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Haplotype analysis of a 100 kb region spanning TNF–LTA identifies a polymorphism in the LTA promoter region that is associated with atopic asthma susceptibility in Japan


Emiko Noguchi, Department of Medical Genetics, Majors of Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Laboratory of Advanced Research D, 1-1-1 Tennodai, Tsukuba City, Ibaraki 305-8577, Japan.


Background The tumour necrosis factor (TNF) gene family, which includes TNF, LTA, and LTB, is located consecutively on human chromosome 6p21 region, which has been linked to asthma by several genome-wide screens. (LTA, lymphotoxin-α; LTB, lymphotoxin-β).

Objective The aim of the present study was to determine whether genes on 6q21 are related to development of atopic asthma.

Methods We screened for mutations in the coding and promoter regions of genes in the TNF–LTA region, including BAT1, NFKBIL1, LTA, TNF, LTB, AIF, and BAT2, and conducted a transmission disequilibrium test of 41 polymorphisms in 137 families identified through pro-bands with childhood-onset atopic asthma. (BAT1, HLA-B-associated transcript 1; NFKBIL1, nuclear factor of κ light polypeptide gene enhancer in B cells inhibitor-like 1; AIF, allograft inflammatory factor 1).

Results  Haplotypes of the LTA/TNF linkage disequilibrium block were associated significantly with asthma (global P=0.0097). Transmission patterns of the common haplotypes to asthmatic offspring were predicted by a single-nucleotide polymorphism in the LTA promoter region. The G allele of the LTA−753G/A polymorphism was transmitted preferentially to asthma-affected individuals (P=0.001). Luciferase reporter assays with constructs containing the 5′ and 3′ flanking regions of the LTA gene showed 30–50% lower transcriptional activity when the −753A allele was present than that of other haplotypes.

Conclusion Our results suggest that LTA is one of the genes that contributes to susceptibility to atopic asthma, and that the association of the TNF/LTA haplotypes to asthma may be defined by the polymorphism in the LTA promoter region in the Japanese population.

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