Two deoxyribonuclease I gene polymorphisms and correlation between genotype and its activity in Japanese population

Deoxyribonuclease I (DNase I) plays important roles for DNA fragmentation and degradation during programmed cell death. The single nucleotide polymorphism (SNP) at DNase I, designated as DNASE1, in exon 8 (A2317G) is considered to be one of the susceptibility genes for gastric and colorectal carcinoma and myocardial infarction. Recent research has shown the presence of a novel 56-bp variable number of tandem repeat (VNTR) polymorphism in intron 4 at DNase I, designated as HumDN1. In the present study, DNASE1 and HumDN1polymorphisms and serum DNase I activities in each different genotype were investigated in 137 Japanese populations. The allele frequencies of A and G in DNASE1 were 0.5839 and 0.4161, respectively. The allelic frequencies of alleles 2, 3, 4, and 5 in HumDN1 were 0.0219, 0.5803, 0.2226, and 0.1752, respectively. In the DNASE1 polymorphism, the activities of genotypes GG and AG were significantly higher than that of AA. As for the HumDN1 polymorphism, the activity of genotype 55 was significantly higher than the activities of 33 and 34. In addition, a significant difference was observed between haplotypes AA/33 and GG/55. The analysis of the correlation between genotype and DNase I activity may be potentially useful for clinical purposes.     

Clinical applications of DNase I, a genetic marker already used for forensic identification

This review primarily summarizes the clinical applications of deoxyribonuclease I (DNase I). Human DNase I exhibits polymorphism at both the protein and DNA level, and thus is potentially one of the best biochemical markers for forensic practice. Clinically, DNase I activity in serum can be used as a novel diagnostic marker for the early detection of acute myocardial infarction and transient myocardial ischemia. Furthermore, the DNase I gene is considered to be one of the susceptibility genes for gastric and colorectal carcinoma, and myocardial infarction. Over the last decade since the discovery of the utility of its genetic polymorphism for forensic purposes, research on DNase I has expanded into clinical applications.     

Usefulness of deoxyribonuclease I (DNase I) polymorphism for individualization from small aged urine stains

We devised a procedure that combines a simple extraction method, isoelectric focusing and activity staining using the dried agarose film overlay method, for deoxyribonuclease I (DNase I) typing from aged urine stains. DNase I types were determined without difficulty from urine stains kept at room temperature for 3 months or more in all of the samples tested. The amounts of urine stains required for typing after 3 months of storage were estimated to be equivalent to 60-120 microl of liquid urine. Therefore, considering that useful PCR-based DNA typing has not yet been developed for urine stains, DNase I polymorphism could be considered the first biochemical marker found to be well suited for individualization from small aged urine stains.     

Induction of chromosomal aberrations by DNase I.

Chinese hamster ovary (CHO) cells were treated with bovine pancreatic DNase I using the method of electroporation. The enzyme induced chromosomal aberrations in a S-phase independent manner. The frequencies of polycentric chromosomes induced in the G1 phase of the cell cycle are positively correlated with the dose of DNase I. The distributions of DNase I-induced polycentric chromosomes were overdispersed.     

Autopsy and postmortem examination case study on genetic risk factors for cardiac death: polymorphisms of endothelial nitric oxide synthase gene Glu298Asp variant and T-786C mutation, human paraoxonase 1 (PON1) gene and alpha2beta-adrenergic receptor gene

BACKGROUND/AIM: The Glu298Asp variant in exon 7 and T-786C mutation in the 5'-flanking region of the endothelial nitric oxide synthase (eNOS) gene, paraoxonase I gene (PON1), and alpha2beta-adrenergic receptor gene (alpha2beta-AR) have been reported to be genetic risk factors for coronary heart disease (CHD). The aim of this study was to investige the effects of these four genetic polymorphisms on the probability of death due to CHD, using data obtained from medico-legal autopsies. METHODS: Blood samples from three groups: healthy controls, dead cases with CHD and without CHD (the latter as a control for dead cases) were used. After DNA extraction, genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) test. RESULTS: The frequency of the T allele in Glu298Asp variant in the dead cases with CHD was significantly higher than that in the healthy control (p < 0.001, OR = 4.47) and that in the dead cases without CHD (p < 0.001, OR = 7.62). The gene frequency of PON1 was significandy different (p = 0.007) between dead cases with and without CHD, and was also significantly different (p = 0.025) between the healthy control and dead cases without CHD. The gene frequency of PON1 was not significantly different (p = 0.401) between the healthy controls and dead cases with CHD. Hence this gene was not associated with death due to CHD. The other polymorphisms (T-786C mutation, alpha2beta-AR) also showed no effect on death due to CHD. CONCLUSION: The polymorphism of Glu298Asp eNOS gene in dead cases may be useful for determining the cause of death in CHD cases in the Japanese population.     

A hypervariable STR polymorphism in the CFI gene: Mutation rate and no linkage disequilibrium with FGA

A hypervariable short tandem repeat (STR) polymorphism in intron 7 of the human complement factor I gene (CFI) was investigated to estimate the mutation rate in Japanese samples and to test linkage disequilibrium (LD) with an STR in the fibrinogen alpha chain gene (FGA). The expected heterozygosity and the mutation rate of CFI were estimated to be 0.917 and 0.002, respectively. No LD was observed between CFI and FGA. CFI is a useful supplementary marker for forensic science.     

Induction of Chromosomal Aberrations by DNase I

Summary

Chinese hamster ovary (CHO) cells were treated with bovine pancreatic DNase I using the method of electroporation. The enzyme induced chromosomal aberrations in a S-phase independent manner. The frequencies of polycentric chromosomes induced in the G₁ phase of the cell cycle are positively correlated with the dose of DNase I. The distributions of DNase I-induced polycentric chromosomes were overdispersed.     

COL11A1 gene is associated with limbus vertebra in gymnasts

Several studies have shown higher frequencies of radiological abnormalities among gymnasts. Recently, the gene encoding the α1 chain of type XI collagen, (COL11A1) (rs 1676486), was associated with lumbar disc herniation in the Japanese population. We hypothesized that there was a significant relationship between abnormal magnetic resonance imaging (MRI) findings of the lumbar spine and the COL11A1 4603C/T gene polymorphism in collegiate gymnasts. Our study participants included 103 Japanese collegiate gymnasts (70 men and 33 women). Radiological abnormalities were evaluated using T1- and T2-weighted MRI. Genotyping for COL11A1 was performed for all the participants. By using logistic regression analysis, we observed significant associations between limbus vertebra and age (adjusted odds ratio=0.51, 95% confidence interval: 0.27-0.96), sporting experience (adjusted odds ratio=1.49, 95% confidence interval: 1.14-1.94), and a TT genotype (adjusted odds ratio=7.83, 95% confidence interval: 1.33-46.03). We conclude that a TT genotype of COL11A1 polymorphism may be a significant risk factor for limbus vertebra in Japanese collegiate gymnasts.     

A hypervariable STR polymorphism in the complement factor I (CFI) gene: Asian-specific alleles

In this study, a short tandem repeat (STR) polymorphism in intron 7 of the human complement factor I (CFI) gene was studied in 637 DNA samples obtained from African, German, Thai, and Japanese populations and German and Japanese families. A total of 41 alleles were observed and classified into two groups, L and H, based on size differences. Group H, which consisted of 16 alleles, was observed only in Thai and Japanese populations at frequencies of 0.162 and 0.116, respectively, and was strongly associated with c.1217A in exon 11 (CFI*Ah). The heterozygosity values ranged from 0.89 in German to 0.93 in Thai populations. This STR would be a useful supplementary marker for forensic individualization.     

The Y-27H39 polymorphism in a Japanese population

We studied 184 Japanese males for the tetranucleotide TAGA repeat polymorphism at the Y -27H39 locus on the Y chromosome, and discovered a new allele, tentatively named F. Direct sequencing of Y -27H39 alleles revealed that the new allele (206 nt) is larger than allele E (202 nt) by 1 repeat unit. The six alleles differ only in the number of repeats, the flanking sequences being constant. The allele frequencies are different in Japanese and Caucasians.     

Evaluation of two new STR loci 9q2h2 and wg3f12 in a Japanese population

Two short tandem repeat (STR) loci (9q2h2 and wg3f12) have been evaluated in a Japanese population. Ten and seven different alleles were observed in 9q2h2 and wg3f12 respectively. 9q2h2 displayed simple polymorphism in tetrameric repeat structure; by contrast, wg3f12 contained variable numbers of tetrameric repeats and a 30-bp deletion/insertion polymorphism. No "interalleles" were found. The expected heterozygosities of 9q2h2 and wg3fl2 were 0.749 and 0.574, respectively. No deviation from Hardy-Weinberg equilibrium was found.     

The angiotensin converting enzyme I/D polymorphism in long distance runners

AIM: There is an assumption that ACE I/D polymorphism represents one of the possible genetic factors that might be associated with sports excellence. Recent studies have identified an increased frequency of I allele in elite endurance athletes, long distance runners, rowers and mountaineers. The aim of this study was to test the hypothesis that the ACE I/D polymorphism is associated with enhanced endurance performance. METHODS: We examined this hypothesis by determining ACE I/D allele frequency in 215 marathon runners, 222 half-marathon runners and 18 inline skaters classified by performance (marathon competition results). ACE genotype and allele frequencies were compared with 252 healthy controls. RESULTS: ACE genotype frequency in the whole cohort did not differ from that in the sedentary controls (P < 0.56). However, there was an increase of the I/I genotype incidence amongst successful marathon runners scoring on places from 1st to 150th (P < 0.01). These findings were confirmed in the group of inline skaters, similarly demonstrating an increase of the I/I genotype (P < 0.01). There was no association found between half marathon runners and the ACE genotype (P < 0.59). CONCLUSIONS: An excess of the I allele in long distance runners confirms the association between the ACE I/D polymorphism and endurance sports performance.     

Inter-alpha-trypsin inhibitor (ITI): A useful genetic system in paternity testing. Evidence for polymorphic occurrence ofITI*3 and existence of a new allele,ITI*4

Summary The genetic polymorphism of human interalpha-trypsin inhibitor (ITI) has been investigated in sialidase-treated samples by isoelectric focusing on polyarcrylamide gels with a pH range 3.5–9.5 followed by passive blotting with enzyme immunoassay. In 400 blood donors from western Japan, 8 simplified band patterns were observed, 6 of which could be explained by the previously described 3 polymorphic alleles, ITI*1, ITI*2, and ITI*3. The others were products of a new and rare fourth allele designated ITI*4, whose expression is also consistent with autosomal codominant inheritance. The frequency of these alleles was 0.440, 0.526, 0.030 and 0.004, respectively. The theoretical exclusion rate for putative fathers in paternity cases was calculated to be 0.228. The ITI system is a useful genetic marker for forensic hemogenetics in Japanese and in Europeans.Dedicated to Professor I. Tsuchie on the occasion of his 60th birthday     

Sequence analysis of alleles at a microsatellite locus D14S299 (wg1c5) and population genetic comparisons

In order to increase the discriminating power of DNA analysis in personal identification, we evaluated the forensic utility of the microsatellite locus D14S299 (wg1c5) in the Japanese population and also in the Chinese and Caucasian populations. Twelve different alleles were identified in length by gel electrophoresis with silver staining. The major alleles in Japanese were sequenced and designated as the numbers of the variable repeats (GGAT or GGAA). There were five variable regions and extensive homoplasy was found. However, the allele fragment lengths were in 4 bp increments and no “interalleles” were found. The estimated heterozygosity and the polymorphism information content (PIC) were 0.726 and 0.689, respectively in Japanese. Those in Chinese (0.743 and 0.704) were similar to those in Japanese, while those in Caucasians (0.812 and 0.781) were much higher. After adjacent alleles were combined to yield at least five entries, statistical analysis was performed. The power of discrimination (PD) was 0.887 in Japanese, 0.895 in Chinese and 0.935 in Caucasians and no significant deviations from the Hardy-Weinberg equilibrium were found in the three populations. We retyped all apparently homozygous samples using an alternative pair of flanking primers and found them to be true homozygotes. D14S299 appears to be a useful STR locus for forensic practice. Received: 28 September 1998 / Received in revised form: 4 January 1999 / Accepted: 8 February 1999     

Polymorphism of the vWA locus located in the center of the three vWA STRs in the Japanese population

The structural polymorphism of the vWA locus (vWA-T) located between the two polymorphic vWA loci (vWA-K and -P) was analyzed in 100 Japanese individuals using DNA samples isolated from dental pulp. The polymorphism of this locus was based on the difference in the number of tcta repeat. New interallele 11.1 was found in two samples. All together 9 alleles and 19 genotypes were observed. In addition, one mutant allele contained tcga in the common tcta repeat structure. The value of PD was calculated to be 0.900. Inheritance of the polymorphism was confirmed in a family including 23 individuals and 6 matings.     

飞行员血管紧张素转换酶基因插入/缺失多态性及其血清水平的研究

目的了解飞行员血管紧张素转换酶(ACE)基因插入/缺失（I/D）多态性及其血清水平,探讨ACE基因多态性与飞行员耐力可能的关系。方法飞行员118例,健康对照者96例,用聚合酶链反应（PCR）扩增技术检测ACE基因I/D多态性,用比色法测定血清ACE水平。结果位于ACE基因第16内含子的I/D多态性经PCR扩增后呈三种基因型纯合子插入型（II）、纯合子缺失型（DD）和杂合子插入/缺失型（I/D）。飞行员组II基因型（44.07%）和Ⅰ等位基因频率（0.65）显著高于健康对照组(分别为31.25%和0.52)。ACE基因多态性与血清ACE水平明显相关(DD>ID,DD>II)。结论ACEⅠ基因有可能在飞行员的飞行耐力中起重要作用。     

上海地区汉族优秀游泳运动员mtDNA高变区Ⅰ序列多态性分析

目的探讨上海地区汉族不同水平优秀游泳运动员mtDNA高变区Ⅰ序列多态性分布特点.方法分别以89名上海籍汉族优秀游泳运动员和71名上海籍普通人为研究对象,采用PCR产物纯化后直接测序的方法,应用DNASTAR 6.10版序列分析软件对不同人群的序列多态性进行分析,并与剑桥序列进行比对,确定多态位点、类型及频率.结果(1)普通人mtDNA高变区Ⅰ多态位点、碱基变异数及变异率高于运动员,但无明显差异(P＞0.05);(2)普通人和不同等级运动员的多态位点和碱基变异数及变异率存在明显差异(P＜0.05),变化趋势为普通人＞总体运动员＞一级＞健将;运动员和普通人独有位点在本群体中的频率分布都很低(低于5%);(3)游泳运动员和普通人mtDNA高变区Ⅰ序列多态性主要表现为碱基转换、颠换、插入和缺失4种类型;(4)普通人碱基转换发生频率显著高于健将和一级运动员(P＜0.05),颠换发生频率明显低于运动员(P＜0.05).结论上海地区汉族优秀游泳运动员mtDNA高变区Ⅰ序列的突变率明显低于上海汉族普通人,表现出较为明显的人群特征;游泳运动员独有的多态位点数高于普通人,但在本群体中的频率分布均低于总体多态的5%;游泳运动员和普通人在碱基替换、插入和缺失类型与频率方面存在一定差异,同时与我国其它耐力性项目的优秀运动员也存在一定差异.     

Relationship between the 1359 G/A polymorphism of the Central Cannabinoid Receptor 1 (CNR1) gene and susceptibility to cannabis addiction in a Turkish population

In this study, we investigate the existence of a possible genetic association between 1359 G/A polymorphism of the Central Cannabinoid Receptor 1 (CNR1) Gene CNR1 (p.Thr453Thr; rs1049353) single nucleotide polymorphism (SNP) and cannabis addiction. DNA samples used in this work are purified from venous leukocytes of 145 unrelated Turkish cannabis-dependent subjects and 140 Turkish control subjects. No significant difference is observed in genotype or allele frequencies of CNR1 1359 G/A polymorphism between these two groups. We also compared CNR1 1359 G/A polymorphism allele frequency distribution in our healthy Turkish population with other healthy populations. The comparison of healthy Turkish subjects with the healthy subjects from English-Irish, Chinese, European-American, African-American, Italian, German and Japanese populations revealed significant differences in allele frequencies. Data indicate that the 1359 G/A CNR1 polymorphism does not contribute to susceptibility to cannabinoid addiction in Turkish subjects. To the best of our knowledge, this is the first study on 1359 G/A CNR1 polymorphism in the Turkish population.     

Parentally imprinted allele typing at a short tandem repeat locus in intron 1a of imprinted gene KCNQ1

A short tandem repeat (STR) in the intron 1a of paternally imprinted gene, KCNQ1, is evaluated as a new probe for use in parentally imprinting allele (PIA) typing. This typing can determine the inheritance of one allele from father by the methylation difference. Allelic and genotypic frequencies of the STR were determined using samples from 175 unrelated Japanese and 170 unrelated Germans. The polymorphism information contents were 0.652 and 0.634 for the Japanese and the Germans, respectively, indicating usefulness in individual identification. This method was applied to five Japanese families consisting of 19 individuals. Genomic DNA was digested by methylation-sensitive restriction endonucleases, HhaI and HapII, followed by PCR amplification using two-step sandwich primer sets and the products were analyzed on polyacrylamide gel electrophoresis. For all of the families, each child's paternal allele given by PIA typing corresponded to one of the two alleles from father, not the two from mother, that were determined by the STR genotyping. The results demonstrate that this STR probe is feasible for use in PIA typing and that its typing method can contribute to paternity testing.     

Distribution of 42-bp variable tandem repeat polymorphism of the cold-induced autoinflammatory syndrome 1 (CIAS1) gene in eight human populations

We recently identified a 42bp Variable Number of Tandem Repeats polymorphism in intron 4 of Cold-induced autoinflammatory syndrome 1 gene (CIAS1 42bp-VNTR), which are associated with CIAS1 gene expression and some inflammatory disease. The aim of our study is to investigate whether variability of CIAS1 42bp-VNTR allele is difference among races. A total of 1291 subjects from 7 populations (178 Chinese, 95 Korean, 614 Mongolian, 49 Bangladesh, 72 Sri Lanka, 192 African and 91 European) was genotyped on CIAS1 42bp-VNTR polymorphism, which was also compared to previous genotyping data from 508 Japanese subjects. A total of 11 genotypes and 5 alleles were found in 8 populations. The range of allele frequencies of CIAS1?6, CIAS1?7, CIAS1?9, CIAS1?12, and CIAS1?13 were 0.000-0.167, 0.056-0.248, 0.008-0.203, 0.570-0.923, and 0.000-0.104 in eight populations. The CIAS1?12 was the most common allele among all populations. The longest allele CIAS1?13 in African population was extremely high frequent at 0.104 compared to other population. While shortest allele CIAS1?6 was not observed Sri Lankan and African. Frequency (0.924) in the Sri Lankan population. These results showed that the CIAS1 42bp-VNTR polymorphism could represent genetic diversity among different human populations.