Nucleotide Variation And Haplotype Diversity Of TNF Gene Cluster In HLA Region In Six Chinese Populations

After the release of the first draft of Human Genome,the advent of high throughput sequencing and genotyping methods push forward a various genomics projects and lead to portray the human genome in populations scale.Asian population takes a considerable proportion in the world's population,and lots of researchers are engaged in exploring the relationship and diseases susceptibility of different Chinese populations.Population dynamics,migration history and the pressure of natural selection has driven Chinese population into specific sub-groups on the long-term course of human evolution.To specifically investigate the genetic structure and polymorphism in major Chinese populations,we sequenced a 32-kb genomic region from the human Major Histocompatibility Complex with Shandong Han(SH), Guangdong Han(GH),Li(LI),Yi(YI),Tibetan(ZH),and Inner-Mongolian(MG). This will facilitate the researches not only disease mapping,but also in health care-related areas such as prevention,diagnosis,and treatment of disease.The 32-kb region comprises 5 important immune-related genes(LTA,TNF,LTB, LST1,and NCR3) which have relationship with a large number of human immune system diseases,such as myocardial infarction,dyslipidemia,distal colitis,leprosy, ankylosing spondylitis,rheumatoid arthritis,cerebral malaria and Alzheimer disease. In particular,tumor necrosis factor(TNF),a pre-inflammatory cytokine,plays important roles in lipid metabolism,blood coagulation,insulin resistance,and endothelial function.We also estimate the allele frequency of 8 polymorphic sites which are disease-causing mutations of some of those diseases.LTA,+804C-A (rs1041981) in the LTA gene that caused a threonine-to-asparagine substitution at codon 26 is significantly associated with increased risk for myocardial infarction.The LTA+804A allele's MAF of YI is much lower than that of other 5 populations.The low-producing LTA+80A allele is significantly associated with an increase in leprosy risk and LTA+80A's MAF is a little lower in southern Chinese population(GH,LI) than in northern Chinese population(SH,MG).TNF,-308G-A(rs1800629) genetic variants is associated with features of the insulin resistance syndrome and TNF-308A allele's MAF is higher in SH,LI than in GH,YI,ZH.TNF-850T and TNF-863A are associated with Alzheimer disease,TNF-850T allele's MAF is smaller in GH and TNF-863A allele is higher in YI,ZH which come from South-West of China.The different frequency of risk alleles in 6 Chinese populations indicates that various diseases susceptibility of them.From the 6 Chinese populations,273 polymorphic sites,including 242 SNPs,3 STRs,and 28 indels,are identified.133 sites among these are newly-discovered and not present in the dbSNP database(v.127),and 13 newly-discovered SNPs are common SNPs.Rare SNP take the proportion of 73%and there is one SNP per 117bp in the 32-kb region.The allele distributions of polymorphic site in 6 Chinese populations indicate that the northern Chinese are more polymorphic than southern Chinese in the studied region,population expansion in northern Chinese is more severely than that of southern Chinese.Lots of new SNPs was detected indicate that there in Chinese populations the human genome,especially for those rare SNPs and polymorphic sites which represent the differentiation between populations.Thus, using the SNPs from dbSNP to investigate population differentiation,population dynamics and natural selection,the results will lead to deviate from reality.High polymorphism in gene regulatory region,such as promoter,5'UTR and intron will increase the discrepancy of gene expression and improve the adaptation of human. Low polymorphism in coding region agree with the functional constrain of genes and high pressure of natural selection on mutation.Lots of evidences show that Chinese populations experience an expansion in history.A smooth,approximate bell-shaped mismatch distribution,significant negative value of Fs test and radial branches of minimum spanning network for haplotypes indicate expansion of 6 Chinese populations.Northern Chinese population represented by Inner-Mongolian and Shandong Han expand more severely than other 4 populations.We don't detect population expansion of LI who lives alone on the Hainan Island.A large number of low-frequency SNPs also predict the occurrence of natural selection,high DNA polymorphism indicate not only that 5 genes play an important role in human adaptation to environment changes,but also high recombination rate of 32-kb region.Lots of genes in the HLA region participate in immune defense.High polymorphism of these genes will help for immune defense and high chromosome recombination will increase the gene polymorphism.The 32-kb region contains a rather loosely-formed linkage disequilibrium(LD) block and 2 to 3 genomic spots at elevated recombination rate.These lead to the observation of a high number of haplotypes.The recombination rate of some regions is higher relative to the background.Similar trend of recombination rate alone the 32-kb region in 6 Chinese populations,but there is a little different between them.Tibetan's recombination rate is highest and Li's recombination rate is lowest.Recombination rate of northern Chinese population is higher than southern Chinese population.There is only one distinct haplotype-block at LTA gene and intergenic region before it,but in the rest region no distinct haplotype-block exists because of recombination.Recombination events break the LD between loci and make it is difficult to predict the most of common SNPs by tag SNPs through the association study.Many tests have used for detecting natural selection on the 32-kb region,and we found that the pattern and intensity of selection are different in 6 Chinese populations. Balancing selection maybe has acted on LTA gene and intergenic region before it,but only significant in Li and Yi.Negative/positive selection maybe has acted on almost all of other genes and their promoter region,the value is significant in all populations except Li and Yi.Selective sweep has acted on LTB,LST1 and their promoter region in 6 Chinese populations,the Fay and Wu' H statistic is more significant in Guangdong Han,Inner-Mongolian than in other 4 populations.Recombination will decay the pattern constructed by natural selection and population expansion, migration,subpopulation,bottleneck can also cause many selection statistics to be significant negative,thus the natural selection maybe act on the region under study. The International HapMap Project has been instrumental in making well-powered, large-scale,genome-wide association studies a reality.It is now clear that the HapMap can be a useful resource for the design and analysis of disease association studies in populations across the world.The Asian population structure is complex and many populations specific common SNPs are still not identified.Disease association studies in Asian population will deviate from the reality when using tag SNPs from HapMap, because of inherent and intentional bias in sampling and rules used for SNP selection in HapMap project.It's also difficult for association studies to detect common SNPs in the region of recombination hotspot.One must increase the number of tag SNPs if he wants to cover the common SNPs in high recombination rate region when doing association study.In the 32-kb region,HapMap project select 93 SNPs and give 15 tag SNPs for association study.It would loss 1/3 common SNPs information when use these 15 tag SNPs because of high recombination rate of this region and lots of Chinese population specific common SNPs are not identified.A comprehensive search for genetic influences on disease would involve examining all genetic differences in a large number of affected individuals and controls.It may eventually become possible to accomplish this by complete genome resequencing.Finally, comparing to the data of the latest HapMap release in the 32-kb region,our resequencing effort captures more rare and Chinese-specific polymorphic sites.This shows that the Han data from HapMap database is not without problems of ascertainment bias.Extending the resequencing effort in larger genomic regions with Chinese populations will facilitate the researches not only in disease mapping,but also in health care-related areas such as prevention,diagnosis,and treatment of disease.