Cassandra Jabara

Graduate Student
BA, Connecticut College '03
Began in fall 2007

It has been demonstrated that minor, drug resistant variants in a retroviral population can significantly influence therapy outcome, yet standard genotypic screening cannot detect polymorphisms below the 20% level. Moreover, genomic amplification of a retroviral population is an indispensable first step of sequencing, and polymerase introduced recombination, nucleotide misincorporation, and differential template amplification, in combination with PCR resampling, can result in a misrepresentation of the initial viral population after sequencing.

In collaboration with Ron Swanstrom and Jeffrey Anderson, I developed a molecular tagging methodology that resolves single retroviral templates after high throughput, ultra-deep pyrosequencing. This allows for not only laboratory introduced error correction, but also accurate inference to the original viral population, including minor variants present below the 1% level. I am currently examining longitudinally sampled circulating populations of HIV-1, and correlating minor, drug resistant variants to viral rebound and therapy failure.

I have previously worked in the laboratory of Robert Doms at the University of Pennsylvania, under Jackie Reeves, studying the entry dynamics and inhibition of the HIV-1 fusion inhibitor T20’s escape mutants. I have also worked in the laboratory of Frederick Kaplan at the University of Pennsylvania Medical School, Center for Research in FOP and Related Disorders, under Paul Billings characterizing the myoblast and myotubule differentiation pathways. My undergraduate research was in the laboratory of Martha Grossel, studying the roles of cell cycle proteins in a primary astrocyte system.

Publications:

Jabara C, CD Jones, J Roach, JA Anderson, Swanstrom R; Accurate Sampling and deep sequencing of the HIV-1 protease gene using a Primer ID, PNAS early edition
PrimerID Supporting Materials


Anderson JA, Ping LH, Dibben O, Jabara CB, Arney L, Kincer L, Tang Y, Hobbs M, Hoffman I, Kazembe P, Jones CD, Borrow P, Fiscus S, Cohen MS, Swanstrom R; and the Center for HIV/AIDS Vaccine Immunology. HIV-1 Populations in Semen Arise through Multiple Mechanisms. PLoS Pathog. 2010 Aug 19;6(8). pii: e1001053. PMC2924360


Harrington PR, Schnell G, Letendre SL, Ritola K, Robertson K, Hall C, Burch CL, Jabara CB, Moore DT, Ellis RJ, Price RW, Swanstrom R. Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course.
AIDS. 2009 May 15;23(8):907-15.

Reeves JD, Lee FH, Miamidian JL, Jabara CB, Juntilla MM, Doms RW. Enfuvirtide resistance mutations: impact on human immunodeficiency virus envelope function, entry inhibitor sensitivity, and virus neutralization. J Virol. 2005 Apr;79(8):4991-9.

Simmons G, Reeves JD, Rennekamp AJ, Amberg SM, Piefer AJ, Bates P. Characterization of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein-mediated viral entry. Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4240-5. Epub 2004 Mar 9. (contributing researcher)