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

  • Authors:
  • G. B. Ferrara;L. Delfino;F. Masulli;S. Rovetta;R. Sensi

  • Affiliations:
  • INFM-Istituto Nazionale per la Fisica della Materia, Via Dodecaneso 35, 16146 Genova, Italy and IST-Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy;IST-Istituto Nazionale per la Ricerca sul Cancro, Largo R. Benzi 10, 16132 Genova, Italy;INFM-Istituto Nazionale per la Fisica della Materia, Via Dodecaneso 35, 16146 Genova, Italy and Dipartimento di Informatica, Università di Pisa, Via F. Buonarroti 2, 56125 Pisa, Italy;INFM-Istituto Nazionale per la Fisica della Materia, Via Dodecaneso 35, 16146 Genova, Italy and Dipartimento di Informatica e Scienze dell'Informazione, Università di Genova, Via Dodecaneso 3 ...;INFM-Istituto Nazionale per la Fisica della Materia, Via Dodecaneso 35, 16146 Genova, Italy

  • Venue:
  • Fuzzy Sets and Systems
  • Year:
  • 2005

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Abstract

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.