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

Abstract We present an integer programming model for human leukocyte antigen (HLA) association studies based on the parsimony criterion. The model is simple, compact, easy to implement, and able to handle datasets containing up to 200 phenotypes. Computational experiments carried out on patients aff...

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Bibliographic Details
Published in:Human immunology 2010-08, Vol.71 (8), p.783-788
Main Authors: Catanzaro, Daniele, Andrien, Marc, Labbé, Martine, Toungouz-Nevessignsky, Michel
Format: Article
Language:English
Subjects:
Adolescent
Adult
Aged
Aged, 80 and over
Algorithms
Allergy and Immunology
Alopecia areata
Alopecia Areata - genetics
Alopecia Areata - immunology
Branch-and-bound
Child
Child, Preschool
Combinatorial optimization
Computational Biology - methods
Computational immunology
Computer Science
Disease susceptibility
Female
Gene Frequency
Haplotypes
Histocompatibility antigens
HLA Antigens - genetics
Human leukocyte antigen
Humans
Infant
Male
Middle Aged
Mixed-integer programming
Models, Genetic
Operations Research
Phenotype
Psoriasis
Psoriasis - genetics
Psoriasis - immunology
Pure parsimony haplotyping
Reproducibility of Results
Severity of Illness Index
Young Adult
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Summary:Abstract We present an integer programming model for human leukocyte antigen (HLA) association studies based on the parsimony criterion. The model is simple, compact, easy to implement, and able to handle datasets containing up to 200 phenotypes. Computational experiments carried out on patients affected by psoriasis and severe alopecia areata show that the model is consistent with the experimental haplotype frequencies, showing, for the considered diseases at least, a high reliability of the predictions. These promising results provide perspective on computer-aided association studies and encourage the development of efficient exact computational approaches for haplotype estimation.
ISSN:0198-8859
1879-1166
DOI:10.1016/j.humimm.2010.04.003