title: TNF-alpha promoter single nucleotide polymorphisms are markers of human ancestry.
abstract: We present a map of single nucleotide polymorphisms (SNPs) in the human tumor necrosis factor (TNF)-alpha promoter based upon exploratory sequencing of 333 human TNF-alpha gene promoters from individuals of distinct ancestral backgrounds. We detect 10 TNF-alpha promoter SNPs that occur with distinct frequencies in populations of different ancestry. Consistent with these findings, we show that two TNF-alpha SNPs, the -243 SNP and the -856 SNP, are the first SNP markers of a sub-Saharan African-derived extended haplotype and an Amerindian HLA haplotype, respectively. Comparisons of TNF-alpha promoter SNP allele frequencies can thus help elucidate variation of HLA haplotypes and their distribution among existing ethnic groups and shed light into the history of human populations.
authors.affiliation: Center for Blood Research, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: A
authors.initials: A
authors.lastname: Baena
authors.forename: J Y
authors.initials: JY
authors.lastname: Leung
authors.forename: A D
authors.initials: AD
authors.lastname: Sullivan
authors.forename: I
authors.initials: I
authors.lastname: Landires
authors.forename: N
authors.initials: N
authors.lastname: Vasquez-Luna
authors.forename: J
authors.initials: J
authors.lastname: Quiñones-Berrocal
authors.forename: P A
authors.initials: PA
authors.lastname: Fraser
authors.forename: G P
authors.initials: GP
authors.lastname: Uko
authors.forename: J C
authors.initials: JC
authors.lastname: Delgado
authors.forename: O P
authors.initials: OP
authors.lastname: Clavijo
authors.forename: S
authors.initials: S
authors.lastname: Thim
authors.forename: S R
authors.initials: SR
authors.lastname: Meshnick
authors.forename: T
authors.initials: T
authors.lastname: Nyirenda
authors.forename: E J
authors.initials: EJ
authors.lastname: Yunis
authors.forename: A E
authors.initials: AE
authors.lastname: Goldfeld
mesh_terms: D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics; D006239:Haplotypes / Q000235:genetics; D006801:Humans; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D014409:Tumor Necrosis Factor-alpha