title: 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-alpha response to LPS.
authors.affiliation: Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, Quan 5, District 5, Ho Chi Minh City, Vietnam. sdunstan@oucru.org
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Dunstan
authors.forename: Thi Hue
authors.initials: TH
authors.lastname: Nguyen
authors.forename: Kirk
authors.initials: K
authors.lastname: Rockett
authors.forename: Julian
authors.initials: J
authors.lastname: Forton
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Morris
authors.forename: Mahamadou
authors.initials: M
authors.lastname: Diakite
authors.forename: Ngoc Lanh
authors.initials: NL
authors.lastname: Mai
authors.forename: Thi Phuong
authors.initials: TP
authors.lastname: Le
authors.forename: Deborah
authors.initials: D
authors.lastname: House
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Parry
authors.forename: Vinh
authors.initials: V
authors.lastname: Ha
authors.forename: T Hieu
authors.initials: TH
authors.lastname: Nguyen
authors.forename: Gordon
authors.initials: G
authors.lastname: Dougan
authors.forename: Tinh Hien
authors.initials: TH
authors.lastname: Tran
authors.forename: Dominic
authors.initials: D
authors.lastname: Kwiatowski
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Farrar
mesh_terms: D016022:Case-Control Studies; D002874:Chromosome Mapping; D016000:Cluster Analysis; D005190:Family; D005260:Female; D020022:Genetic Predisposition to Disease; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics* / Q000378:metabolism; D014435:Typhoid Fever / Q000235:genetics* / Q000378:metabolism; D014744:Vietnam
chemical_list: D014409:Tumor Necrosis Factor-alpha