Journal of Diabetes Science and Technology·Rina KagawaKazuhiko Ohe
Mar 10, 2018·Current Cardiology Reports·Aeron M SmallScott M Damrauer
Nov 18, 2017·Clinical and Translational Science·Jamie R RobinsonSara L Van Driest
Nov 18, 2017·GigaScience·Jui-Chu LinYao-Sheng Chen
Apr 27, 2018·Pharmacogenomics·Alexandr A KalininBrian D Athey
Apr 28, 2018·Circulation Research·Jane A Leopold, Joseph Loscalzo
Apr 9, 2016·Statistical Methods in Medical Research·Luca Salmasi, Enrico Capobianco
Oct 13, 2018·Nature Reviews. Drug Discovery·Sudeep PushpakomMunir Pirmohamed
Jul 23, 2019·Journal of the American Medical Informatics Association : JAMIA·Spiros DenaxasHarry Hemingway
Aug 23, 2019·AIDS and Behavior·Kirsha S GordonAmy C Justice
May 6, 2016·Annual Review of Genomics and Human Genetics·Joshua C DennyDan M Roden
Jul 12, 2018·Journal of Neurology·Eldbjørg HustadJan O Aasly
Feb 5, 2020·JMIR Medical Informatics·Emily R PfaffAshok Krishnamurthy
Jun 21, 2019·Annual Review of Biomedical Data Science·Juan M BandaNigam H Shah
Sep 12, 2019·JAMA Network Open·QiPing FengC Michael Stein
Jun 26, 2020·Frontiers in Genetics·Liwei WangHongfang Liu
Oct 25, 2017·Wellcome Open Research·Shona M KerrCaroline Hayward
Aug 21, 2018·Journal of the American Medical Informatics Association : JAMIA·Jennifer A PachecoWilliam K Thompson
Jul 4, 2020·Clinical Rheumatology·Laura L DanielCecilia P Chung
Sep 26, 2020·Journal of the American Medical Informatics Association : JAMIA·Neil S ZhengWei-Qi Wei
Aug 28, 2020·Pharmacoepidemiology and Drug Safety·Caitrin W McDonoughWilliam R Hogan
Jun 15, 2020·Digestive Diseases and Sciences·Christopher J DanfordMichelle Lai
Sep 23, 2020·Drug and Alcohol Dependence·Wenyu SongAdam Wright
Sep 23, 2019·Journal of Biomedical Informatics·Ning ShangChunhua Weng

Related Concepts

DNA
Pharmaceutical Preparations
Health Care Systems
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Vision
Extraction
Genetic Research
Drug Response
High Throughput Analysis
Meta Analysis (Statistical Procedure)

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