Advertisement

EPMA Journal

, Volume 9, Issue 3, pp 225–234 | Cite as

Biorepository and integrative genomics initiative: designing and implementing a preliminary platform for predictive, preventive and personalized medicine at a pediatric hospital in a historically disadvantaged community in the USA

  • Rony Jose
  • Robert Rooney
  • Naga Nagisetty
  • Robert Davis
  • David Hains
Research

Abstract

Current healthcare is evolving to emphasize cost-effective care by leveraging results and outcomes of genomic and other advanced research efforts in clinical care and preventive health planning. Through a collaborative effort between the University of Tennessee Health Science Center (UTHSC) and Le Bonheur Children’s Hospital (LBCH), the Biorepository and Integrative Genomics (BIG) Initiative was established to set up a pediatric-based DNA biorepository that can serve as a foundation for successful development of delivery platforms for predictive, preventive, and personalized medical services in Memphis, Tennessee, a historically disadvantaged community in the USA. In this paper, we describe the steps that were followed to establish the biorepository. We focused on domains that are essential for implementation of a biorepository for genomic research as an initial goal and identified patient consent, DNA extraction, storage and dissemination, and governance as essential components. Specific needs in each of these domains were addressed by respective solutions developed by multidisciplinary teams under the guidance of a governance model that involved experts from multiple hospital arenas and community members. The end result was the successful launch of a large-scale DNA biorepository, with patient consent greater than 75% in the first year. Our experience highlights the importance of performing pre-design research, needs assessment, and designing an ethically vetted plan that is cost-effective, easy to implement, and inclusive of the community that is served. We believe this biorepository model, with appropriate tailoring according to organizational needs and available resources, can be adopted and successfully applied by other small- to mid-sized healthcare organizations.

Keywords

Biobank Integrative genomics initiative Predictive preventive personalized medicine Pediatrics Community 

Notes

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Consent for publication

The authors provide consent for publication.

Ethical approval

All the patient investigations conformed to the principles outlined in the Declaration of Helsinki and have been performed with the permission (IRB Approval Number—15-03639-XP) released by the responsible Ethics Committee/Institutional Regulatory Board of the University of Tennessee Health Science Center. All the patients were informed about the purposes of the study and have signed their “consent of the patient.” This article does not contain any studies with animals performed by any of the authors.

References

  1. 1.
    Christensen KD, Dukhovny D, Siebert U, Green RC. Assessing the costs and cost-effectiveness of genomic sequencing. J Pers Med. 2015;5(4):470–86.CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Baker M. Biorepositories: building better biobanks. Nature. 2012;486(7401):141–6.CrossRefPubMedGoogle Scholar
  3. 3.
  4. 4.
    Centers for Disease Control. Behavioral risk factor surveillance system 2016 system data and documentation. 2018. https://www.cdc.gov/brfss/annual_data/annual_2016.html.
  5. 5.
    Knerr S, Wayman D, Bonham VL. Inclusion of racial and ethnic minorities in genetic research: advance the spirit by changing the rules? J Law Med Ethics. 2011;39(3):502–12.CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Wright ML, Housman D, Taylor JY. A perspective for sequencing familial hypercholesterolaemia in African Americans. NPJ Genom Med. 2016;1:16012.CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Popejoy AB, Fullerton SM. Genomics is failing on diversity. Nature. 2016;538:161–4.CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Garber KB, Vincent LM, Alexander JJ, Bean LJ, Bale S, Hegde M. Reassessment of genomic sequence variation to harmonize interpretation for personalized medicine. Am J Hum Gen. 2016;99(5):1140–9.CrossRefGoogle Scholar
  9. 9.
    Landry LG, Rehm HL. Association of racial/ethnic categories with the ability of genetic tests to detect a cause of cardiomyopathy. JAMA Cardiol. 2018;3(4):341–5.CrossRefPubMedGoogle Scholar
  10. 10.
    Lu M, Zhan X. The crucial role of multiomic approach in cancer research and clinically relevant outcomes. EPMA J. 2018;9(1):77–102.CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Ozgüç M. Genetic testing: predictive value of genotyping for diagnosis and management of disease. EPMA J. 2011;2(2):173–9.CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Wysocki K. Lung disease and genomics. AACN Adv Crit Care. 2018;29(1):74–83. SpringCrossRefPubMedGoogle Scholar
  13. 13.
    Amare AT, Schubert KO, Baune BT. Pharmacogenomics in the treatment of mood disorders: strategies and opportunities for personalized psychiatry. EPMA J. 2017;8(3):211–27.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Relling MV, Evans WE. Pharmacogenomics in the clinic. Nature. 2015;526(7573):343–50.CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Berg AT, Coryell J, Saneto RP, Grinspan ZM, Alexander JJ, Kekis M, et al. Early-life epilepsies and the emerging role of genetic testing. JAMA Pediatr. 2017;171(9):863–71.CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    McGregor TL, Van Driest SL, Brothers KB, Bowton EA, Muglia LJ, Roden DM. Inclusion of pediatric samples in an opt-out biorepository linking DNA to de-identified medical records: pediatric BioVU. Clin Pharmacol Ther. 2013;93(2):204–11.CrossRefPubMedGoogle Scholar
  17. 17.
    National Human Research Institute. NHGRI implementation of the NIH Genomic Data Sharing (GDS) Policy. https://www.genome.gov/27562511#al-2.
  18. 18.
    U.S. Department of Health & Human Services. Federal policy for the protection of human subjects (‘Common Rule’). https://www.hhs.gov/ohrp/regulations-and-policy/regulations/common-rule/index.html.
  19. 19.
    Golubnitschaja O, Costigliola V, EPMA. General report & recommendations in predictive, preventive and personalised medicine 2012: white paper of the European association for predictive, preventive and personalised medicine. EPMA J. 2012;3(1):14.CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Golubnitschaja O, Baban B, Boniolo G, Wang W, Bubnov R, Kapalla M, et al. Medicine in the early twenty-first century: paradigm and anticipation - EPMA position paper 2016. EPMA J. 2016;7:23.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Campbell LD, Astrin JJ, DeSouza Y, Giri J, Patel AA, Rawley-Payne M, et al. The 2018 revision of the ISBER best practices: summary of changes and the editorial Team's development process. Biopreserv Biobank. 16(1):3–6.21.Google Scholar
  22. 22.
    CFR Parts 50 and 56: Additional Safeguards for Children in Clinical Investigations of Food and Drug Administration-Regulated Products https://www.gpo.gov/fdsys/pkg/FR-2013-02-26/pdf/2013-04387.pdf.
  23. 23.
    Title 45: Public Welfare, Part 46, Protection of Human Subjects. https://www.hhs.gov/ohrp/regulations-and-policy/regulations/45-cfr-46/index.html.
  24. 24.
  25. 25.
  26. 26.
    45 CFR Part 160 and Subparts A and E for Professionals: https://www.hhs.gov/hipaa/for-professionals/privacy/index.html.
  27. 27.
    The Genetic Information Nondiscrimination Act of 2008, Information for Researchers and Health Care Professionals: https://www.genome.gov/pages/policyethics/geneticdiscrimination/ginainfodoc.pdf.
  28. 28.
    Final NIH Policy on the Use of a Single Institutional Review Board for Multi-Site Research: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-16-094.html.
  29. 29.
    Federal Policy for the Protection of Human Subjects; Final Rule: https://www.gpo.gov/fdsys/pkg/FR-2017-01-19/html/2017-01058.htm.
  30. 30.
    Federal Policy for the Protection of Human Subjects; Rules and Regulations: https://www.gpo.gov/fdsys/pkg/FR-2018-01-22/pdf/2018-00997.pdf.
  31. 31.
    Brothers KB, Lynch JA, Aufox SA, Connolly JJ, Gelb BD, Holm IA, et al. Practical guidance on informed consent for pediatric participants in a biorepository. Mayo Clin Proc. 2014;89:1471–80.CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Harris PA, Taylor R, Thielke R, Payne J, Gonzalez N, Conde JG. Research electronic data capture (REDCap) – a metadata-driven methodology and workflow process for providing translational research informatics support. J Biomed Inform. 2009;42(2):377–81.CrossRefPubMedGoogle Scholar
  33. 33.
    Redcap (Research Electronic Data Capture) https://www.project-redcap.org.
  34. 34.
    Evans RS, Lloyd JF, Pierce LA. Clinical use of an enterprise data warehouse. AMIA Ann Symp Proc. 2012;2012:189–98.Google Scholar
  35. 35.
    Northwestern Medicine Enterprise Data Warehouse (NMEDW): http://nucats.northwestern.edu/resources/data-science-and-informatics/nmedw/index.html.
  36. 36.
    VCU and VCU Health System, single Enterprise Data Warehouse (EDW) https://cctr.vcu.edu/informatics/edw/index.html.
  37. 37.
    NIH’s Certificates of Confidentiality Policy Enhances Confidentiality of Participants Enrolled in Clinical Research Studies: https://nexus.od.nih.gov/all/2017/09/07/nih-new-certificates-of-confidentiality-policy.
  38. 38.
    NIH Certificates of Confidentiality (CoC): https://humansubjects.nih.gov/coc/index.

Copyright information

© European Association for Predictive, Preventive and Personalised Medicine (EPMA) 2018

Authors and Affiliations

  1. 1.Center for Biomedical Informatics, Department of PediatricsUniversity of Tennessee Health Science CenterMemphisUSA
  2. 2.Department of Pediatrics, Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisUSA
  3. 3.Department of PediatricsUniversity of Tennessee Health Science CenterMemphisUSA
  4. 4.Department of Pediatrics, University of Tennessee Health Science Center, Center for Innate Immunity Translational ResearchChildren’s Foundation Research Institute at Le Bonheur Children’s HospitalMemphisUSA
  5. 5.Division of Pediatric Nephrology, Riley Hospital for ChildrenIndiana University School of MedicineIndianapolisUSA

Personalised recommendations