A statistical framework for modeling HLA-dependent T cell response data

PLoS Computational Biology

Volumn 3, Issue 10, 2007, Pages 1879-1886

  Listgarten, Jennifer ^a   Frahm, Nicole ^b   Kadie, Carl ^a   Brander, Christian ^b   Heckerman, David ^a  

^a MICROSOFT RESEARCH   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; COST EFFECTIVENESS; DISEASES; EPITOPES; T-CELLS;

CELLULARS; CLASS I; HUMAN LEUKOCYTE ANTIGEN; LABORATORY TECHNIQUES; RAPID SCREENING; RESPONSE DATA; STATISTIC MODELING; STATISTICAL FRAMEWORK; T-CELL EPITOPES; T-CELL RESPONSE;

VACCINES;

EPITOPE; HLA ANTIGEN CLASS 1; LEUKOCYTE ANTIGEN;

ALLELE; ARTICLE; COST EFFECTIVENESS ANALYSIS; DONOR; ENZYME LINKED IMMUNOSPOT ASSAY; HLA SYSTEM; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNE RESPONSE; LABORATORY DIAGNOSIS; PREDICTION; PROBABILITY; STATISTICAL MODEL; T LYMPHOCYTE; VACCINATION;

EID: 35748979698     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030188     Document Type: Article

References (27)

1. Johnston MI, Fauci AS (2007) An HIV vaccine - Evolving concepts. N Engl J Med 20: 2073-2081.
2. McMichael A, Hanke T (2002) The quest for an AIDS vaccine: Is the CD8+ T cell approach feasible? Nat Rev 2: 283-291.
3. Hertz T, Yanover C (2007) Identifying HLA supertypes by learning distance functions. Bioinformatics 23: e148-e155. doi:10.1093/Bioinformatics/btl324
4. Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, et al. (2007) CD8+ T cell responses to different HIV proteins have discordant associations with viral load. Nat Med 13: 46-53.
5. Fischer W, Perkins S, Theiler J, Bhattacharya T, Yusim K, et al. (2007) Polyvalent vaccines for optimal coverage of potential T cell epitopes in global HIV-1 variants. Nat Med 1: 100-106.
6. Nickle DC, Rolland M, Jensen MA, Pond SLK, Deng W, et al. (2007) Coping with viral diversity in HIV vaccine design. PLoS Comput Biol 3: e75. doi:10.1371/journal.pcbi.0030075
7. Goulder P, Addo M, Altfeld M, Rosenberg E, Tang Y, et al. (2001) Rapid definition of five novel HLA-A*3002-restricted human immunodeficiency virus-specific cytotoxic T-lymphocyte epitopes by Elispot and intracellular cytokine staining assays. J Virol 75: 1339-1347.
8. Zhanga GL, Bozic I, Kwoh CK, August JT, Brusic V (2007) Prediction of supertype-specific HLA class I binding peptides using support vector machines. J Immunol Methods 320: 143-154.
9. Sette A, Bui HH, Sidney J, Bourne P, Buus S, et al. (2006) The Immune Epitope Database and analysis resource. In: Rajapakse JC, Wong L, Acharya R, editors. Proceedings of the Pattern Recognition in Bioinformatics International Workshop, PRIB 2006; 20 August 2006; Hong Kong, China. Berlin: Springer. pp. 126-132. Available: http://www.immuneepitope.org/references.do. Accessed 11 September 2007.
10. Lund O, Nielsen M, Lundegaard C, Kesmir C, Brunak S (2005) Immunological bioinformatics (computational molecular biology). Cambridge (Massachusetts): MIT Press.
11. Heckerman D, Kadie CM, Listgarten J (2007) Leveraging information across HLA alleles/supertypes improves epitope prediction. J Comput Biol 14: 736-746.
12. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc 57: 289-300.
13. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
14. Frahm N, Goulder PJ, Brander C (2004). Broad HIV-1 specific CTL responses reveal extensive HLA class I binding promiscuity of HIV-derived, optimally defined CTL epitopes. In: HIV molecular immunology database. Los Alamos (New Mexico): Los Alamos National Laboratory, Theoretical Biology and Biophysics.
15. Heckerman D, Breese J (1996) Causal independence for probability assessment and inference using Bayesian networks. IEEE Trans Syst Man Cybern 26: 826-831.
16. Shwe M, Middleton B, Heckerman D, Henrion M, Horvitz E, et al. (1991) Probabilistic diagnosis using a reformulation of the INTERNIST-1/QMR knowledge base: Part I. The probabilistic model and inference algorithms. Methods Inf Med 30: 241-250.
17. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Auto Control 19: 716-723.
18. Kass R, Raftery A (1995) Bayes factors. J Am Stat Assoc 90: 773-795.
19. MacKay DJC (2003) Information theory, inference, and learning algorithms. Cambridge (United Kingdom): Cambridge University Press.
20. Casella G, Berger R (2001) Statistical inference. Duxbury (Massachusetts): Duxbury Press.
21. Listgarten J, Heckerman D (2007) Determining the number of nonspurious arcs in a learned DAG model: Investigation of a Bayesian and a frequentist approach. In: UAI '07: Proceedings of the 23rd Conference in Uncertainty in Artificial Intelligence; University of British Columbia, Vancouver, British Columbia, Canada, 19-22 July 2007. San Francisco: Morgan Kaufmann.
22. Friedman N, Koller D (2003) Being bayesian about network structure. A bayesian approach to structure discovery in bayesian networks. Mach Learn 50: 95-125.
23. Frahm N, Adams S, Kiepiela P, Linde C, Hewitt H, et al. (2005) HLA-B63 presents HLA-B57/B58-restricted cytotoxic T-lymphocyte epitopes and is associated with low human immunodeficiency virus load. J Virol 79: 10218-10225.
24. Frahm N, Kiepiela P, Adams S, Linde C, Hewitt H, et al. (2006) Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nat Immunol 2: 173-178.
25. Jurgelenaite R, Heskes T (2006) Symmetric causal independence models for classification. In: Studeny M, Vomlel J, editors. Proceedings of the Third European Workshop on Probabilistic Graphical Models; 12-15 September 2006; Prague, Czech Republic.
26. Frahm N, Yusim K, Suscovich T, Adams S, Sidney J, et al. (2007) Extensive HLA class I allele promiscuity among viral CTL epitopes. Eur J Immunol 37: 2419-2433.
27. Sette A, Sidney J (1999) Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism. Immunogenetics 50: 201-212.