HLA Similarity

The transmission index of an HIV sequence estimates its relative fitness for transmission. This estimate is predominantly derived from the similarity of protein sequences to those circulating in the population. ()
Details 

We define the adaptation similarity of two HLA alleles to be the Pearson product-moment correlation coefficient between the adaptation scores of the two alleles over a panel of reference HIV sequences. Similarity the adaptaiton similarity of two HLA profiles is the correlation of those profiles over the viral panel. This definition defines similarity based on the shared escape mutations between the two alleles. Intuitively, two alleles are similar if the same viruses appear highly adapted to both alleles.

For this tool, you must choose which HLA adaptation model to choose from, based on HIV subtype. This choice also defines the reference panel of viruses (the same panel used to train the model). Note that Subtype B using a panel of viruses that includes the entire proteome; subtype C includes only Gag, Pol and Nef. For now, we have pre-computed similarity based on this panel for all HLA alleles registered in hla.alleles.org as of 2010, roughly corresponding to when our training data were collected. While adaptation similarity can be comptued against any reference panel, for now it is fixed to the training data.

For technical details and to cite, please see
Jonathan M. Carlson#, Victor Y. Du*, Nico Pfeifer*, Anju Bansal, Vincent Y.F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung’u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter#, Paul A. Goepfert#
Nature Medicine, doi: 10.1038/nm.4100, May 2016.

By using this tool you confirm you have consent from subjects to submit their data.


 
HIV subtype (): load example
Sequences ():
Proteins ():
()
HLAs ():
Subject pairs ():
indicates a required field



Jonathan M. Carlson#, Victor Y. Du*, Nico Pfeifer*, Anju Bansal, Vincent Y.F. Tan, Karen Power, Chanson J. Brumme, Anat Kreimer, Charles E. DeZiel, Nicolo Fusi, Malinda Schaefer, Mark A. Brockman, Jill Gilmour, Matt A. Price, William Kilembe, Richard Haubrich, Mina John, Simon Mallal, Roger Shapiro, John Frater, P. Richard Harrigan, Thumbi Ndung’u, Susan Allen, David Heckerman, John Sidney, Todd M. Allen, Philip J.R. Goulder, Zabrina L. Brumme, Eric Hunter#, Paul A. Goepfert#
Nature Medicine, doi: 10.1038/nm.4100, May 2016.