Duke HIV Database and Biorepository

Background

The Duke HIV Research Database and Repository has served as an immense resource to conduct translational and clinical research at Duke University since it was first developed in 1998.  As one of the largest and most comprehensive of its kind, the biorepository contains over 70,000 plasma samples on patients with HIV in longitudinal follow-up (median: 12 years) and remains the only clinical biorepository at Duke that exclusively includes HIV-infected persons.

Treatment strategies for HIV and its complications evolve as our understanding of the disease improves, and as our HIV-infected patients live longer. The epidemiology of HIV has gradually shifted away from AIDS-related illnesses to instead focus on HIV comorbidities such as cancer, cardiovascular disease and liver disease, which now constitute the leading causes of death in HIV-infected patients. As a result, significant interest has been generated across funding agencies, including the National Institutes of Health, to investigate pathogenesis of these HIV-associated, non-AIDS related conditions. The clinical investigator community has multiple research applications utilizing this resource, including but not limited to successful ongoing projects and grants. The Duke HIV biorepository has aided a host of multidisciplinary research projects (Table 1) combining the field of infectious diseases with cardiovascular disease, pulmonary disease, oncology, hepatology and gastroenterology, endocrinology, and aging.

Accessing the Biorepository

The Duke HIV Database and Repository serves a diverse group of investigators both internally and externally. As a Duke Core Research Facility, the biorepository resides within the Department of Medicine with Dr. Susanna Naggie as the Principal Investigator. Although the biorepository holds >70,000 plasma samples, each individual sample is unique and thus requests for usage must be reviewed and considered on the basis of merit and potential for scientific contribution.

To ensure an effective, transparent process for reviewing requests, we maintain an oversight committee representing multiple institutes and departments at Duke. The committee employs the following peer-reviewed approach to assess all requests for both biospecimens and database information.

  1. Three primary reviewers are assigned to each proposal
  2. Proposals are discussed on 1-hour conference call to the full committee on an as needed-basis.
  3. Use of database resource will be approved or denied via email response

In order to request Duke HIV biorepository data and/or specimens, please submit a Request Form.

Operations and Logistics

The biorepository is housed with The OneDukebio Integrated biospecimen Network (ODIN), a shared resource created in 2021 that provides full-service biospecimen allocation and management. All specimens undergo de-identification, bar-coding, and 24/7 monitoring in accordance with stringent GLP/GMP standards. ODIN is located in the Snyderman Building (Genome Science Research Building I) on the medical campus of Duke University (595 LaSalle St, Durham, NC), occupying approximately 3000 square feet and in MSRBIII. Rooms housing freezers are equipped with alarm systems for each freezer, emergency power, and two-fold redundant environmental control systems (air conditioning). Access to the facility is controlled by magnetic card-activated door locks, ensuring sample security, confidentiality, and GCLP compliance.  

Rates

All research users have a $20.00 per-sample fee.
Additional fees for more involved data requisition services to accompany Biorepository samples can be discussed with investigators based on the scope of their proposed project.  

Table 1: Publications and Presentations resulting from the Duke HIV Database and Biorepository

User

Publication or National Presentation
Presented in Chronologic Order

Shanti Narayanasamy, Thuy Le

Narayanasamy S, Dougherty J, van Doorn HR, Le T. Pulmonary Talaromycosis: A Window into the Immunopathogenesis of an Endemic Mycosis  Mycopathologia. 2021 Oct;186(5):707-715. doi: 10.1007/s11046-021-00570-0. Epub 2021 Jul 6. PMID: 34228343, PMCID: PMC8536569

Shanti Narayanasamy, Thuy Le

Narayanasamy S, Dat VQ, Thanh NT, Ly VT, Chan JF, Yuen KY, Ning C, Liang H, Li L, Chowdhary A, Youngchim S, Supparatpinyo K, Aung NM, Hanson J, Andrianopoulos A, Dougherty J, Govender NP, Denning DW, Chiller T, Thwaites G, van Doorn HR, Perfect J, Le T.  A global call for talaromycosis to be recognised as a neglected tropical disease

Lancet Glob Health. 2021 Nov;9(11):e1618-e1622. doi: 10.1016/S2214-109X(21)00350-8. PMID: 34678201

Susanna Naggie

Naggie S, Lusk S, Thompson JW, Mock M, Moylan C, Lucas JE, Dubois L, St John-Williams L, Moseley MA, Patel K. Metabolomic signature as a predictor of liver disease events in patients with HIV/HCV co-infection [published online ahead of print, 2020 Jun 5]. J Infect Dis. 2020;jiaa316. doi:10.1093/infdis/jiaa316. PMID: 32502252

Susanna Naggie, Anna Mae Diehl

Du, K, Chitneni, S, Suzuki A, Wang Y, Henao R, Hyun J, Premont R, Naggie S, Moylan C, Mustafa B, Abdelmalek M, Diehl AM. Increased Glutaminolysis Marks Active Scarring in Nonalcoholic Steatohepatitis Progression. Cellular and Molecular Gastroenterology and Hepatology. 2020;10(1):1-21. doi:10.1016/j.jcmgh.2019.12.006. PMID: 31881361 PMCID: PMC7215180

Susanna Naggie

Naggie S, Clement M, Lusk S, Osinusi A, Himmel T, Lucas JE, Thompson WJ, Dubois L, Moseley MA, Clark PJ, Kottilil S, Patel K. Using Stepwise Pharmacogenomics and Proteomics to Predict Hepatitis C Treatment Response in Difficult to Treat Patient Populations. Proteomics Clin. Appl. 2019 May;13(3):e1800006. doi: 10.1002/prca.201800006. PMID: 30058111; PMCID: PMC6353701

Lauren Collins

Collins, L. F., Chan, A., Zheng, J., Chow, S.-C., Wilder, J. M., Muir, A. J., & Naggie, S. (2018). Direct-Acting Antivirals Improve Access to Care and Cure for Patients With HIV and Chronic HCV Infection. Open Forum Infectious Diseases, 5(1). 2017 Dec 9.

Lauren Collins

Collins L, Chan A, Zheng J, Chow S, Wilder J, Muir A, Naggie S.  Direct-Acting Anitvirals Improve Access to Care and Cure for Patients with HIV-HCV.  February 2017.  Conference on Retroviruses and Opportunistic Infections (CROI).  Seattle, WA. Abstract #552.  PubMed

Lance Okeke

Okeke, N.L., Craig, D.M., Muehlbauer, M.J., Ilkayeva, O., Clement, M., Naggie, S., Shah. S.H. Metabolites predict cardiovascular disease events in persons living with HIV: a pilot case–control study. Metabolomics 14: 23. 31 January 2018 https://link.springer.com/article/10.1007%2Fs11306-018-1318-z

Lance Okeke

Okeke L, Craig DM, Muehlbauer MJ, Ilkayeva O, Clement ME, Naggie S, Shah SH. Elevations of Short Chain Dicarboxylacylcarnitine (SCDA) Levels Precede Major Cardiovascular Events in HIV-Infected Persons. October 2016. ID Week, Infectious Diseases Society of America. New Orleans, LA. Abstract #2138.

Susanna Naggie

Naggie S, Meissner E, St. Johns-Williams L, Thompson W, Cyr D, Lucas J, Moseley A, Kottili S, Patel K. Oxylipin Metabolites as Markers of Inflammation and Liver Disease in HCV Infection.  February 2016.  Conference on Retroviruses and Opportunistic Infections (CROI) Meeting, Boston, MA.  Abstract #595.

Mehri McKellar

Khoury, A. L., Morey, M. C., Wong, T. C., McNeil, D. L., Humphries, B., Frankey, K., Pieper, C.F., Hicks, C.C., Huffman, K. McKellar, M. S. (2017). Diminished physical function in older HIV-infected adults in the Southeastern U.S. despite successful antiretroviral therapy. PLoS ONE, 12(6), e0179874. http://doi.org/10.1371/journal.pone.0179874

Mehri McKellar

McKellar M, Bain, J, Ilkayeva O, Muehlbauer M, O’Connell T, Stevens R, Morey M, Pieper C, Kraus W, Huffman K.  Metabolic Alterations and Physical Function in Older HIV-Infected Adult.  February 2016.  Conference on Retroviruses and Opportunistic Infections (CROI) Meeting, Boston, MA.  Abstract #705. 

Mehri McKellar

Jacobson JM, Routy JP, Welles S, DeBenedette M, Tcherepanova I, Angel JB, Asmuth DM, Baril JG, McKellar M, Margolis DM, Trottier B, Wood K, Nicolette C.  Dendritic Cell Immunotherapy for HIV-1 Infection Using Autologous HIV-1 RNA: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.  J Acquir Immune Defic Syndr. 2016 Jan 8.  PubMed

Susanna Naggie

Wong T, Lan A, Kiser J, Anderson PL, Patel K, Tillman H, Naggie S. Novel Quantification of TDF adherence in HIV-hepatitis B co-infected patients with incomplete HBV viral suppression. Hepatology. 2015 December 23, in press.  PubMed

Mehri McKellar

Lan A, Morey M, Chin T, McNeil L, Humphries B, Frankey K, Pieper C, Hicks C, McKellar M.  Diminished Physical Function in Older HIV+ Adults Despite Successful Antiretroviral Therapy.  July 2014.  AIDS Conference, Melbourne Australia.  Abstract #PE056.  PubMed

Susanna Naggie

Norton BL, Park L, McGrath LJ, Proeschold Bell RJ, Muir AJ, Naggie S. Healthcare Utilization in HIV-Infected Patients: Assessing the Burden of Chronic Hepatitis C Coinfection. AIDS Patient Care STDS 2012; 26:541-5. PMID: 22860997.  PubMed

Bart Haynes

Bonsignori M, Moody MA, Parks RJ, Holl TM, Kelsoe G, Hicks CB, Vandergrift N, Tomaras GD, Haynes BF.  HIV-1 Envelope Induces Memory B Cell Responses That Correlate with Plasma Antibody Levels after Envelope gp120 Protein Vaccination or HIV-1 Infection.  PLoS Pathog. 2011 Sep; 7(9): e1002209.  PubMed

Bart Haynes

Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, Decamp AC, Magaret CA, Schief WR, Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B.  Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections.  PLoS Pathog. 2011 Sep; 7(9):e1002209. doi: 10.1371/journal.ppat.1002209. Epub 2011 Sep 29.  PubMed

Nella Goswami

Wang D, Hicks CB, Goswami ND, Tafoya E, Ribeiro RM, Cai F, Perelson AS, Gao F.  Evolution of drug-resistant viral populations during interruption of antiretroviral therapy. 

Journal of Virol. 2011 Jul; 85(13):6403-15. doi: 10.1128/JVI.02389-10. Epub 2011 Apr 13.  PubMed

Feng Gao

Wang D, Hicks CB, Goswami N, Tafoya E, Ribeiro R, Cai F, Perelson A, Gao F.  Evolution of Drug-Resistant Viral Populations during Interruption of Antiretroviral Therapy.  J Virol. 2011 Jul; 85(13): 6403–6415.  PubMed

Susanna Naggie

Naggie S, Yang LY, Chow SC, McCarthy J, McHutchinson J, Hicks C.  Hepatitis C Viral Load Increases in HIV/HCV Co-infected Patients Initiating Antiretroviral Therapy and Correlates with Increases in vLDL Particle Apolipoprotein CIII.  Poster 2010, 17th Conference on Retroviruses and Opportunistic Infections, San Francisco, CA.  

Wanda Lakey

Lakey W, Hicks C.  Lipid changes associated with antiretroviral therapy: results differ by reporting.  Current HIV Research 2009 Sep; 7(5):547-54.  PubMed

Susanna Naggie

Naggie S, Hseih T, Reckleff J, Castellano J, Hicks C.  Treatment and CD4+ T cell count recovery among antiretroviral therapy-naïve patients with HIV/AIDS.  Clin Infect Diseases 2009; 49:1619-20. PMID: 19857170.  PubMed

Kim Hanson

Hanson KE, Reckleff J, Hicks L, Castellano C, Hicks CB.  Unsuspected HIV infection in patients presenting with acute meningitis.  Clinical Infectious Diseases. 2008 Aug 1; 47(3):433-4. doi: 10.1086/589931.  PubMed

Bart Haynes

Alam SM, Scearce RM, Parks RJ, Plonk K, Plonk SG, Sutherland LL, Gorny MK, Zolla-Pazner S, Vanleeuwen S, Moody MA, Xia SM, Montefiori DC, Tomaras GD, Weinhold KJ, Karim SA, Hicks CB, Liao HX, Robinson J, Shaw GM, Haynes BF.  Human Immunodeficiency Virus Type 1 gp41 Antibodies That Mask Membrane Proximal Region Epitopes: Antibody Binding Kinetics, Induction, and Potential for Regulation in Acute Infection.  J Virol. 2008 Jan; 82(1):115-25. Epub 2007 Oct 17. PubMed

Feng Gao

Cai F, Chen H, Hicks CB, Bartlett JA, Zhu J, Gao F.  Detection of Minor Drug-Resistant Populations by Parallel Allele-specific Sequencing.  Nat Methods. 2007 Feb; 4(2):123-5. Epub 2007 Jan 7.  PubMed

Susan Sufka

Sufka SA, Ferrari G, Gryszowka VE, Wrin T, Fiscus SA, Tomaras GD, Staats HF, Patel DD, Sempowski GD, Hellmann NS, Weinhold KJ, Hicks CB.  Prolonged CD4+ cell/virus load discordance during treatment with protease inhibitor-based highly active antiretroviral therapy: immune response and viral control.  J Infect Dis. 2003 Apr 1; 187(7):1027-37. Epub 2003 Mar 13.  PubMed