To meet the challenges of HIV/AIDS research in prevention, pathogenesis, drug discovery and the natural history in the treatment era, it has been necessary to create a new CFAR Genomics Core. The overall goal of the core is to provide investigators access to cutting-edge genomics resources and methodologies designed to facilitate and strengthen the quality of genetic, genomic, and molecular studies in HIV/AIDS related research. The Genomics Core emphasis on new genomic services, coupled with the microbiome resource and the companion bioinformatics services, provides CFAR investigators with unique resources that will allow for avenues of research in alignment with the 4 pillars of the CFAR scientific mission of prevention, pathogenesis, drug discovery and the natural history in the treatment area era.
Explore resources from March 2015 Microbiome Resources Workshop
Click Here for access to presentations, particpant and speaker contacts, abstracts and other useful information
CFAR investigators will now have access to genome genotyping, gene expression, and methylation arrays, low and high throughput custom genotyping and gene expression, and both standard and next generation sequencing (NGS). A new component has been developed by the core that will provide microbiome analytical capabilities. This component currently provides 16S rRNA gene microbiome analysis and in the future its services will include microbial metagenome, transcriptome and possibly virome analysis. The Core provides guidance for microbiome analysis and the selection of genomic assays and analyses. The specialized knowledge of the core leadership makes this Genomics Core unique in providing not only methodological but also content expertise. The provision of bioinformatics resources and support to help investigators analyze and understand the datagenerated by the genomics core will continue to be a priority through the CFAR Molecular and Genetics Bioinformatics Facility (MGBF).
2014 Publications Supported by the Core
*CFAR Members are Bolded
1. Kumar, R., P. Eipers, R.B. Little, M. Crowley, D.K. Crossman, E.J. Lefkowitz and C.D. Morrow. 2014. Getting Started with Microbiome Analysis: Sample Acquisition to Bioinformatics. Current Protocols in Human Genetics.18.8.1-18.8.29, July 2014 Published online July 2014 in Wiley Online Library (wileyonlinelibrary.com). DOI: 10.1002/0471142905.hg1808s82. PMID: 25042718
2. Brawner, K.M., C.D. Morrow and P. D. Smith. 2014. Gastric Microbiome and Gastric Cancer. The Cancer Journal: The Journal of Principles & Practice of Oncology. 20:211. PubMed PMID: 24855010; PubMed Central PMCID: PMC4149312.
3. Muzny CA, Sunesara IR, Kumar R, Mena LA, Martin DH, Griswold M, Lefkowitz EJ, Schwebke JR, Swiatlo E. Characterization of the Vaginal Microbiota Among Sexual Risk Behavior Groups of Women with Bacterial Vaginosis. PLoS One 2013; 8(11): e80254. PMID: 24236175; PubMed Central PMCID: PMC3827412.
4. Muzny CA, Sunesara IR, Griswold M, Kumar R, Lefkowitz EJ, Mena LA, Schwebke JR, Martin DH, Swiatlo E. Association Between BVAB1 and High Nugent Scores among Women with Bacterial Vaginosis. Diagn Microbiol Infect Dis. PubMed PMID: 25262105. PMCID: PMC4326426.
5. Stoll, M.L., Kumar, R. Morrow, C.D., Lefkowitz, E.J., Cui, X., Genin, A., Cron, R.Q. and C. O. Elson Altered microbiota triggering abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis. Arthritis Res Ther. 2014 Nov30;16(6):486. PMID: 25434931; PMCID: PMC4272554.
6. Hildebrandt E, Zhang Q, Cant N, Ding H, Dai Q, Peng L, Fu Y, DeLucas LJ, Ford R, Kappes JC,Urbatsch IL (2014). A survey of detergents for the purification of stable, active human cystic fibrosis transmembrane conductance regulator (CFTR). Biochim Biophys Acta:.1838(11):2825-37. PMID: 25065669 PMCID: PMC4170525.
7. Jonathan M. Carlson, Malinda Schaefer, Daniela C. Monaco, Rebecca Batorsky, Daniel T. Claiborne, Jessica Prince, Martin J. Deymier, Zachary S. Ende, Nichole R. Klatt, Charles E. DeZiel, Tien-Ho Lin, Jian Peng, Aaron M. Seese, Roger Shapiro, John Frater, Thumbi Ndung’u, Jianming Tang, Paul Goepfert, Jill Gilmour, Matt A. Price, William Kilembe, David Heckerman, Philip J.R. Goulder, Todd M. Allen, Susan Allen, and Eric Hunter. Selection bias at the heterosexual HIV-1 transmission bottleneck. 2014. Science 345(6193). Doi:10.1126/science.1254031. PMCID:4289910
8. Sainski AM, Dai H, Natesampillai S, Pang YP, Bren GD, Cummins NW, Correia C, Meng XW, Tarara JE, Ramirez-Alvarado M, Katzmann DJ, Ochsenbauer C, Kappes JC, Kaufmann SH, Badley AD. 2014. Casp8p41 generated by HIV protease kills CD4 T cells through direct Bak activation.J Cell Biol. 2014 Sep 29;206(7):867-76. doi: 10.1083/jcb.201405051. Epub 2014 Sep 22. Erratum in: J Cell Biol. 2014 Oct 13;207(1):159. PMCID:4178959
9. Yue L, Pfafferott KJ, Baalwa J, Conrod K, Dong CC, Chui C, Rong R, Claiborne DT, Prince JL, Tang J, Ribeiro RM, Cormier E, Hahn BH, Perelson AS, Shaw GM, Karita E, Gilmour J, Goepfert P, Derdeyn CA, Allen SA, Borrow P, Hunter E. Transmitted virus fitness and host T cell responses collectively define divergent infection outcomes in two HIV-1 recipients.PLoS Pathog. 2015 Jan 8;11(1):e1004565. doi: 10.1371/journal.ppat.1004565. PMCID:4287535
10. Deymier MJ, Claiborne DT, Ende Z, Ratner HK, Kilembe W, Allen S, Hunter E. 2014.Particle infectivity of HIV-1 full-length genome infectious molecular clones in a subtype C heterosexual transmission pair following high fidelity amplification and unbiased cloning.Virology Nov;468-470:454-61. doi: 10.1016/j.virol.2014.08.018. PMCID:4252503
11. Yang W, Lee YH, Jones AE, Woolnough JL, Zhou D, Dai Q, Wu Q, Giles KE, Townes TM, Wang H. 2014. The histone H2A deubiquitinase Usp16 regulates embryonic stem cell gene expression and lineage commitment.Nat Commun. 2014 May 2;5:3818. doi: 10.1038/ncomms4818. PMCID:4060806
12. Zhang Z, Jones A, Joo HY, Zhou D, Cao Y, Chen S, Erdjument-Bromage H, Renfrow M, He H, Tempst P, Townes TM, Giles KE, Ma L, Wang H. 2013 USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing. Genes Dev. Jul 15;27(14):1581-95. doi: 10.1101/gad.211037.112. PMCID:3731547
13. Trad A, Tanasa RI, Lange H, Zemlin M, Schroeder HW Jr, Lemke H. 2014 Clonal Progression during the T Cell-Dependent B Cell Antibody Response Depends on the Immunoglobulin DH Gene Segment Repertoire. Front Immunol. Aug 11;5:385. doi: 10.3389/fimmu.2014.00385. eCollection 2014. PMCID:4158299
14. Prentice HA, Pajewski NM, He D, Zhang K, Brown EE, Kilembe W, Allen S, Hunter E, Kaslow RA, Tang J. 2014. Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort. Genes Immun. Jul-Aug;15(5):275-81. doi: 10.1038/gene.2014.16. PMCID:4111776
Pictured: Drs. Michael Crowley, Casey Morrow and Elliot Lefkowitz
Contact for Microbiome Analysis
Casey Morrow, PhD
Contact for Next Generation & DNA Sequencing and Microarrays
Michael Crowley, PhD
Contact for the CFAR Molecular and Genetic Bioinformatics Facility (MGBF)
Elliot Lefkowitz, PhD
University of Alabama at Birmingham
720 20th Street South
Kaul Human Genetics Building, Rooms 406-412
Birmingham, AL 35233