UnitBar
Core Genomics

Core G redTo 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.

Services


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).

Publications


Baalwa J, Wang S, Parrish NF, Decker JM, Keele BF, Learn GH, Yue L, Ruzagira E, Ssemwanga D, Kamali A, Amornkul PN, Price MA, Kappes JC, Karita E, Kaleebu P, Sanders E, Gilmour J, Allen S, Hunter E, Montefiori DC, Haynes BF, Cormier E, Hahn BH, Shaw GM. Molecular identification, cloning and characterization of transmitted/founder HIV-1 subtype A, D and A/D infectious molecular clones. Virology. 2013 Feb 5;436(1):33-48. doi: 10.1016/j.virol.2012.10.009. Epub 2012 Nov 1. PMCID: PMC3545109.

Bar KJ, Tsao CY, Iyer SS, Decker JM, Yang Y, Bonsignori M, Chen X, Hwang KK, Montefiori DC, Liao HX, Hraber P, Fischer W, Li H, Wang S, Sterrett S, Keele BF, Ganusov VV, Perelson AS, Korber BT, Georgiev I, McLellan JS, Pavlicek JW, Gao F, Haynes BF, Hahn BH, Kwong PD, Shaw GM. Early low-titer neutralizing antibodies impede HIV-1 replication and select for virus escape. PLoS Pathog. 2012;8(5):e1002721. doi: 10.1371/journal.ppat.1002721. Epub 2012 May 31. PMCID: PMC3364956.

Basu D, Kraft CS, Murphy MK, Campbell PJ, Yu T,Hraber PT, Irene C, Pinter A, Chomba E, Mulenga J, Kilembe W, Allen SA, Derdeyn CA, Hunter E. HIV-1 subtype C superinfected individuals mount low autologous neutralizing antibody responses prior to intrasubtype superinfection. Retrovirology. 2012 Sep 20;9:76. doi: 10.1186/1742-4690-9-76. PMCID: PMC3477039.

Bibollet-Ruche F, Heigele A, Keele BF, Easlick JL, Decker JM, Takehisa J, Learn G, Sharp PM, Hahn BH, Kirchhoff F. Efficient SIVcpz replication in human lymphoid tissue requires viral matrix protein adaptation. J Clin Invest. 2012 May 1;122(5):1644-52. doi: 10.1172/JCI61429. Epub 2012 Apr 16. PMCID: PMC3336991.

Boehme, A. K., L. Moneyham, J.McLeod, M. W. Walcott, L. Wright, P. Seal, M. Mugavero, W. E. Norton and M. C. Kempf (2012). "HIV-infected women's relationships with their health care providers in the rural deep south: an exploratory study." Health Care Women Int 33(4): 403-419. PMID: 22420680.

Broker, T. R. (2012). "Global prevention and management of human papillomavirus related diseases: the pressing challenges and the compelling opportunities. Foreword." Vaccine 30 Suppl 5: vii-x. PMID: 23199970.

Broor, S., W. Sullender, K. Fowler, V. Gupta, M. A. Widdowson, A. Krishnan and R. B. Lal (2012). "Demographic shift of influenza A(H1N1)pdm09 during and after pandemic, rural India." Emerg Infect Dis 18(9): 1472-1475. PMID: 22932477; PMCID: PMC3437708.

Brown BK, Wieczorek L, Kijak G, Lombardi K, Currier J, Wesberry M, Kappes JC, Ngauy V, Marovich M, Michael N, Ochsenbauer C, Montefiori DC, Polonis VR. The role of natural killer (NK) cells and NK cell receptor polymorphisms in the assessment of HIV-1 neutralization. PLoS One.2012;7(4):e29454. doi: 10.1371/journal.pone.0029454. Epub 2012 Apr 11. PMCID: PMC3324450.

Chawla, M., P. Parikh, A. Saxena, M. Munshi, M. Mehta, D. Mai, A. K. Srivastava, K. V. Narasimhulu, K. E. Redding, N. Vashi, D. Kumar, A. J. Steyn and A. Singh (2012). "Mycobacterium tuberculosis WhiB4 regulates oxidative stress response to modulate survival and dissemination in vivo." Mol Microbiol 85(6): 1148-1165. PMID: 22780904; PMCID: PMC3438311.

Cornelius, D. C., D. A. Robinson, C. A. Muzny, L. A. Mena, D. M. Aanensen, W. B. Lushbaugh and J. C. Meade (2012). "Genetic characterization of Trichomonas vaginalis isolates by use of multilocus sequence typing." J Clin Microbiol 50(10): 3293-3300. PMID: 22855512; PMCID: PMC3457461.

Contact Information


Genomics Team                                              Pictured: Drs. Michael Crowley, Casey Morrow and Elliot Lefkowitz

Director
Casey Morrow, PhD
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Co-Directors

Michael Crowley
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Elliot Lefkowitz 
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Contact for Microbiome Analysis

Casey Morrow, PhD
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Contact for Next Generation Sequencing and Microarrays

Michael Crowley, PhD
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Contact for the CFAR Molecular and Genetic Bioinformatics Facility (MGBF)

Elliot Lefkowitz, PhD
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Contact for CFAR DNA Sequencing:
Maria Salazar
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University of Alabama at Birmingham
720 20th Street South
Kaul Human Genetics Building, Rooms 406-412
Birmingham, AL 35233