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March 17, 2014

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Alpha chpbts promoter single nucleotide polymorphisms are markers cheap beats by dre studio of human ancestry Top of pageabstractwe present a map of single nucleotide polymorphisms(Snps)In the human tumor necrosis factor(Tnf)Promoter based upon exploratory sequencing of 333 human tnf gene promoters from individuals of distinct ancestral backgrounds.We detect 10 tnf promoter snps that occur with distinct frequencies in populations of different ancestry.Consistent with these findings, we show that two tnf snps, the snp and the snp, are the first snp markers of a subsaharan africanderived extended haplotype and an amerindian hla haplotype, respectively.Comparisons of tnf 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.Additionally, the and snps have been associated with hla haplotypes that do not contain complotype information in individuals of japanese ancestry.8A critical question in the genetic origin of humans is what types of nuclear DNA sequence variation have accumulated.Previously taking a phylogenetic approach, we identified phylogenetic footprints or conserved regions in primate tnf promoters and presented evidence for a mechanism by which the human tnf regulatory region evolved.6 That is, sequences containing functional activator binding sites have been conserved in the primate lineage, whereas regions that are not essential for regulation display a high density of variable sites.To determine the degree of variability of human tnf promoters, we undertook largescale sequencing of 333 fulllength tnf promoters from ethnically distinct human populations. (Iii)Tnf snps are markers of ethnicspecific hla haplotypes.Taken together, these data are consistent with the hypothesis6 that accumulation of snps in the tnf promoter has been nonrandom and driven by the conservation of tnf activator binding sites.Tnf snps appear to have been maintained as silent substitutions in different ancestral human genetic backgrounds where they were incorporated into conserved or extended haplotypes, which became haplospecific in populations of different ethnic groups.Top of pageresults and discussionexploratory sequencing of the tnf promoter region of individuals of caucasian(North american), Asian(Cambodian), African(Malawian, southern nigerian, africanamerican and africancaribbean), and Amerindian(Quechua and paez)Descent revealed nine previously reported snps located at and nt and one novel snp a c to g transversion, at nt relative to the tnf transcription start site.The snp was found in two individuals from malawi and in one individual from nigeria;All three were heterozygous for the variant g nucleotide(Table 1).Inspection of the distribution of snps reveals that the three african populations studied have the highest relative diversity of tnf snps(Table 1).This finding is consistent with the africa hypothesis based upon human mitochondrial dna analyses, 18 which contends that the genetic variation occurring in subsaharan africa gave rise to the variation in populations outside of africa.Our analysis here of the nuclear dna diversity of the human tnf promoter supports this hypothesis and is consistent with other recent nuclear dna snp surveys.1, 19 We note that using the principles of probability, there is a 95 probability that an analysis of direct sequencing of 333 kb of DNA could detect any existent SNP in the TNF promoter in the human population with a heterozygosity rate of 0.0090 or greater(See legend to Table 1).Thus, the 10 snps detected in this study likely represent the majority of human tnf promoter snps that exist.The and tnf snps are the most frequently observed snps among the 43 caucasian(35 and 26 respectively)And 40 cambodian(30 and 25 respectively)Tnf promoters evaluated(Table 1).The and snps are also frequently observed in the 66 malawian(17 and 11 respectively), 54 Nigerian(7 and 7 and 34 AfricanAmerican samples(29 and 8 respectively)Relative to the frequencies of the other tnf snps in these populations.However, their relative frequencies are lower when compared to the caucasian and cambodian samples(Table 1).The and snps were also detected in the 54 quechua(9 and 7 respectively)And 42 paez(7 and 2 respectively)Promoters examined;However, their relative frequencies were also significantly less as compared to caucasian and cambodian samples examined(Table 1).Furthermore, the snp always occurred in association with the snp in all the ethnic groups studied.Of the 333 promoters studied, 273 were wild type at both positions, and 40 carried both the and and 20 carried the snp alone(Table 1).Thus, these snps likely became linked before human migration out of africa(Table 1).Unexpectedly, the tnf snp, a relatively highfrequency snp in caucasian(14 and Cambodian(13 samples, was absent in the Malawian promoters and found in only one of the Nigerian promoters analyzed and was absent in the AfricanAmerican promoters(Table 1).Strikingly, by contrast, the tnf snp was found in 30 of the quechua promoters and 45 of the paez promoters studied(Table 1).Furthermore, the snp, which occurs with relative high frequency in caucasian(21 Malawian(12 Nigerian(13 AfricanAmerican(12 and Cambodian(8 promoters, was not detected in any of the 96 TNF promoters derived from the two distinct indigenous Amerindian populations analyzed(Table 1).Consistent with our results, the snp was not detected in examples of other amerindian(Chachi indians from ecuador and pima indians of arizona)Samples previously analyzed.10, 13 Thus, these data establish that TNF SNPs occur with distinct patterns in ethnically distinct populations.The dramatic increase of the and absence of the tnf snp in the amerindian samples examined led us to speculate that this snp pattern was not random and was likely to be associated with neighboring hla genes in amerindians where it may be a haplospecific marker.We thus next performed highresolution hla typing of the hlac, b, and drb1 loci of the paez samples where 45 of the 42 samples examined contained the tnf snp.Of the 19 examples of the snp in the paez samples, only six were random and not associated with a known amerindian haplotype(Table 2).We note that where it was detected, the snp occurred as the sole tnf snp in each of the haplotypes evaluated(Table 2).Since the hlacw and b hla fragment has been observed in indigenous populations from taiwan, new zealand(Maori), Northeast China(Orochon), Inuit, and Tlingit, 24 our results are consistent with the hypothesis that Amerindians may have originated from a postneolithic migration from Asia to South America.25In addition to the Amerindian samples, we also detected the SNP in promoters of all three Africanderived populations.Although the variant has previously been reported in caucasians9 and asians, 8 we did not detect it in the caucasian or cambodian samples evaluated(Table 1), consistent with its very low frequency in these groups.By contrast, the snp was not detected in any of the nonafrican samples examined(Table 1).Furthermore, the four malawians carrying the snp also carried the snp on the same chromosome, which we determined by cloning promoter fragments of the snppositive individuals and sequencing individual alleles(Table 1 and Data not shown).Since we previously detected the snp in two old world monkeys(Baboon and macaque)And in a new world monkey(Aotus trivirgatus), 6 our data are consistent with the hypothesis that the SNP entered the primate lineage before the split of the old and new world monkeys and sometime after the migration out of Africa became associated with the SNP in African populations that remained behind.Intriguingly, we also detected the snp on the same chromosome as the snp in three cases(In a paece, table 2)And in two individuals of the africanamerican group(Data not shown).We imagine that those tnf snps, which are found randomly and in no apparent association with other tnf variants or mhc genes in individuals of all continents, may have occurred in the human population before the migration out of africa and then in certain cases were integrated into a conserved mhc haplotype or linked with another tnf variant.The snp that was previously detected in south american black people10 was enriched in malawians(9 and in 17 individuals of AfricanAmerican or AfricanCaribbean background(26 where highresolution MHC typing was available and previous family studies allowed us to determine the haplotypes of particular individuals17(Table 1).Remarkably, among six examples of the subsaharan africanderived extended haplotype of hlacw b fc(1, 90)0, DRB1 contained in this sample set, five carried the SNP.One individual was homozygous for both the extended haplotype and the snp(Haplotypes 1 and 2, table 3).We also found the snp in an individual who carried a fragment of the extended haplotype and had a distinct complotype(Haplotype7).In two other individuals, the variant appeared to be in nonrandom association with their mhc(Haplotypes 8 and 9).To test the hypothesis that the snp was indeed a part of the extended subsaharan haplotype, we sequenced the tnf promoter in a cell line(Rsh, homozygous for the haplotype26 and, strikingly, we found that it was also homozygous for the variant(Data not shown).This analysis thus establishes the variant as the first tnf snp linked to an africanderived extended hla haplotype.We have also shown that these patterns are at least in part secondary to beats by dre pro cheap the nonrandom association of tnf snps with neighboring hla genes that differ in distinct ancestral backgrounds.Genes that are in linkage disequilibrium with neighboring genes are thought to reflect a more ancient evolutionary history since it requires a long time for genetic segments to be united by recombination events.1 The enrichment of the SNP in African populations and the SNP in Amerindian populations thus appears to be ancient since they were incorporated into African and Amerindian HLA haplotypes, respectively.The fact that examples of the snp in nonafricanderived populations are rare suggests that it was adaptive to natural selection within the african context where it became a marker for neighboring genes including hla class i, class ii, and complement genes that may have functional importance in infectious diseases.Despite this high level of variation, here we have shown that the sequences involved in enhanceosome formation involved in the regulation of the gene3, 4, 5 are highly conserved in humans of distinct ancestral backgrounds since we did not detect a single snp in this region.By contrast, human tnf snps including the novel variant described here occur within or immediately adjacent to regions of the promoter with high variability in the primate lineage.6 Furthermore, statistical analyses of sample configurations of TNF promoter SNPs suggest that they are effectively neutral and act as silent substitutions.27 Taken together, we conclude that similar to coding regions, promoter region variation is evolutionarily constrained, and substitutions in sequences critical for TNF regulation are not tolerated.One explanation for the high number of snps in the tnf promoter that is consistent with our data is that they have accumulated in regions of the promoter not essential for gene regulation and that they have been incorporated into hla haplotypes where they are in nonrandom association with neighboring genes that in the course of human history have been stratified and maintained in specific ethnic groups.Finally, this compilation of a tnf promoter snp map not only provides insight into the evolution of noncoding sequences in the promoter region of a gene of critical importance in the human immune response, but also demonstrates that comparisons of snp allele frequencies in different populations can help elucidate the history of human populations.Top of pagereferencestop of pageacknowledgementswe are grateful to dan hartl for helpful discussions and to terrie taylor for support of the study in malawi, and we thank adele uglialoro for technical assistance and pedro floresvillanueva for helpful discussions.This work was supported by grants from the american heart association and the nih(Gm56492)To aeg and from the nih(Hl5983 To aeg and ejy