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DNA microarray analysis of chromosomal susceptibility regions to identify candidate genes for allergic disease: a pilot study.

Journal article
Authors Mikael Benson
Per-Arne Svensson
Mikael Adner
Helena Carén
Björn Carlsson
Lena M S Carlsson
Tommy Martinsson
Mats Rudemo
Lars Olaf Cardell
Published in Acta Oto-Laryngologica
Volume 124
Issue 7
Pages 813-9
ISSN 0001-6489
Publication year 2004
Published at Department of Mathematical Statistics
Institute for the Health of Women and Children, Dept of Paediatrics
Institute of Internal Medicine, Dept of Body Composition and Metabolism
Pages 813-9
Language en
Subject categories Medical and Health Sciences

Abstract

OBJECTIVE: To examine whether DNA microarray analysis of chromosomal susceptibility regions for allergy can help to identify candidate genes. MATERIAL AND METHODS: Nasal biopsies were obtained from 23 patients with allergic rhinitis and 12 healthy controls. RNA was extracted from the biopsies and pooled into three patient and three control pools. These were then analysed in duplicate with DNA microarrays containing 12626 genes. Candidate genes were further examined in nasal biopsies (real-time polymerase chain reaction) and blood samples (single nucleotide polymorphisms) from other patients with allergic rhinitis and from controls. RESULTS: A total of 37 differentially expressed genes were identified according to criteria involving both the size and consistency of the gene expression levels. The chromosomal location of these genes was compared with the chromosomal susceptibility regions for allergic disease. Using a statistical method, five genes were identified in these regions, including serine protease inhibitor, Kazal type, 5 (SPINK5) and HLA-DRB2. The relevance of these genes was examined in other patients with allergic rhinitis and in controls; none of the genes were differentially expressed in nasal biopsies. Moreover, no association between allergic rhinitis and SPINK5 polymorphisms was found, at either the genotype or haplotype level. CONCLUSIONS: DNA microarray analysis of chromosomal susceptibility regions did not lead to identification of candidate genes that could be validated in a new material. However, because gene polymorphisms may cause differential gene expression, further studies, including validation data, are needed to examine this approach.

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