Position:
Assistant Professor
Division:
AIDS
Vision Statement:

The core theme of Dr. Poon’s research career is the development of methods of next-generation sequence analysis to address key issues in HIV treatment and prevention. He draws on a highly multidisciplinary background that covers mathematical biology1, experimental virology2, and bioinformatics3. More recently, he has been developing bioinformatic techniques to detect compensatory interactions from the comparative analysis of genetic sequence data.

Dr. Poon is an Assistant Professor in the division of AIDS at UBC Department of Medicine and an Associate Research Scientist (bioinformatics) for the BC Centre for Excellence in HIV/AIDS’s Laboratory Program. Dr. Poon is also an active member of Canadian HIV Cure Enterprise (CanCURE).

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Research Sumary:

I am actively developing computational tools to analyze next-generation sequencing (NGS) data. NGS is a major challenge for bioinformatics because of the overwhelming amounts of sequence data generated by these technologies. For example, a single Roche/454 Genome Sequencer FLX run typi- cally generates approximately 100,000,000 bps of data. The vast majority of HIV studies have limited themselves to straight-forward analyses such as quantifying the number of rare sequence variants in an HIV-1 population. My objective is to test the limits of what can be inferred from these data. Additionally, I have been developing techniques to reconstruct the complete history of HIV evolution within hosts from longitudinal NGS data. For example, I have used these techniques to reconstruct the mutational pathways leading to the first CXCR4-using ancestors, thereby recreating the evolutionary dynamics of the ‘HIV coreceptor switch’.

Education:
Ph.D. University of California, San Diego, US
M.S. University of British Columbia, Vancouver, BC
B.S. honors. University of Toronto, Toronto, Ontario
Recent Publications:
  1. Gonzalez-Serna A, McGovern RA, Harrigan PR, Vidal F, Poon AFY, Ferrando-Martinez S, Abad MA, Genebat M, Leal M, Ruiz-Mateos E. Correlation of the virological response to short-term Maraviroc monotherapy with standard and deep sequencing-based genotypic tropism methods. Antimicrobial Agents and Chemotherapy, 2012;56(3): 1202-1207.
  2. Knapp, DJHF, RA McGovern, W Dong, AFY Poon, LC Swenson, X Zhong, C Woods, and PR Harrigan. Factors influencing the sensitivity and specificity of conventional sequencing in Human Immunodeficiency Virus-1 tropism testing. J Clin Microbiol, in press. (2012).
  3. Poon AFY, Swenson LC, Bunnik EM, D Edo-Matas, Schuitemaker H, van’t Wout AB, Harrigan PR. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data. PLoS Comput Biol 2012;8(11): e1002753.
  4. Lee GQ, Swenson LC, Poon AFY, Martin JN, Hatano H, Deeks SG, Harrigan PR. Prolonged and Substantial Discordance in Prevalence of Raltegravir-resistant HIV-1 in Plasma versus PBMC Samples Revealed by 454 “Deep’’ Sequencing. PLoS ONE2012; 7(9): e46181.
  5. Aldous JL, Pond SK, Poon A, Jain S, Qin H, Kahn JS, Kitahata M, Rodriguez B, Dennis AM, Boswell SL, Haubrich R, Smith DM. Characterizing HIV Transmission Networks across the United States. Clinical Infectious Diseases 2012;55(8): 1135-1143.
  6. Pond SLK, Murrell B, Poon AFY. Evolution of viral genomes — interplay between selection, recombination and other forces. Methods Mol Biol 2012;856: 239-72.
  7. Rang CU, Peng AY, Poon AF, Chao L. Aging in Escherichia coli requires damage by an extrinsic agent. Microbiology 2012;158: 1553-1559.
  8. Lamers SL, Poon AFY, McGrath MS. HIV-1 nef protein structures associated with brain infection and dementia pathogenesis. PLoS ONE 2011;6(2): e16659.
  9. Knapp DJHF, Harrigan PR, Poon AFY, Brumme ZL, Brockman M, Huang S, Cheung PK. In vitro selection of clinically-relevant bevirimat resistance mutations revealed by deep sequencing of serially-passaged, quasispecies-containing recombinant HIV-1. Journal of Clinical Microbiology 2011;49(1): 201-208.
  10. Poon AFY, Aldous JL, Mathews CW, Kitahata M, Kahn JS, Saag MS, Rodriguez B, Boswell SL, Frost SDW, Haubrich RH. Transmitted Drug Resistance in the CFAR Network of Integrated Clinical Systems Cohort: Prevalence and Effects on Pre-Therapy CD4 and Viral Load. PLoS ONE 2011;6(6): e21189.
Awards & Recognition:
  • Micheal Smith Foundataion for Health Research (MSFHR)/ St. Paul’s Hospital Foundation-Providence Health Care Research Institute (SPHF-PHCRI) Career Investigator Scholar Award, 2012 – 2020.
  • CIHR Fellowhsips Award; Biomedical/Clinical HIV/AIDS Research, 2008 – 2010.
  • NSERC PGS A Award 1998 – 2000.