Practical considerations for implementing genomic information resources

Luke V. Rasmussen; Casey L. Overby; John Connolly; Christopher G. Chute; Joshua C. Denny; Robert R. Freimuth; Andrea L. Hartzler; Ingrid A. Holm; Shannon Manzi; Jyotishman Pathak; Peggy L. Peissig; Maureen Smith; Marc S. Williams; Brian H. Shirts; Elena M. Stoffel; Peter Tarczy-Hornoch; Carolyn R. Rohrer Vitek; Wendy A. Wolf; Justin Starren

doi:10.4338/ACI-2016-04-RA-0060

Applied Clinical Informatics, Table of Contents

Appl Clin Inform 2016; 07(03): 870-882
DOI: 10.4338/ACI-2016-04-RA-0060

Research Article

Schattauer GmbH

Practical considerations for implementing genomic information resources

Experiences from eMERGE and CSER

Authors

Luke V. Rasmussen

¹Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
Casey L. Overby

²Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD

³Genomic Medicine Institute, Geisinger Health System, Danville, PA
John Connolly

⁴The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA
Christopher G. Chute

²Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
Joshua C. Denny

⁵Vanderbilt University Medical Center, Vanderbilt University Medical Center, Nashville, TN
Robert R. Freimuth

⁶Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
Andrea L. Hartzler

⁷Group Health Research Institute, Group Health Cooperative, Seattle, WA
Ingrid A. Holm

⁸Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children’s Hospital, Boston, MA

⁹Department of Pediatrics, Harvard Medical School, Boston, MA
Shannon Manzi

¹⁰Department of Pharmacy and Division of Genetics & Genomics, Boston Children’s Hospital, Boston MA
Jyotishman Pathak

¹¹Division of Health Informatics, Weill Cornell Medical College, Cornell University, New York City, NY
Peggy L. Peissig

¹²Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield WI
Maureen Smith

¹³Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago IL
Marc S. Williams

³Genomic Medicine Institute, Geisinger Health System, Danville, PA
Brian H. Shirts

¹⁴Department of Laboratory Medicine, University of Washington, Seattle, WA
Elena M. Stoffel

¹⁵Department of Internal Medicine, University of Michigan, Ann Arbor, MI
Peter Tarczy-Hornoch

¹⁶Departments of Biomedical Informatics and Medical Education; Pediatrics; Computer Science and Engineering, University of Washington Seattle WA
Carolyn R. Rohrer Vitek

¹⁷Center for Individualized Medicine, Mayo Clinic, Rochester, MN
Wendy A. Wolf

¹⁰Department of Pharmacy and Division of Genetics & Genomics, Boston Children’s Hospital, Boston MA

¹⁸Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA

¹⁹Unitio, Inc., Boston, MA
Justin Starren

¹Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago IL

Abstract

Summary

Objectives

To understand opinions and perceptions on the state of information resources specifically targeted to genomics, and approaches to delivery in clinical practice.

Methods

We conducted a survey of genomic content use and its clinical delivery from representatives across eight institutions in the electronic Medical Records and Genomics (eMERGE) network and two institutions in the Clinical Sequencing Exploratory Research (CSER) consortium in 2014.

Results

Eleven responses representing distinct projects across ten sites showed heterogeneity in how content is being delivered, with provider-facing content primarily delivered via the electronic health record (EHR) (n=10), and paper/pamphlets as the leading mode for patient-facing content (n=9). There was general agreement (91%) that new content is needed for patients and providers specific to genomics, and that while aspects of this content could be shared across institutions there remain site-specific needs (73% in agreement).

Conclusion

This work identifies a need for the improved access to and expansion of information resources to support genomic medicine, and opportunities for content developers and EHR vendors to partner with institutions to develop needed resources, and streamline their use – such as a central content site in multiple modalities while implementing approaches to allow for site-specific customization.

Citation: Rasmussen LV, Overby CL, Connolly J, Chute CG, Denny JC, Freimuth RR, Hartzler AL, Holm IA, Manzi S, Pathak J, Peissig PL, Smith M, Williams MS, Shirts BH, Stoffel EM, Tarczy-Hornoch P, Rohrer Vitek CR, Wolf WA, Starren J. Practical considerations for implementing genomic information resources – experiences from eMERGE and CSER.

Keywords

Electronic health records - genetics - clinical decision support - medicine - education

Full Text

References

References
1 Green ED, Guyer MS. Charting a course for genomic medicine from base pairs to bedside. Nature 2011; 470 7333 204-213.
2 Klitzman R, Chung W, Marder K, Shanmugham A, Chin L, Stark M. et al. Attitudes and Practices Among Internists Concerning Genetic Testing. Journal of Genetic Counseling 2013; 22 (01) 90-100.
3 Calzone KA, Cashion A, Feetham S, Jenkins J, Prows CA, Williams JK. et al. Nurses transforming health care using genetics and genomics. Nurs Outlook 2010; 58 (01) 26-35.
4 Selkirk CG, Weissman SM, Anderson A, Hulick PJ. Physicians’ preparedness for integration of genomic and pharmacogenetic testing into practice within a major healthcare system. Genet Test Mol Biomarkers 2013; 17 (03) 219-225.
5 Dodson C. Knowledge and attitudes concerning pharmacogenomics among healthcare professionals. Personalized Medicine 2011; 08 (04) 421-428.
6 Johansen KATaber, Dickinson BD. Pharmacogenomic knowledge gaps and educational resource needs among physicians in selected specialties. Pharmgenomics Pers Med 2014; 07: 145-162.
7 Overby CL, Erwin AL, Abul-Husn NS, Ellis SB, Scott SA, Obeng AO. et al. Physician Attitudes toward Adopting Genome-Guided Prescribing through Clinical Decision Support. J Pers Med 2014; 04 (01) 35-49.
8 Stanek EJ, Sanders CL, Taber KAJ, Khalid M, Patel A, Verbrugge RR. et al. Adoption of Pharmacogenomic Testing by US Physicians: Results of a Nationwide Survey. Clin Pharmacol Ther 2012; 91 (03) 450-458.
9 Katsanis SH, Minear MA, Vorderstrasse A, Yang N, Reeves JW, Rakhra-Burris T. et al. Perspectives on genetic and genomic technologies in an academic medical center: the duke experience. J Pers Med 2015; 05 (02) 67-82.
10 Passamani E. Educational challenges in implementing genomic medicine. Clin Pharmacol Ther 2013; 94 (02) 192-195.
11 Devine EB, Lee CJ, Overby CL, Abernethy N, McCune J, Smith JW. et al. Usability evaluation of pharmacogenomics clinical decision support aids and clinical knowledge resources in a computerized provider order entry system: a mixed methods approach. Int J Med Inform 2014; 83 (07) 473-483.
12 Overby CL, Devine EB, Abernethy N, McCune JS, Tarczy-Hornoch P. Making pharmacogenomic-based prescribing alerts more effective: A scenario-based pilot study with physicians. J Biomed Inform 2015; 55: 249-259.
13 Reiff M, Bernhardt BA, Mulchandani S, Soucier D, Cornell D, Pyeritz RE. et al. „What does it mean?”: uncertainties in understanding results of chromosomal microarray testing. Genet Med 2012; 14 (02) 250-258.
14 Houfek JF, Soltis-Vaughan BS, Atwood JR, Reiser GM, Schaefer GB. Adults’ perceptions of genetic counseling and genetic testing. Appl Nurs Res 2015; 28 (01) 25-30.
15 National Library of Medicine. Genetics Home Reference. [July 30, 2016]; Available from: http://ghr.nlm.nih.gov/
16 Pagon R, Adam M, Ardinger H, Wallace S, Amemiya A, Bean L. et al. GeneReviews®. Seattle, WA: University of Washington, Seattle; [July 30, 2016]; Available from: http://www.ncbi.nlm.nih.gov/books/NBK1116/
17 Caudle KE, Klein TE, Hoffman JM, Muller DJ, Whirl-Carrillo M, Gong L. et al. Incorporation of pharmacogenomics into routine clinical practice: the Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline development process. Curr Drug Metab 2014; 15 (02) 209-217.
18 Gottesman O, Scott SA, Ellis SB, Overby CL, Ludtke A, Hulot JS. et al. The CLIPMERGE PGx Program: clinical implementation of personalized medicine through electronic health records and genomics-pharmacogenomics. Clin Pharmacol Ther 2013; 94 (02) 214-217.
19 Bielinski SJ, Olson JE, Pathak J, Weinshilboum RM, Wang L, Lyke KJ. et al. Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol. Mayo Clin Proc 2014; 89 (01) 25-33.
20 Manolio TA, Chisholm RL, Ozenberger B, Roden DM, Williams MS, Wilson R. et al. Implementing genomic medicine in the clinic: the future is here. Genet Med 2013; 15 (04) 258-267.
21 Peissig P, Nikolai A, Glurich I, Brilliant M. Personalized Medicine. In: Hock FJ. editor. Drug Discovery and Evaluation: Pharmacological Assays: Springer International Publishing. 2016 4235-4249.
22 Pulley JM, Denny JC, Peterson JF, Bernard GR, Vnencak-Jones CL, Ramirez AH. et al. Operational implementation of prospective genotyping for personalized medicine: the design of the Vanderbilt PREDICT project. Clin Pharmacol Ther 2012; 92 (01) 87-95.
23 Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA. et al. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med 2013; 15 (10) 761-771.
24 Rasmussen-Torvik LJ, Stallings SC, Gordon AS, Almoguera B, Basford MA, Bielinski SJ. et al. Design and anticipated outcomes of the eMERGE-PGx project: a multicenter pilot for preemptive pharmacogenomics in electronic health record systems. Clin Pharmacol Ther 2014; 96 (04) 482-489.
25 National Human Genome Research Institute. Clinical Sequencing Exploratory Research (U01). [July 30, 2016]; Available from: http://grants.nih.gov/grants/guide/rfa-files/RFA-HG-10-017.html
26 Herr T, Bielinski S, Bottinger E, Brautbar A, Brilliant M, Chute C. et al. Practical considerations in genomic decision support: The eMERGE experience. J Pathol Inform. 2015 06. 01
27 Shirts BH, Salama JS, Aronson SJ, Chung WK, Gray SW, Hindorff LA. et al. CSER and eMERGE: current and potential state of the display of genetic information in the electronic health record. J Am Med Inform Assoc 2015; 22 (06) 1231-1242.
28 Tarczy-Hornoch P, Amendola L, Aronson SJ, Garraway L, Gray S, Grundmeier RW. et al. A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record. Genet Med 2013; 15 (10) 824-832.
29 Health Level Seven (HL7) International. Clinical Genomics. 2016 [July 30, 2016]; Available from: http://www.hl7.org/Special/committees/clingenomics/index.cfm
30 Siu LL, Lawler M, Haussler D, Knoppers BM, Lewin J, Vis DJ. et al. Facilitating a culture of responsible and effective sharing of cancer genome data. Nat Med 2016; 22 (05) 464-471.
31 Overby CL, Rasmussen LV, Hartzler A, Connolly JJ, Peterson JF, Hedberg RE. et al. A Template for Authoring and Adapting Genomic Medicine Content in the eMERGE Infobutton Project. AMIA Annu Symp Proc 2014; 2014: 944-953.
32 Heale B, Overby C, Del Fiol G, Rubinstein W, Maglott D, Nelson T. et al. Integrating Genomic Resources with Electronic Health Records using the HL7 Infobutton Standard. Appl Clin Inform [In press]. 2016
33 Cimino JJ, Jing X, Del Fiol G. Meeting the electronic health record „meaningful use” criterion for the HL7 infobutton standard using OpenInfobutton and the Librarian Infobutton Tailoring Environment (LITE). AMIA Annu Symp Proc 2012; 2012: 112-120.
34 Alterovitz G, Warner J, Zhang P, Chen Y, Ullman-Cullere M, Kreda D. et al. SMART on FHIR Genomics: facilitating standardized clinico-genomic apps. J Am Med Inform Assoc 2015; 22 (06) 1173-1178.
35 Institute of Medicine. Representing Genomic Information in the EHR Ecosystem. Genomics-enabled learning health care systems: Gathering and using genomic information to improve patient care and research: Workshop summary. Washington, DC: The National Academies Press; 2015
36 Rohrer CRVitek, Nicholson WT, Schultz C, Caraballo PJ. Evaluation of the use of clinical decision support and online resources for pharmacogenomics education. Pharmacogenomics 2015; 16 (14) 1595-1603.
37 Del Fiol G, Huser V, Strasberg HR, Maviglia SM, Curtis C, Cimino JJ. Implementations of the HL7 Context-Aware Knowledge Retrieval („Infobutton”) Standard: challenges, strengths, limitations, and uptake. J Biomed Inform 2012; 45 (04) 726-735.
38 CDS Hooks – Home. 2015 [July 30, 2016]; Available from: https://github.com/cds-hooks/cds-hooks/wiki
39 Overby CL, Heale B, Aronson S, Cherry JM, Dwight S, Milosavljevic A. et al. Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup. Clin Pharmacol Ther 2016; 99 (02) 157-160.
40 Goel MS, Brown TL, Williams A, Cooper AJ, Hasnain-Wynia R, Baker DW. Patient reported barriers to enrolling in a patient portal. J Am Med Inform Assoc 2011; 18 (Suppl. 01) i8-i12.
41 Davis SE, Osborn CY, Kripalani S, Goggins KM, Jackson GP. Health Literacy, Education Levels, and Patient Portal Usage During Hospitalizations. AMIA Annu Symp Proc 2015; 2015: 1871-1880.
42 Irizarry T, DeVito ADabbs, Curran CR. Patient Portals and Patient Engagement: A State of the Science Review. J Med Internet Res 2015; 17 (06) e148.
43 Stuckey H, Williams JL, Fan AL, Rahm AK, Green J, Feldman L. et al. Enhancing genomic laboratory reports from the patients’ view: A qualitative analysis. Am J Med Genet A 2015; 167a (10) 2238-2243.
44 Williams J, Rahm A, Stuckey H, Green J, Feldman L, Zallen D. et al. Enhancing Genomic Laboratory Reports: A Qualitative Analysis of Provider Review. Am J Med Genet A 2016; 170 (05) 1134-1141.

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