A biochemical and genetic study on all non-synonymous single nucleotide polymorphisms of the gene encoding human deoxyribonuclease I potentially relevant to autoimmunity

A reduction of deoxyribonuclease I (DNase I) activity levels in the serum of patients with autoimmune diseases has been reported. The objectives of this study were to clarify genetic and biochemical aspects of 12 non-synonymous SNPs in the human gene (DNASE1), potentially giving rise to an alteration in the in vivo DNase I activity levels. Genotyping of all the non-synonymous SNPs was performed in healthy subjects of three ethnic groups including 15 populations using newly developed methods. Among them, only four SNPs, R-21S, Y95S, G105R, and Q222R were polymorphic in all or some populations; Asian group showed a relatively low genetic diversity of these SNPs. Furthermore, the distribution pattern of the common SNP Q222R was classified into three ethnic groups. The activity levels of the amino acid-substituted DNase I forms derived from SNPs R-21S, G105R, P132A, and P197S were significantly high compared with that of the wild-type; the polymorphic SNPs R-21S and G105R gave rise to a high activity-harboring DNase I isoform. On the other hand, activity levels from Q35H, R85G, V89M, C209Y, Q222R, and A224P were significantly low, but these SNPs, except Q222R, were not distributed in any of the populations. However, since these SNPs may produce potentially low levels of in vivo DNase I activity, a minor allele in each SNP will be served as a genetic risk factor for autoimmune diseases. These findings on non-synonymous SNPs in DNASE1 may provide a biochemical-genetic basis for the clarification of a possible relationship between DNase I and the diseases.     

Geographical north-south decline in DNASE1*2 in Japanese populations

Allele frequencies for human deoxyribonuclease I (DNase I) phenotypes were determined using blood samples from about 2000 Japanese subjects living in nine prefectures, and compared with one another. DNase I phenotyping was performed principally using isoelectric focusing electrophoresis and activity staining. The DNase I system was shown to have enhanced potential for anthropologic, genetic, and clinical studies of Japanese populations. DNase I phenotypes were analyzed to evaluate the degree of genetic variation at the DNASE1 locus. Our examination of DNase I types revealed a decreasing north-to-south gradient in the DNASE1 allele.     

Deoxyribonuclease I gene polymorphism in Han Chinese population: frequency and effect on glucose and lipid parameters

DNASE1, the encoding gene of deoxyribonuclease I (DNase I), exhibits polymorphisms, including a single nucleotide polymorphism (SNP A2317G) in exon 8 and a 56 bp variable number of tandem repeat, designated as HumDN1 in intron 4. Several different ethnic population studies have revealed both A2317G and HumDN1 demonstrate genetic heterogeneity in the worldwide distribution. Recently, G2317 allele was proposed as an independent risk factor for myocardial infarction in Japanese population. In the present study, we identified A2317G and HumDN1 genotypes in 402 unrelated healthy Han Chinese individuals. At the same time, the impact of different genotypes and diplotypes of DNase I on plasma lipids levels and fasting blood glucose was also illuminated. Polymerase chain reaction and restriction fragment length polymorphism were used for the detection of HumDN1 and A2317G polymorphisms. Plasma glucose and lipids were measured in fasting state by biochemical methods. Three genotypes of A2317G and 9 genotypes of HumDN1 were detected in Han Chinese population. Among them, the most predominate alleles were A2317 (frequency = 53.6%) and HumDN1*3 (frequency = 47.4%) respectively. Linkage disequilibrium between A2317G and HumDN1 polymorphisms was also observed (D' = 0.717). Haplotype A-3, presented in frequency of 46.5%, was most common. Compared to other ethnic populations, Han Chinese had its own unique DNase I gene distribution characteristics. As for the influence of DNase I gene polymorphisms on lipids and glucose levels, no association was found between either genotype or diplotype and these parameters. (all P > 0.05). Results obtained in this study could be used for anthropological investigation, probing into relations between DNase I gene and diseases.     

Nonsynonymous single-nucleotide polymorphisms of the human apoptosis-related endonuclease--DNA fragmentation factor beta polypeptide, endonuclease G, and Flap endonuclease-1--genes show a low degree of genetic heterogeneity

DNA fragmentation factor beta (DFFB) polypeptide, endonuclease G (EndoG), and Flap endonuclease-1 (FEN-1) are responsible for DNA fragmentation, a hallmark of apoptosis. Although the human homologs of these genes show three, four, and six nonsynonymous single-nucleotide polymorphisms (SNPs), respectively, data on their genotype distributions in populations worldwide are limited. In this context, the objectives of this study were to elucidate the genetic heterogeneity of all these SNPs in wide-ranging populations, and thereby to clarify the genetic background of these apoptosis-related endonucleases in human populations. We investigated the genotype distribution of their SNPs in 13 different populations of healthy Asians, Africans, and Caucasians using novel genotyping methods. Among the 13 SNPs in the 3 genes, only 3 were found to be polymorphic: R196K and K277R in the DFFB gene, and S12L in the EndoG gene. All 6 SNPs in the FEN-1 gene were entirely monoallelic. Although it remains unclear whether each SNP would exert any effect on endonuclease functions, these genes appear to exhibit low degree of genetic heterogeneity with regard to nonsynonymous SNPs. These findings allow us to conclude that human apoptosis-related endonucleases, similarly to other human DNase genes, revealed previously, are well conserved at the protein level during the course of human evolution.     

Analysis of Genetic Polymorphism of Deoxyribonuclease I in Ovambo and Turk Populations Using a Genotyping Method

Deoxyribonuclease I (DNase I) polymorphism has been used as a valuable marker in genetic and clinical investigations. Six codominant alleles are known for DNase I, DNASE1*1, *2, *3, *4, and the recently discovered alleles *5 and *6. To detect these two new alleles, we added a new DNase I genotyping method based on both an allele-specific amplification and mismatched polymerase chain reaction (PCR). These methods were used to examine the distribution of DNase I genotypes in unrelated individuals from bloodstains of Ovambo and Turkish populations. The DNASE1*1 allele was found to be most dominant in the Ovambos. In contrast, Turks showed the highest allele frequency for DNASE1*2. This study is the first to demonstrate that there is a certain genetic heterogeneity in the worldwide distribution of DNase I polymorphism using the genotyping method of human DNase I polymorphism with PCR.     

Human serum deoxyribonuclease I (DNase I) polymorphism: pattern similarities among isozymes from serum, urine, kidney, liver, and pancreas.

We have devised a zymogram method with high sensitivity and resolution for investigating molecular heterogeneity and genetic polymorphism of deoxyribonuclease I. A combination technique of polyacrylamide-gel isoelectric-focusing electrophoresis and the newly developed zymogram method have led to the discovery of genetic polymorphism of human serum DNase I. Family studies showed that the three common phenotypes--DNASE1 1, DNASE1 1-2, and DNASE1 2--and the other five relatively rare phenotypes--DNASE1 1-3, DNASE1 2-3, DNASE1 2-4, and DNASE1 3-4--represent homozygosity or heterozygosity for four autosomal codominant alleles, DNASE1 *1, DNASE1 *2, DNASE1 *3, and DNASE1 *4. The frequencies of DNASE1 *1, DNASE1 *2, DNASE1 *3, and DNASE1 *4 calculated in a Japanese population were .5517, .4358, .0104, and .0021, respectively. Moreover, it was found that urine and extracts of kidney, liver, and pancreas, as well as serum, can be used for DNase I phenotyping.     

Extremely high prevalence of DNASE1*1 allele in African populations

The single nucleotide polymorphism (SNP) at deoxyribonuclease I (DNase I), designated as DNASE1 (NCBI SNP number; 1053874), in exon 8 (A2317G) has been shown to be associated with liver disease, colorectal carcinoma, and gastric carcinoma in Japanese patients. In this study, we investigated the frequency of the DNASE1 polymorphism in Ghanaian (n = 96) and Xhosa (n = 78) populations and compared the results with those of other studies. The single nucleotide polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The frequencies of DNASE1*1 in the Ghanaian and Xhosa populations were 0.90 and 0.88, respectively. These two African populations had an extremely high frequency of DNASE1*1, similar to that of the Ovambos living in Namibia. Caucasians and Asians had a lower frequency of DNASE1*1 than the African groups. This study is the first to reveal an extremely high frequency of DNASE1*1 among African populations.     

‘Satellite DNA transcripts have diverse biological roles in Drosophila'

Recent years have seen considerable progress in applying single nucleotide polymorphisms (SNPs) to population genetics studies. However, relatively few have attempted to use them to study the genetic differentiation of wild bird populations and none have examined possible differences of exonic and intronic SNPs in these studies. Here, using 144 SNPs, we examined population genetic differentiation in the saker falcon (Falco cherrug) across Eurasia. The position of each SNP was verified using the recently sequenced saker genome with 108 SNPs positioned within the introns of 10 fragments and 36 SNPs in the exons of six genes, comprising MHC, MC1R and four others. In contrast to intronic SNPs, both Bayesian clustering and principal component analyses using exonic SNPs consistently revealed two genetic clusters, within which the least admixed individuals were found in Europe/central Asia and Qinghai (China), respectively. Pairwise D analysis for exonic SNPs showed that the two populations were significantly differentiated and between the two clusters the frequencies of five SNP markers were inferred to be influenced by selection. Central Eurasian populations clustered in as intermediate between the two main groups, consistent with their geographic position. But the westernmost populations of central Europe showed evidence of demographic isolation. Our work highlights the importance of functional exonic SNPs for studying population genetic pattern in a widespread avian species.     

Single-nucleotide polymorphisms and haplotype analysis in beta-defensin genes in different ethnic populations

Beta-defensins are cationic antimicrobial peptides expressed by epithelial cells and exhibit antibacterial, antifungal, and antiviral properties. The defensins are part of the innate host defense network and may have a significant protective role in the oral cavity and other mucosa. Defects or alteration in expression of the beta-defensins may be associated with susceptibility to infection and mucosal disorders. We examined the occurrence of single-nucleotide polymorphisms (SNPs) in the human beta-defensin genes DEFB1 and DEFB2 encoding human beta-defensin-1 and -2 (hBD-1, hBD-2), respectively, in five ethnic populations and defined haplotypes in these populations. Fifteen SNPs were identified in both DEFB1 and DEFB2. Coding region SNPs were found in very low frequency in both genes. One nonsynonymous DEFB1 SNP, G1654A (Val --> Ile), and one nonsynonymous DEFB2 SNP, T2312A (Leu --> His), were identified. Seven sites in each gene exhibited statistically significant differences in frequency between ethnic groups, with the greatest variation in the promoter and in the 5'-untranslated region of DEFB1. DEFB1 displayed 10 common haplotypes, including one cosmopolitan haplotype. Eight common haplotypes were found in DEFB2, including one cosmopolitan haplotype shared among all five ethnic groups. Our results show that genotypic variability among ethnic groups will need to be addressed when performing associative genetic studies of innate defense mechanisms and susceptibility to disease.     

Identification of the nucleotide substitution that generates the fourth polymorphic site in human deoxyribonuclease I (DNase I)

In addition to the three polymorphic sites responsible for protein polymorphism, a new polymorphic site has been identified in intron 7 of the human deoxyribonuclease I (DNase I) gene. Three phenotypes were observed on single-strand conformational polymorphism analysis of a 266-bp polymerase chain reaction-amplified fragment containing exon 7 and part of intron 7 of the human DNase I gene. DNA sequencing analysis demonstrated that a C-G substitution occurred at position 1978 in intron 7. This substitution was confirmed by restriction fragment length polymorphism analysis, since a new Msp1 site is created by the substitution. Population and family studies showed that the inheritance of the genotypes for DNase I C1978G polymorphism is controlled by two codominant alleles, tentatively designated DNASE1*1978C and *1978G. The gene frequencies in a Japanese population were significantly different from those in a Caucasian (German) population. The C1978G polymorphism is in linkage disequilibrium with the common DNase I protein phenotypes 1, 1–2, and 2. Received: 20 March 1996 / Revised: 14 May 1996     

中国内蒙古鄂伦春族线粒体DNA高变区Ⅰ和高变区Ⅱ遗传多态性

收集50份鄂伦春族无关人群外周血样本, 用ABI PRISM377测序仪对其mtDNA HVRⅠ和HVRⅡ进行测序, 计算多态性位点数、单倍型数目、单倍型频率、平均核苷酸差异数目等多态性指标; 结合已发表的其他民族mtDNA遗传资料, 根据Nei法计算鄂伦春族与各群体之间的遗传距离, 进行聚类分析, 绘制系统发生树。鄂伦春族群体mtDNA两个高变区与CRS序列比对, 分别发现52和24个多态性位点, 分别界定了38和27种单倍型, 单倍型多态性分别为0.964±0.018和0.929±0.019; 平均核苷酸差异分别为7.379和2.408; 用HVRⅠ序列多态性数据计算Fst和dA两种遗传距离, 相关系数r为0.993(P<0.01); 基于HVRⅠ序列的系统树显示鄂伦春族与中国台湾、南方汉族和中国香港人群遗传距离较近, 与北方汉族、蒙古族及其国外人群遗传距离相对较远。我国鄂伦春族人群mtDNA具有相对独特的遗传特征, 其遗传多态性和个体识别力较高, 可用于民族起源、迁徙、法医学个体识别等领域研究。     

Adaptations to climate-mediated selective pressures in humans

Humans inhabit a remarkably diverse range of environments, and adaptation through natural selection has likely played a central role in the capacity to survive and thrive in extreme climates. Unlike numerous studies that used only population genetic data to search for evidence of selection, here we scan the human genome for selection signals by identifying the SNPs with the strongest correlations between allele frequencies and climate across 61 worldwide populations. We find a striking enrichment of genic and nonsynonymous SNPs relative to non-genic SNPs among those that are strongly correlated with these climate variables. Among the most extreme signals, several overlap with those from GWAS, including SNPs associated with pigmentation and autoimmune diseases. Further, we find an enrichment of strong signals in gene sets related to UV radiation, infection and immunity, and cancer. Our results imply that adaptations to climate shaped the spatial distribution of variation in humans.     

Human SNPs reveal no evidence of frequent positive selection

We compared the single-nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Using mouse as a second species for computing sequence divergences, we found no evidence of positive selection: for both housekeeping and tissue-specific genes, the ratio of nonsynonymous to synonymous common SNPs per site showed no significant difference from that of divergence. Similarly, we observed no evidence of positive selection for the 289 and 149 genes that have orthologs available for divergence calculation between humans and chimpanzees and between humans and Old World monkeys, respectively. A comparison with previous SNP studies suggests that approximately 20% of the nonsynonymous SNPs in the human population are nearly neutral and that positive selection in the human genome might not be as frequent as previously thought.     

Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases

Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations.     

Lack of association between AQP4 polymorphisms and risk of inflammatory demyelinating disease in a Korean population

Multiple sclerosis (MS) and neuromyelitis optica (NMO) are demyelinating autoimmune inflammatory diseases that affect the central nervous system (CNS). Previous genome-wide or candidate gene studies have suggested that genetic variants might be associated with the risk of MS or NMO. Aquaporin 4 (AQP4) is a commonly distributed water channel in astrocytes of the CNS, and its expression is decreased in NMO lesions due to astrocyte cytotoxicity. Previous studies have suggested the associations of AQP4 single nucleotide polymorphisms (SNPs) with MS and/or NMO. However, there have been few replication studies in various ethnic populations. This study, as the first of its kind performed in an Asian population, investigated associations of AQP4 SNPs with the risk of inflammatory demyelinating disease (IDD), including MS and NMO, in a Korean population. A total of seven common AQP4 SNPs were selected based on status of linkage disequilibrium (LD), and then genotyped in 178 IDD cases (79 MS and 99 NMO patients) and 237 normal controls. Statistical analyses showed no significant associations between AQP4 SNPs/haplotypes and development of IDD, including MS and NMO (P > 0.05). Further replications in larger cohorts and other ethnic groups are needed.     

Characterization of 48 polymorphic loci as potential markers for the risk of ischemic stroke

With the aim to determine specific genetic characteristics of the population of Moscow region, we determined allele frequencies of 48 polymorphic loci (SNP) associated with the increased risk of ischemic stroke development. The genotype frequency distribution for all the SNPs corresponds to Hardy–Weinberg equilibrium. Comparison of the allele frequencies with those obtained for Caucasian populations from the databases dbSNP and 1000 Genomes Project revealed significant differences for two SNPs (rs556621 and rs556512) and seven SNPs (rs556621, rs556512, rs1801133, rs1799983, rs5918, rs328, and rs2398162), respectively. The revealed genetic features of the population make it possible to increase the accuracy and reliability of the individual genetic risk assessment of development for multifactorial diseases in the examined population.     

Genetic polymorphism of human urine deoxyribonuclease I

Summary A genetic polymorphism of human urine deoxyribonuclease I (DNase I) has been detected by the technique of polyacrylamide gel isoelectric focusing (IEF-PAGE) followed by immunoblotting with anti-DNase I antibody. Family studies showed that the three common phenotypes —DNASE1 1, 1–2, and 2 — and the other four rare phenotypes — DNASE1 1–3, 2–3, 2–4, and 3–4 — represent homozygosity or heterozygosity for four autosomal codominant alleles, DNASE1 ^* 1, ^* 2, ^* 3, and ^* 4. The frequencies of the DNASE1 ^* 1, DNASE1 ^* 2, DNASE1 ^* 3, and DNASE1 ^* 4 alleles in a studied Japanese population were 0.5453, 0.4396, 0.0117, and 0.0034, respectively.     

Allele frequency and genotype distribution of polymorphisms within disease-related genes is influenced by ethnic population sub-structuring in Sudan

Four single nucleotide polymorphisms (SNPs) and a variable number of tandem repeats (VNTR) polymorphism located within disease associated/causing genes were typed in four populations of different tribal and ethnic affiliation from the Sudan. The genotype and allele frequencies were compared with those of other groups from published and unpublished data of world populations. The combined Sudanese sample conformed with Hardy–Weinberg equilibrium (HWE) expectation. However, population sub-structuring according to ethnic/linguistic group indicated at least two SNPs in departure from HWE. Differences in allele frequencies and genotype distribution between groups was also noted in three of the four SNPs. The other loci were distributed homogeneously within the populations studied with genotype frequencies in agreement with HWE expectation. These results highlight the importance of inter-population stratification for polymorphic markers, as well as the potential influence of evolutionary history and ethnic variation of loci, in the general distribution of SNPs and other polymorphisms.