title: Nucleotide polymorphism of the TNF gene cluster in six Chinese populations.
abstract: DNA variants in a 31-kb region of the human major histocompatibility complex, encompassing the tumor necrosis factor (TNF) gene cluster, were surveyed by direct sequencing of 283 unrelated individuals from six Chinese populations. A total of 273 polymorphic sites were identified, with nearly half of them novel. We observed an excess of rare variants and negative values of selection tests of the region, implying either that these populations experienced a historical expansion or that the surveyed region was subjected to natural selection. Different characteristics of the sequence variation in the six populations outline the genetic differentiation between Northern and Southern Chinese populations. The distributions of recombination rates are similar among all the populations, with variation in the magnitude and/or in the fine location of hot spots. Tag single-nucleotide polymorphisms (SNPs) selected from HapMap (Phase II) CHB data accounted for an average of 64% of common SNPs from the six Chinese populations. We also observed a limited transferability of tag SNPs between Chinese populations on the 31-kb region with an excess of untaggable SNPs and ragged linkage disequilibrium blocks. It suggested that the design and interpretation of future association studies should be more cautious, and that a resequencing approach may refine tag SNP selection on Chinese-specific disease mapping.
authors.affiliation: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, PR China.
authors.forename: Yongbiao
authors.initials: Y
authors.lastname: Zhang
authors.forename: Feng
authors.initials: F
authors.lastname: Zhang
authors.forename: Hongbin
authors.initials: H
authors.lastname: Lin
authors.forename: Lei
authors.initials: L
authors.lastname: Shi
authors.forename: Panpan
authors.initials: P
authors.lastname: Wang
authors.forename: Li
authors.initials: L
authors.lastname: Shi
authors.forename: Qiang
authors.initials: Q
authors.lastname: Gong
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jiayou
authors.initials: J
authors.lastname: Chu
authors.forename: Duen-Mei
authors.initials: DM
authors.lastname: Wang
mesh_terms: D044466:Asian People / Q000235:genetics*; D002681:China; D004194:Disease / Q000235:genetics*; D006239:Haplotypes; D006801:Humans; D008285:Major Histocompatibility Complex / Q000235:genetics; D005810:Multigene Family; D020641:Polymorphism, Single Nucleotide; D011153:Population / Q000235:genetics; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D048069:Tumor Necrosis Factors / Q000235:genetics*
chemical_list: D048069:Tumor Necrosis Factors