A fuzzy approach to image analysis in HLA typing using oligonucleotide microarrays

The human leukocyte antigen (HLA) region is a part of genome which spans over 4 Mbases of DNA. The HLA system is strongly connected to immunological response and its compatibility between tissues is critical in transplantation. We have developed an application of oligonucleotide microarrays to HLA typing. In this paper, we present a method based on a fuzzy system which interactively supports the user in analyzing the hybridization results, speeding-up the decision process moving from raw array data obtained from the scanner to their interpretation (genotyping). The two-level procedure starts with evaluation of spot activity, then it estimates probe hybridization levels from activity levels. The method is designed for being readily usable by the biologist, by adopting fuzzy linguistic variables which are familiar to the user and by featuring a standard and complete graphical interface.