Development of a Genomic Data Flow Framework: Results of a Survey Administered to NIH-NHGRI IGNITE and EMERGE Consortia Participants

Overview

Journal AMIA Annu Symp Proc

Specialty Medical Informatics

Date 2020 Apr 21

PMID 32308829

Citations 2

Authors

Paul Dexter

Henry Ong

Amanda Elsey

Gillian Bell

Nephi Walton

Wendy Chung

Luke Rasmussen

Kevin Hicks

Aniwaa Owusu-Obeng

Stuart Scott

Steve Ellis

Josh Peterson

Affiliations

Soon will be listed here.

Abstract

Precision health's more individualized molecular approach will enrich our understanding of disease etiology and patient outcomes. Universal implementation of precision health will not be feasible, however, until there is much greater automation of processes related to genomic data transmission, transformation, and interpretation. In this paper, we describe a framework for genomic data flow developed by the Clinical Informatics Work Group of the NIH National Human Genome Research Institute (NHGRI) IGNITE Network consortium. We subsequently report the results of a genomic data flow survey administered to sites funded by NIH-NHGRI for large scale genomic medicine implementations. Finally, we discuss insights and challenges identified through these survey results as they relate to both the current and a desirable future state of genomic data flow.

Citing Articles

Addressing biomedical data challenges and opportunities to inform a large-scale data lifecycle for enhanced data sharing, interoperability, analysis, and collaboration across stakeholders.

Sriram V, Conard A, Rosenberg I, Kim D, Saponas T, Hall A Sci Rep. 2025; 15(1):6291.

PMID: 39984563 PMC: 11845626. DOI: 10.1038/s41598-025-90453-x.

Impact of integrating genomic data into the electronic health record on genetics care delivery.

Lau-Min K, McKenna D, Asher S, Bardakjian T, Wollack C, Bleznuck J Genet Med. 2022; 24(11):2338-2350.

PMID: 36107166 PMC: 10176082. DOI: 10.1016/j.gim.2022.08.009.

The Role of Electronic Health Records in Advancing Genomic Medicine.

Linder J, Bastarache L, Hughey J, Peterson J Annu Rev Genomics Hum Genet. 2021; 22:219-238.

PMID: 34038146 PMC: 9297710. DOI: 10.1146/annurev-genom-121120-125204.

References

Harris P, Taylor R, Thielke R, Payne J, Gonzalez N, Conde J . Research electronic data capture (REDCap)--a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform. 2008; 42(2):377-81. PMC: 2700030. DOI: 10.1016/j.jbi.2008.08.010. View

He K, Ge D, He M . Big Data Analytics for Genomic Medicine. Int J Mol Sci. 2017; 18(2). PMC: 5343946. DOI: 10.3390/ijms18020412. View

Kohane I, Hsing M, Kong S . Taxonomizing, sizing, and overcoming the incidentalome. Genet Med. 2012; 14(4):399-404. PMC: 3821385. DOI: 10.1038/gim.2011.68. View

Deckard J, McDonald C, Vreeman D . Supporting interoperability of genetic data with LOINC. J Am Med Inform Assoc. 2015; 22(3):621-7. PMC: 5566197. DOI: 10.1093/jamia/ocu012. View

Dunnenberger H, Crews K, Hoffman J, Caudle K, Broeckel U, Howard S . Preemptive clinical pharmacogenetics implementation: current programs in five US medical centers. Annu Rev Pharmacol Toxicol. 2014; 55:89-106. PMC: 4607278. DOI: 10.1146/annurev-pharmtox-010814-124835. View

Aziz N, Zhao Q, Bry L, Driscoll D, Funke B, Gibson J . College of American Pathologists' laboratory standards for next-generation sequencing clinical tests. Arch Pathol Lab Med. 2014; 139(4):481-93. DOI: 10.5858/arpa.2014-0250-CP. View

Manzi S, Fusaro V, Chadwick L, Brownstein C, Clinton C, Mandl K . Creating a scalable clinical pharmacogenomics service with automated interpretation and medical record result integration - experience from a pediatric tertiary care facility. J Am Med Inform Assoc. 2016; 24(1):74-80. PMC: 7654081. DOI: 10.1093/jamia/ocw052. View

Dewey F, Grove M, Pan C, Goldstein B, Bernstein J, Chaib H . Clinical interpretation and implications of whole-genome sequencing. JAMA. 2014; 311(10):1035-45. PMC: 4119063. DOI: 10.1001/jama.2014.1717. View

Welch B, Loya S, Eilbeck K, Kawamoto K . A proposed clinical decision support architecture capable of supporting whole genome sequence information. J Pers Med. 2014; 4(2):176-99. PMC: 4234046. DOI: 10.3390/jpm4020176. View

10.

Al Kawam A, Sen A, Datta A, Dickey N . Understanding the Bioinformatics Challenges of Integrating Genomics into Healthcare. IEEE J Biomed Health Inform. 2018; 22(5):1672-1683. DOI: 10.1109/JBHI.2017.2778263. View

11.

Masys D, Jarvik G, Abernethy N, Anderson N, Papanicolaou G, Paltoo D . Technical desiderata for the integration of genomic data into Electronic Health Records. J Biomed Inform. 2012; 45(3):419-22. PMC: 3328607. DOI: 10.1016/j.jbi.2011.12.005. View

12.

Collins F, Varmus H . A new initiative on precision medicine. N Engl J Med. 2015; 372(9):793-5. PMC: 5101938. DOI: 10.1056/NEJMp1500523. View

13.

Roy S, LaFramboise W, Nikiforov Y, Nikiforova M, Routbort M, Pfeifer J . Next-Generation Sequencing Informatics: Challenges and Strategies for Implementation in a Clinical Environment. Arch Pathol Lab Med. 2016; 140(9):958-75. DOI: 10.5858/arpa.2015-0507-RA. View

14.

Welch B, Kawamoto K . Clinical decision support for genetically guided personalized medicine: a systematic review. J Am Med Inform Assoc. 2012; 20(2):388-400. PMC: 3638177. DOI: 10.1136/amiajnl-2012-000892. View

15.

Leipzig J . A review of bioinformatic pipeline frameworks. Brief Bioinform. 2016; 18(3):530-536. PMC: 5429012. DOI: 10.1093/bib/bbw020. View

16.

Jalali Sefid Dashti M, Gamieldien J . A practical guide to filtering and prioritizing genetic variants. Biotechniques. 2017; 62(1):18-30. DOI: 10.2144/000114492. View

17.

Payne T, Corley S, Cullen T, Gandhi T, Harrington L, Kuperman G . Report of the AMIA EHR-2020 Task Force on the status and future direction of EHRs. J Am Med Inform Assoc. 2015; 22(5):1102-10. PMC: 5009932. DOI: 10.1093/jamia/ocv066. View

18.

Aronson S, Rehm H . Building the foundation for genomics in precision medicine. Nature. 2015; 526(7573):336-42. PMC: 5669797. DOI: 10.1038/nature15816. View

19.

Aronson S, Clark E, Babb L, Baxter S, Farwell L, Funke B . The GeneInsight Suite: a platform to support laboratory and provider use of DNA-based genetic testing. Hum Mutat. 2011; 32(5):532-6. PMC: 3082613. DOI: 10.1002/humu.21470. View

20.

Hazin R, Brothers K, Malin B, Koenig B, Sanderson S, Rothstein M . Ethical, legal, and social implications of incorporating genomic information into electronic health records. Genet Med. 2013; 15(10):810-6. PMC: 3926430. DOI: 10.1038/gim.2013.117. View