Founder effects in the assessment of HIV polymorphisms and HLA allele associations

T. Bhattacharya; M. Daniels; D. Heckerman; B. Foley; N. Frahm; C. Kadie; J. Carlson; K. Yusim; B. McMahon; B. Gaschen; S. Mallal; J.I. Mullins; D.C. Nickle; J. Herbeck; C Rousseau; G.H. Learn; T. Miura; C. Brander; B. Walker; B. Korber

doi:10.1126/science.1131528

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Founder effects in the assessment of HIV polymorphisms and HLA allele associations

Journal article

Peer reviewed

Founder effects in the assessment of HIV polymorphisms and HLA allele associations

T. Bhattacharya, M. Daniels, D. Heckerman, B. Foley, N. Frahm, C. Kadie, J. Carlson, K. Yusim, B. McMahon, B. Gaschen, …

Science, Vol.315(5818), pp.1583-1586

2007

DOI: https://doi.org/10.1126/science.1131528

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Abstract

Escape from T cell–mediated immune responses affects the ongoing evolution of rapidly evolving viruses such as HIV. By applying statistical approaches that account for phylogenetic relationships among viral sequences, we show that viral lineage effects rather than immune escape often explain apparent human leukocyte antigen (HLA)–mediated immune-escape mutations defined by older analysis methods. Phylogenetically informed methods identified immune-susceptible locations with greatly improved accuracy, and the associations we identified with these methods were experimentally validated. This approach has practical implications for understanding the impact of host immunity on pathogen evolution and for defining relevant variants for inclusion in vaccine antigens.

Details

Title: Founder effects in the assessment of HIV polymorphisms and HLA allele associations
Authors/Creators: T. Bhattacharya (Author/Creator) - Los Alamos National Laboratory
M. Daniels (Author/Creator) - Los Alamos National Laboratory
D. Heckerman (Author/Creator) - Microsoft (Canada)
B. Foley (Author/Creator) - Los Alamos National Laboratory
N. Frahm (Author/Creator) - Harvard University
C. Kadie (Author/Creator) - Microsoft (United States)
J. Carlson (Author/Creator) - Microsoft (United States)
K. Yusim (Author/Creator) - Los Alamos National Laboratory
B. McMahon (Author/Creator) - Los Alamos National Laboratory
B. Gaschen (Author/Creator) - Los Alamos National Laboratory
S. Mallal (Author/Creator) - Royal Perth Hospital
J.I. Mullins (Author/Creator) - University of Washington
D.C. Nickle (Author/Creator) - University of Washington
J. Herbeck (Author/Creator) - University of Washington
C Rousseau (Author/Creator) - University of Washington
G.H. Learn (Author/Creator) - University of Washington
T. Miura (Author/Creator) - Harvard University
C. Brander (Author/Creator) - Harvard University
B. Walker (Author/Creator) - Harvard University
B. Korber (Author/Creator) - Los Alamos National Laboratory
Publication Details: Science, Vol.315(5818), pp.1583-1586
Publisher: American Association for the Advancement of Science
Identifiers: 991005540096407891
Copyright: 2007 American Association for the Advancement of Science
Murdoch Affiliation: Institute for Immunology and Infectious Diseases
Language: English
Resource Type: Journal article

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Collaboration types: Industry collaboration; Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.66 HIV; 1.66.46 HIV Pathogenesis
Web Of Science research areas: Immunology
ESI research areas: Immunology