Adaptation

Computes adaptation of HIV sequence to HLA-I alleles and to individual's HLA-I profiles. Will compute autologous, heterologous and circulating adaptation. ()
Details 

This tool computes the adaptation of HIV sequences to HLA-I alleles. Three types of adaptation are computed:

  • Autologous adaptation:The extent to which autologous viruses are adapted to their host alleles. The level of autologous adaptation has been linked to host VL and CD4 counts.
  • Heterologous adaptation:The extent to which non-autologous viruses are adapted to a different host's alleles. Heterologous adaptation provides a useful baseline to estimate how much more adapted autologous viruses are than expected.
  • Circulating adaptation:The average heterologous adaptation of a panel of viruses to a given host's alleles. This provides an estimate for the expected extent of pre-adaptation of the founder virus to the host, and has been linked with host VL and CD4 levels.

Circulating adaptation is always computed for all HLA profiles provided against all HIV sequences. Autologous adaptation requires mapping of sequence ID's to HLA ID's, and is only computed for IDs that can be successfully mapped. Heterologous adaptation is computed for a random sample of HLA-sequence pairs, based on a user-specified parameter.

By default, autologous adaptation is computed by mapping the provided sequence IDs to the provided HLA IDs. However, an alternative mapping can be provided.

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 ():
ID map ():
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.