Computer-aided human leukocyte antigen association studies: A case study for psoriasis and severe alopecia areata

Human Immunology

Volumn 71, Issue 8, 2010, Pages 783-788

  Catanzaro, Daniele ^a   Andrien, Marc ^b   Labbé, Martine ^a   Toungouz Nevessignsky, Michel ^b  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b ERASME HOSPITAL   (Belgium)

Author keywords

Alopecia areata; Branch and bound; Combinatorial optimization; Computational immunology; Disease susceptibility; Histocompatibility antigens; Human leukocyte antigen; Mixed integer programming; Psoriasis; Pure parsimony haplotyping

Indexed keywords

HLA A ANTIGEN; HLA ANTIGEN; HLA B ANTIGEN; HLA DQB1 ANTIGEN; HLA DR ANTIGEN;

ADOLESCENT; ADULT; AGED; ALOPECIA AREATA; ARTICLE; CASE STUDY; CHILD; COMPUTER ANALYSIS; DISEASE SEVERITY; FEMALE; GENE FREQUENCY; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; MALE; MATHEMATICAL MODEL; PHENOTYPE; PREDICTION; PRESCHOOL CHILD; PRIORITY JOURNAL; PSORIASIS; RELIABILITY; SCHOOL CHILD;

EID: 77954762505     PISSN: 01988859     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.humimm.2010.04.003     Document Type: Article

References (32)

1. The international HapMap project. Nature 2003, 426:789-796. International HapMap Consortium.
2. A second generation human haplotype map of over. 3.1 Million SNPs. Nature 2007, 449:851-861. International HapMap Consortium.
3. Risch N., Merikangas K. The future of genetic studies of complex human diseases. Science 1996, 273:1516-1517.
4. Li W.H., Sadler L.A. Low nucleotide diversity in man. Genetics 1991, 129:513-523.
5. Lancia G., Pinotti M.C., Rizzi R. Haplotyping populations by pure parsimony: Complexity of exact and approximate algorithms. Informs J Comput 2004, 16:348-359.
6. Excoffier L., Slatkin M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995, 12:921-927.
7. Bonizzoni P., Della Vedova G., Dondi R., Jing L. The haplotyping problem: A view of computational models and solutions. Int J Comput Sci Technol 2003, 18:675-688.
8. Zhang X.S., Wang R.S., Wu L.Y., Chen L. Models and algorithms for haplotyping problem. Curr Bioinformatics 2006, 1:105-114.
9. Gusfield D., Orzack S.H. Haplotype inference. Handbook on Bioinformatics 2005, 1-28. CRC Press, Boca Raton. S. Aluru (Ed.).
10. Catanzaro D., Labbé M. The pure parsimony haplotyping problem: Overview and computational advances. Int Transact Operat Res 2009, 16:561-584.
11. Gusfield D. Inference of haplotypes from samples of diploid populations: Complexity and algorithms. J Comput Biol 2001, 8:305-324.
12. Wang L., Xu Y. Haplotype inference by maximum parsimony. Bioinformatics 2003, 19:1773-1780.
13. Clark A.G. Inference of haplotypes from PRC-amplified samples of diploid populations. Mol Biol Evol 1990, 7:111-122.
14. Catanzaro D. The minimum evolution problem: Overview and classification. Networks 2009, 53:112-125.
15. Li J., Jiang T. Efficient inference of haplotype from genotype on a pedigree. J Bioinform Comput Biol 2003, 1:41-69.
16. Schmitt-Egenolf M., Eiermann T.H., Boehncke W.H., Ständer M., Sterry W. Familial juvenile onset psoriasis is associated with the human leukocyte antigen (HLA) class I side of the extended haplotype Cw6-B57-DRB1*0701-DQA1*0201-*03: A population and family-based study. J Invest Dermatol 1996, 106:711-714.
17. Marques Da Costa C., Dupont E., Van der Cruys M., Andrien M., Hidajat M., Song M., Stene J.J. Earlier occurrence of severe alopecia areata in HLA-DRB1*11-positive patients. Dermatol 2006, 213:12-14.
18. Lancia G., Rizzi R. A polynomial case of the parsimony haplotyping problem. Oper Res Lett 2006, 34:289-295.
19. Gusfield D. Haplotype inference by pure parsimony. Annual Symposium in Combinatorial Pattern Matching, volume 2676 2003, 144-155. Lecture Note in Computer Science (ed), Springer-Verlag, Berlin, Germany.
20. Hidajat M., Andrien M., De Canck I., Dupont E. Caucasian belgian normal. HLA 1998 1998, 119-121. American Society for Histocompatibility and Immunogenetics. D. Gjertson, P.I. Terasaki (Eds.).
21. Catanzaro D., Godi A., Labbé M. A class representative model for pure parsimony haplotyping. Informs J Comput 2009, in press.
22. Colombe B.W., Price V.H., Khoury E.L., Garavoy M.R., Lou C.D. HLA class II antigens associations help to define two types of alopecia areata. J Am Acad Dermatol 1995, 33:757-764.
23. Price V.H., Colombe B.W. Heritable factors distinguish two types of alopecia areata. Clin Dermatol 1996, 14:679-689.
24. Colombe B.W., Lou C.D., Price V.H. The genetic basis of alopecia areata: HLA associations with patchy alopecia areata versus alopecia totalis and alopecia universalis. J Invest Dermatol 1999, 4:216-219.
25. Frentz G., Thomsen K., Jakobsen B.K., Svejgaard A. HLA-DR4 in alopecia areata. J Am Accademy Dermatol 1986, 14:129-130.
26. Welsh E.A., Clarck H.H., Epstein S.Z., Duvic M. Human leukocyte antigen *alleles are associated with alopecia areata. J Invest Dermatol 1994, 103:758-763.
27. Christopher E., Henseler T. Patient subgroups and the inflammatory pattern in psoriasis. Acta Dermatol Venereol 1989, 69:88-92.
28. Hanson I.M., Poustka A., Trowsdale J. New genes in the class II region of the human major histocompatibility complex. Genomics 1991, 10:417-424.
29. Sargent C.A., Dunham I., Campbell R.D. Identification of multiple HTF-Island associated genes in the human major histocompatibility complex class III region. EMBO J 1989, 8:2305-2312.
30. Trowsdale J., Ragoussis J., Campbell R.D. Map of the human MHC. Immunol Today 1991, 12:443-446.
31. Dugoujon J.M., Hazout S., Loirat F., Mourrieras B., Crouau-Roy B., Sanchez-Mazas A. GM haplotype diversity of 82 populations over the world suggests a centrifugal model of human migrations. Am J Phys Anthropol 2004, 125:175-192.
32. Sanchez-Mazas A. An appointment of human HLA diversity. Tissue Antigens 2007, 69:198-202.