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A TNF region haplotype offers protection from typhoid fever in Vietnamese patients

Abstract

The genomic region surrounding the TNF locus on human chromosome 6 has previously been associated with typhoid fever in Vietnam (Dunstan et al. in J Infect Dis 183:261–268, 2001). We used a haplotypic approach to understand this association further. Eighty single nucleotide polymorphisms (SNPs) spanning a 150 kb region were genotyped in 95 Vietnamese individuals (typhoid case/mother/father trios). A subset of data from 33 SNPs with a minor allele frequency of >4.3% was used to construct haplotypes. Fifteen SNPs, which tagged the 42 constructed haplotypes were selected. The haplotype tagging SNPs (T1–T15) were genotyped in 380 confirmed typhoid cases and 380 Vietnamese ethnically matched controls. Allelic frequencies of seven SNPs (T1, T2, T3, T5, T6, T7, T8) were significantly different between typhoid cases and controls. Logistic regression results support the hypothesis that there is just one signal associated with disease at this locus. Haplotype-based analysis of the tag SNPs provided positive evidence of association with typhoid (posterior probability 0.821). The analysis highlighted a low-risk cluster of haplotypes that each carry the minor allele of T1 or T7, but not both, and otherwise carry the combination of alleles *12122*1111 at T1–T11, further supporting the one associated signal hypothesis. Finally, individuals that carry the typhoid fever protective haplotype *12122*1111 also produce a relatively low TNF-α response to LPS.

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Acknowledgments

We acknowledge with thanks the directors and the staff of the Hospital for Tropical Disease, Dong Thap Provincial Hospital, Dong Nai Pediatric Hospital and Hung Vuong Hospital, Viet Nam for the clinical and microbiological work associated with this study. We thank the Vietnamese individuals who took part in this study. The Wellcome Trust funded this work.

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Correspondence to Sarah J. Dunstan.

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Dunstan, S.J., Hue, N.T., Rockett, K. et al. A TNF region haplotype offers protection from typhoid fever in Vietnamese patients. Hum Genet 122, 51–61 (2007). https://doi.org/10.1007/s00439-007-0372-9

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Keywords

  • Major Histocompatibility Complex Class
  • Typhoid Fever
  • Protective Haplotype
  • Haplotype Construction
  • Typhoid Case