PhyloD Odds Ratio
PhyloDOR measures and compares the strength of selection pressure placed upon viral sequences by various external factors, such as HLA alleles, antiretroviral drugs, etc.
It does so using a phylogenetically-corrected odds ratio, which compares the odds of escape in the presence or absence of the given HLA allele (for example), conditioned on the phylogeny.
Odds of escape can be computed for a single HLA, two HLA alleles can be compared to see if they drive differential selection, or interaction effects can be tested to see if an HLA allele
drives escape differentially in one context compared to another. Learn more...
- Jonathan M. Carlson, Jennifer Listgarten, Nico Pfeifer, Vincent Tan, Carl Kadie, Bruce D. Walker, Thumbi Ndung'u, Roger Shapiro, John Frater, Zabrina L. Brumme, Philip J. R. Goulder, David Heckerman
(2012) Widespread Impact of HLA Restriction on Immune Control and Escape Pathways in HIV-1.
Journal of Virology, 86(9):5230-5243, May 2012.
Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.
Jonathan M. Carlson, Zabrina Brumme, Christine Rousseau, Chanson Brumme, Philippa Matthews, Carl Kadie, James Mullins, Bruce D. Walker, P. Richard Harrigan, Philip J.R. Goulder, David Heckerman.
PLoS Computational Biology, 4(11):
e1000225, November 2008.