Positional candidate gene approach and functional genomics strategy in atopy gene discovery

As part of our effort in searching for genetic factors contributing to the susceptibility to atopy and asthma, we have focused on a 'positional candidate' approach in identifying CC chemokine gene polymorphisms and their functional correlates. To date, a single-nucleotide polymorphism was found in the RANTES proximal promoter region, and a high degree of sequence variation was identified in the 3'-untranslated region -of the eotaxin gene. Also, we are pursuing a series of functional genomics' studies designed to identify differentially expressed genes in a panel of allergen-specific human Th2 cells and in antigen-induced hyperreactive murine airways. This is performed using a combination of protocols including suppression-subtractive hybridization and cDNA array hybridizations with 18,363 nonredundant sequences. A data base is being generated from a list of subtracted cDNA sequences and array-positive clones to categorize differentially expressed genes. Sequences are being placed in biologically relevant categories on the basis of function (i.e., receptor, signal transduction pathways, transcription, and translation). With the increasing amount of sequence information compiled by the Human Genome Project, it will be particularly challenging to integrate functional gene-mapping efforts to define and compare aberrant genotypes/phenotypes in atopic diseases.