Literature DB >> 33930535

Genomic considerations for FHIR®; eMERGE implementation lessons.

Mullai Murugan1, Lawrence J Babb2, Casey Overby Taylor3, Luke V Rasmussen4, Robert R Freimuth5, Eric Venner6, Fei Yan7, Victoria Yi7, Stephen J Granite3, Hana Zouk8, Samuel J Aronson9, Kevin Power10, Alex Fedotov11, David R Crosslin12, David Fasel13, Gail P Jarvik14, Hakon Hakonarson15, Hana Bangash16, Iftikhar J Kullo16, John J Connolly15, Jordan G Nestor17, Pedro J Caraballo18, WeiQi Wei19, Ken Wiley20, Heidi L Rehm21, Richard A Gibbs6.   

Abstract

Structured representation of clinical genetic results is necessary for advancing precision medicine. The Electronic Medical Records and Genomics (eMERGE) Network's Phase III program initially used a commercially developed XML message format for standardized and structured representation of genetic results for electronic health record (EHR) integration. In a desire to move towards a standard representation, the network created a new standardized format based upon Health Level Seven Fast Healthcare Interoperability Resources (HL7® FHIR®), to represent clinical genomics results. These new standards improve the utility of HL7® FHIR® as an international healthcare interoperability standard for management of genetic data from patients. This work advances the establishment of standards that are being designed for broad adoption in the current health information technology landscape.
Copyright © 2021 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Clinical decision support; Clinical genomics; Electronic health record (EHR); Genetic test results; HL7® FHIR® standard; Interoperability

Mesh：

Year:  2021        PMID： 33930535      PMCID： PMC8583906          DOI： 10.1016/j.jbi.2021.103795

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN： 1532-0464            Impact factor:   8.000


  17 in total

Review 1.  Cytogenetic Nomenclature: Changes in the ISCN 2013 Compared to the 2009 Edition.

Authors:  A Simons; L G Shaffer; R J Hastings
Journal:  Cytogenet Genome Res       Date:  2013       Impact factor: 1.636

2.  CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record.

Authors:  Brian H Shirts; Joseph S Salama; Samuel J Aronson; Wendy K Chung; Stacy W Gray; Lucia A Hindorff; Gail P Jarvik; Sharon E Plon; Elena M Stoffel; Peter Z Tarczy-Hornoch; Eliezer M Van Allen; Karen E Weck; Christopher G Chute; Robert R Freimuth; Robert W Grundmeier; Andrea L Hartzler; Rongling Li; Peggy L Peissig; Josh F Peterson; Luke V Rasmussen; Justin B Starren; Marc S Williams; Casey L Overby
Journal:  J Am Med Inform Assoc       Date:  2015-07-03       Impact factor: 4.497

3.  Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network.

Authors: 
Journal:  Am J Hum Genet       Date:  2019-08-22       Impact factor: 11.025

4.  Molecular findings among patients referred for clinical whole-exome sequencing.

Authors:  Yaping Yang; Donna M Muzny; Fan Xia; Zhiyv Niu; Richard Person; Yan Ding; Patricia Ward; Alicia Braxton; Min Wang; Christian Buhay; Narayanan Veeraraghavan; Alicia Hawes; Theodore Chiang; Magalie Leduc; Joke Beuten; Jing Zhang; Weimin He; Jennifer Scull; Alecia Willis; Megan Landsverk; William J Craigen; Mir Reza Bekheirnia; Asbjorg Stray-Pedersen; Pengfei Liu; Shu Wen; Wendy Alcaraz; Hong Cui; Magdalena Walkiewicz; Jeffrey Reid; Matthew Bainbridge; Ankita Patel; Eric Boerwinkle; Arthur L Beaudet; James R Lupski; Sharon E Plon; Richard A Gibbs; Christine M Eng
Journal:  JAMA       Date:  2014-11-12       Impact factor: 56.272

Review 5.  Strategic vision for improving human health at The Forefront of Genomics.

Authors:  Eric D Green; Chris Gunter; Leslie G Biesecker; Valentina Di Francesco; Carla L Easter; Elise A Feingold; Adam L Felsenfeld; David J Kaufman; Elaine A Ostrander; William J Pavan; Adam M Phillippy; Anastasia L Wise; Jyoti Gupta Dayal; Britny J Kish; Allison Mandich; Christopher R Wellington; Kris A Wetterstrand; Sarah A Bates; Darryl Leja; Susan Vasquez; William A Gahl; Bettie J Graham; Daniel L Kastner; Paul Liu; Laura Lyman Rodriguez; Benjamin D Solomon; Vence L Bonham; Lawrence C Brody; Carolyn M Hutter; Teri A Manolio
Journal:  Nature       Date:  2020-10-28       Impact factor: 49.962

6.  The variant call format and VCFtools.

Authors:  Petr Danecek; Adam Auton; Goncalo Abecasis; Cornelis A Albers; Eric Banks; Mark A DePristo; Robert E Handsaker; Gerton Lunter; Gabor T Marth; Stephen T Sherry; Gilean McVean; Richard Durbin
Journal:  Bioinformatics       Date:  2011-06-07       Impact factor: 6.937

7.  Returning Results in the Genomic Era: Initial Experiences of the eMERGE Network.

Authors:  Georgia L Wiesner; Alanna Kulchak Rahm; Paul Appelbaum; Sharon Aufox; Sarah T Bland; Carrie L Blout; Kurt D Christensen; Wendy K Chung; Ellen Wright Clayton; Robert C Green; Margaret H Harr; Nora Henrikson; Christin Hoell; Ingrid A Holm; Gail P Jarvik; Iftikhar J Kullo; Philip E Lammers; Eric B Larson; Noralane M Lindor; Maddalena Marasa; Melanie F Myers; Josh F Peterson; Cynthia A Prows; James D Ralston; Hila Milo Rasouly; Richard R Sharp; Maureen E Smith; Sara L Van Driest; Janet L Williams; Marc S Williams; Julia Wynn; Kathleen A Leppig
Journal:  J Pers Med       Date:  2020-04-27

8.  Genomic Information for Clinicians in the Electronic Health Record: Lessons Learned From the Clinical Genome Resource Project and the Electronic Medical Records and Genomics Network.

Authors:  Marc S Williams; Casey Overby Taylor; Nephi A Walton; Scott R Goehringer; Samuel Aronson; Robert R Freimuth; Luke V Rasmussen; Eric S Hall; Cynthia A Prows; Wendy K Chung; Alexander Fedotov; Jordan Nestor; Chunhua Weng; Robb K Rowley; Georgia L Wiesner; Gail P Jarvik; Guilherme Del Fiol
Journal:  Front Genet       Date:  2019-10-29       Impact factor: 4.599

Review 9.  Implementing genomic medicine in the clinic: the future is here.

Authors:  Teri A Manolio; Rex L Chisholm; Brad Ozenberger; Dan M Roden; Marc S Williams; Richard Wilson; David Bick; Erwin P Bottinger; Murray H Brilliant; Charis Eng; Kelly A Frazer; Bruce Korf; David H Ledbetter; James R Lupski; Clay Marsh; David Mrazek; Michael F Murray; Peter H O'Donnell; Daniel J Rader; Mary V Relling; Alan R Shuldiner; David Valle; Richard Weinshilboum; Eric D Green; Geoffrey S Ginsburg
Journal:  Genet Med       Date:  2013-01-10       Impact factor: 8.822

10.  FHIR Genomics: enabling standardization for precision medicine use cases.

Authors:  Gil Alterovitz; Bret Heale; James Jones; David Kreda; Fan Lin; Lei Liu; Xin Liu; Kenneth D Mandl; David W Poloway; Rachel Ramoni; Alex Wagner; Jeremy L Warner
Journal:  NPJ Genom Med       Date:  2020-03-18       Impact factor: 8.617
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  5 in total

1.  Applying FHIR Genomics for Research - From Sequencing to Database.

Authors:  Sean Hernandez; Karen Fairchild; Mark Pemberton; Jonathan Dahmer; Wei Zhang; Matvey B Palchuk; Umit Topaloglu
Journal:  AMIA Annu Symp Proc       Date:  2022-05-23

Review 2.  HL7 FHIR-based tools and initiatives to support clinical research: a scoping review.

Authors:  Stephany N Duda; Nan Kennedy; Douglas Conway; Alex C Cheng; Viet Nguyen; Teresa Zayas-Cabán; Paul A Harris
Journal:  J Am Med Inform Assoc       Date:  2022-08-16       Impact factor: 7.942

3.  A research agenda to support the development and implementation of genomics-based clinical informatics tools and resources.

Authors:  Ken Wiley; Laura Findley; Madison Goldrich; Tejinder K Rakhra-Burris; Ana Stevens; Pamela Williams; Carol J Bult; Rex Chisholm; Patricia Deverka; Geoffrey S Ginsburg; Eric D Green; Gail Jarvik; George A Mensah; Erin Ramos; Mary V Relling; Dan M Roden; Robb Rowley; Gil Alterovitz; Samuel Aronson; Lisa Bastarache; James J Cimino; Erin L Crowgey; Guilherme Del Fiol; Robert R Freimuth; Mark A Hoffman; Janina Jeff; Kevin Johnson; Kensaku Kawamoto; Subha Madhavan; Eneida A Mendonca; Lucila Ohno-Machado; Siddharth Pratap; Casey Overby Taylor; Marylyn D Ritchie; Nephi Walton; Chunhua Weng; Teresa Zayas-Cabán; Teri A Manolio; Marc S Williams
Journal:  J Am Med Inform Assoc       Date:  2022-07-12       Impact factor: 7.942

Review 4.  Pharmacogenomic Clinical Decision Support: A Review, How-to Guide, and Future Vision.

Authors:  Dyson T Wake; D Max Smith; Sadaf Kazi; Henry M Dunnenberger
Journal:  Clin Pharmacol Ther       Date:  2021-08-29       Impact factor: 6.903

5.  Genetic testing in ambulatory cardiology clinics reveals high rate of findings with clinical management implications.

Authors:  David R Murdock; Eric Venner; Donna M Muzny; Ginger A Metcalf; Mullai Murugan; Trevor D Hadley; Varuna Chander; Paul S de Vries; Xiaoming Jia; Aliza Hussain; Ali M Agha; Aniko Sabo; Shoudong Li; Qingchang Meng; Jianhong Hu; Xia Tian; Michelle Cohen; Victoria Yi; Christie L Kovar; Marie-Claude Gingras; Viktoriya Korchina; Chad Howard; Daniel L Riconda; Stacey Pereira; Hadley S Smith; Zohra A Huda; Alexandria Buentello; Patricia R Marino; Lee Leiber; Ashok Balasubramanyam; Christopher I Amos; Andrew B Civitello; Mihail G Chelu; Ronald Maag; Amy L McGuire; Eric Boerwinkle; Xander H T Wehrens; Christie M Ballantyne; Richard A Gibbs
Journal:  Genet Med       Date:  2021-08-06       Impact factor: 8.864
  5 in total

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