Viral Genetic Analysis Facility
Director: Feng Gao, MD

Shared Resource Summary:
The Viral Genetic Analysis facility offers large scale florescent DNA sequencing, sequence analysis, and PCR purification to serve the viral genetic analysis needs of researchers at the Center for AIDS Research (CFAR), the Duke Human Vaccine Institute (DHVI), and the Duke community. The facility is equipped with an ABI 3730XL DNA analyzer, a 3100 Genetic Analyzer, a Beckman Coulter Biomek FX^p Laboratory Automation workstation, an Eppendorf epMotion automated pipetting system, a PerkinElmer ScanArray Express, and a Genepix 4000 microarray scanner. Our state of the art fluorescent DNA sequencing yields high quality sequences of 800 or more bases per read. The facility is well equipped to handle large orders and offers discounts for multiple reaction requests greater than 48. In addition to basic sequencing, extensive analysis of sequence data is also offered. These services include primer design, multiple sequence alignments, construction of phylogenetic trees, determination of genetic distances and mutation rates, recombinant viral genome analysis, and detection of drug resistance mutations.
Personnel/Contact Information:
Director: Feng Gao, MD Office Phone: (919) 668-6433 Fax: (919) 668-6435 Email: fgao@duke.edu	Manager: Yi Yang Office Phone: (919) 681-2140 Lab Phone: (919) 684-8364 Fax: (919) 681-8251 Email: yiyang@duke.edu
Location: Research Park I, Room 105, DUMC Box 103020, Durham, NC 27710
Getting Started:
Please see the Common Tools sidebar to register to use facilities, schedule or request a job, and to retrieve data. A sequencing request form or PCR purify request form must accompany all facility service requests. Sequencing Request Form PCR Purification Request Form For a schedule of fees for services, please contact DHVI Shared Resources business office.
Facilities and Instruments:
ABI 3730XL DNA Analyzer (photo) ABI 3100 Genetic Analyzer (photo) Beckman Coulter FX^pLaboratory Automation workstation (photo) Eppendorf epMotion 5075 automated pipetting system (photo) PerkinElmer ScanArray Express (photo) Genepix 4000 microarray scanner (photo)
Services Provided:
Large scale DNA sequencing PCR product purification Sequence analysis Primer design for amplification of diverse HIV-1 strains and other genes Sequence alignments Phylogenetic tree analysis Calculation of genetic diversity and mutation rates Identification of recombinant viral genomes and signature sequences Determination of low frequency drug resistance mutations by parallel allele-specific sequencing (PASS) Detection of drug resistance mutations by direct PCR product sequencing
Protocols and Documents:
DNA Sequencing Instructions DNA Sequencing Sample Form PCR Purification Sample Form
Affiliated Centers:
Duke Center for AIDS Research (www.cfar.duke.edu) Center for HIV-AIDS Vaccine Immunology (www.chavi.org)
Publications:
2006-2008 Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A. 105:7552-7. 2008. Abstract Ramadani HO, Thielman NM, Landman KZ, Ndosi EM, Gao F,Kirchherr JL, Shah R, Shao HJ, Morpeth SC, McNeill, JD, Shao JF, Bartlett JA and Crump JA. Predictors of maladherence, virologic failure and drug resistance among HIV-infected persons receiving antiretroviral therapy in Tanzania. Clinical Infectious Diseases. 45:1492-8. 2007. Abstract Masse S, Lu X, Dekhtyar T, Lu L, Koev G, Gao F, Mo H, Kempf D, Bernstein B, Hanna GJ, Molla A. In vitro selection and characterization of human immunodeficiency virus type 2 (HIV-2) with decreased susceptibility to lopinavir. Antimicrob Agents Chemother. 51:3075-80. 2007. Abstract Kirchherr JL, Lu X, Kasongo W, Chalwe V, Mwananyanda L, Musonda RM, Xia SM, Scearce RM, Liao HX, Montefiori DC, Haynes BF, Gao F. High throughput functional analysis of HIV-1 env genes without cloning. J Virol Methods. 143:104-111. 2007. Abstract Alam SM, McAdams M, Boren D, Rak M, Scearce RM, Gao F, Camacho ZT, Gewirth D, Kelsoe G, Chen P, Haynes BF. The role of antibody polyspecificity and lipid reactivity in binding of broadly neutralizing anti-HIV-1 envelope human monoclonal antibodies 2F5 and 4E10 to glycoprotein 41 membrane proximal envelope epitopes. J Immunol. 178:4424-35. 2007. Abstract Cai F, ChenH, HicksCB, BartlettJA, Zhu J and Gao F.Detection of minor drug-resistance populations by parallel allele-specific sequencing. Nat. Methods. 4:123-125. 2007. Abstract Li M, Salazar-Gonzalez JF, Derdeyn CA, Morris L, Williamson C, Robinson JE, Decker JM, Li Y, Salazar MG, Polonis VR, Mlisana K, Karim SA, Hong K, Greene KM, Bilska M, Zhou J, Allen S, Chomba E, Mulenga J, Vwalika C, Gao F, Zhang M, Korber BT, Hunter E, Hahn BH, Montefiori DC. Genetic and Neutralization Properties of Acute and Early Subtype C Human Immunodeficiency Virus Type 1 Molecular env Clones from Heterosexually Acquired Infections in Southern Africa. J Virol. 80:6745-6756. 2006. Abstract Weaver EA, Lu Z, Camacho ZT, Moukdar F, Liao H-X, Ma B-J, Muldoon M, Theiler J, Nabel GJ, Letvin NL, Korber BT, Hahn BH, Haynes BF and Gao F. Cross-subtype T Cell Immune Responses induced by an HIV-1 Group M Consensus Env Immunogen. J. Virol. 80:6745-6756. 2006. Abstract