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

Benson, M; Svensson, PA; Adner, M; Caren, H; Carlsson, B; Carlsson, LMS; Martinsson, T; Rudemo, M and Cardell, Lars-Olaf LU (2004) In Acta Oto-Laryngologica 124(7). p.813-819
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... (More)
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. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
allergic rhinitis, expression profiling, microarray, linkage analysis
in
Acta Oto-Laryngologica
volume
124
issue
7
pages
813 - 819
publisher
Taylor & Francis
external identifiers
  • pmid:15370566
  • wos:000223997900010
  • scopus:4644233904
ISSN
1651-2251
DOI
10.1080/00016480410018025
language
English
LU publication?
yes
id
b2605cb4-833f-4cb7-ad8c-fa6f394f2eb3 (old id 898479)
date added to LUP
2008-01-10 11:22:14
date last changed
2017-01-01 07:05:18
@article{b2605cb4-833f-4cb7-ad8c-fa6f394f2eb3,
  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.},
  author       = {Benson, M and Svensson, PA and Adner, M and Caren, H and Carlsson, B and Carlsson, LMS and Martinsson, T and Rudemo, M and Cardell, Lars-Olaf},
  issn         = {1651-2251},
  keyword      = {allergic rhinitis,expression profiling,microarray,linkage analysis},
  language     = {eng},
  number       = {7},
  pages        = {813--819},
  publisher    = {Taylor & Francis},
  series       = {Acta Oto-Laryngologica},
  title        = {DNA microarray analysis of chromosomal susceptibility regions to identify candidate genes for allergic disease: A pilot study},
  url          = {http://dx.doi.org/10.1080/00016480410018025},
  volume       = {124},
  year         = {2004},
}