Association between a high-expressing interferon-gamma allele and a lower frequency of kidney angiomyolipomas in TSC2 patients

Tuberous sclerosis complex (TSC) is a familial hamartoma syndrome in which renal involvement is common and, at times, life threatening. We have investigated the potential effect of a non-TSC gene on renal disease in a cohort of 172 TSC patients with TSC2 mutations. Patients were genotyped for an interferon-gamma (IFN-gamma) microsatellite polymorphism, within intron 1, for which one common allele (allele 2, with 12 CA repeats) has been shown to have a higher expression of IFN-gamma. A chi(2) analysis was used to examine the association between IFN-gamma allele 2 and the development of kidney angiomyolipomas (KAMLs) in this TSC2 cohort. Because of the age-dependent development of KAMLs in TSC, we initially focused on the 127 patients who were >5 years old. Additional subgroup analyses were done to investigate the influence of age and gender. The transmission/disequilibrium test (TDT) was also performed in a subset of this cohort (46 probands) for whom parent and/or sibling samples were available for analysis. Both chi(2) analysis and TDT suggested an association between IFN-gamma allele 2 and the absence of KAMLs in patients who have known TSC2 mutations. Among the 127 patients who were >5 years old, KAMLs were present in 95 (75%) and were absent in 32 (25%). In the group with KAML present, the frequency of IFN-gamma allele 2 was 56%; in the group with KAML absent, the frequency of IFN-gamma allele 2 was significantly higher, at 78% (P=.02, by chi(2) analysis). The family-based TDT analysis gave similar results, with a TDT statistic (TDT chi2=5.45) corresponding to a P value of.02. Subgroup analyses show that both age and gender may influence the impact of this association. Although these results should be replicated in other populations with TSC, the present study suggests that modifier genes play a role in the variable expression of TSC and also suggests a potential therapy for KAMLs in patients with TSC.     

CCR5-Delta32 allele frequencies in Ashkenazi Jews

This study was carried out to determine the 32-bp deletion allele frequencies in the CCR5 gene (CCR5-Delta32) in various populations of Jews of eastern European origin (Ashkenazi Jews). The total population sample (n = 351) represented Ashkenazi Jews originating from seven geographic groups in Europe. The overall frequency of the CCR5-Delta32 allele was elevated (13.7%), although some important differences in frequencies occurred among the seven countries included in the survey; the frequency was highest (25.9%) in those of Lithuanian origin. There is an apparent trend (r = 0.74) involving a lowering of the Delta32 allele frequencies moving from north to south in the seven populations tested. The Delta32 frequencies obtained were compared to those already published for non-Jewish populations inhabiting the same countries and the differences in frequencies were not significant, with the exception of Lithuania (chi(2) = 2.20, p < 0.03). Founder effect and genetic drift are proposed to explain the elevated values observed in Ashkenazi Jews and those originating from Lithuania.     

Polymorphism of length of tetranucleotide repeat from the 5'-side from the myelin basic protein gene in multiple sclerosis in Russians

The myelin basic protein gene (MBP) can confer the susceptibility to multiple sclerosis, because its protein product is the main protein component of myelin of the central nervous system and a potential autoimmune antigen in the disease. A possible association of multiple sclerosis with alleles and genotypes of a microsatellite repeat (TGGA)n, located to the 5' side from the first exon of MBP in ethnic Russians (126 patients with reliable multiple sclerosis and 142 healthy controls from Central Russia) was analyzed using the case-control method. Upon separation of the tetranucleotide repeat site amplification products in 1.5% agarose gel, one can see two distinct bands that can be analyzed as two allele groups (A and B). The distribution of allele A and B group frequencies as well as frequency of allele group B and genotype A/A reliably differs in multiple sclerosis patients and healthy controls. Alleles A and the A/A genotype are associated with the development of multiple sclerosis. We also analyzed the association of multiple sclerosis with combined bearing of alleles and genotypes A and B of MBP and groups of alleles of the DRB1 gene of the major histocompatibility complex that correspond to serospecificities DR1-DR18. The comparison of subgroups of multiple sclerosis patients and healthy individuals, formed on the basis of the DRB1 phenotype, has shown a reliable increase in the frequency of allele B in healthy individuals and the genotype A/A frequency in patients, only among DR4- and DR5-positive individuals. No reliable difference was found in the MBP allele and genotype distribution between multiple sclerosis patients and healthy individuals in combined groups of (DR4,DR5)-negative individuals, i.e., no carriers of any phenotype except DR4 and DR5 were revealed. Thus, MBP or some other nearby gene is involved in the multiple sclerosis development in Russians, predominantly (or exclusively) among DR4 and DR5 carriers. In this case, without stratification of analyzed individuals by the MBP alleles, multiple sclerosis is reliably associated only with DR2(15), but not of DR4 and DR5 alleles of DRB1. The results obtained are in favor of the genetic heterogeneity of multiple sclerosis, and suggest the possibility of epistatic interactions between the MBP and DRB1 genes.     

Association of cytochrome P450 genes polymorphisms (CYP1A1 and CYP1A2) with the development of chronic obstructive pulmonary disease in Bashkortostan

To assess the role that polymorphisms of cytochrome P450 genes play in genetic predisposition to chronic obstructive pulmonary disease (COPD), the allele and genotype distributions of CYPIA1 (2455 A/G, 3801T/C) and CYP1A2 (-2464T/delT, -163C/A) genes were studied in Tatar and Russian COPD patients and in cases of healthy individuals (Russian, Tatar and Bashkir), residents of Bashkortostan. It was shown that the CYP1A1 and CYP1A2 genes haplotypes frequency distribution patterns do not differed between Tatars and Russians ethnic groups (chi2 = 0.973, df = 3, p = 1.00 and chi2 = 1.546, df = 3, p = 0.92, respectively). Analysis of the the CYP1A1 and CYP1A2 genes haplotypes revealed statistically significant differences in the haplotypes frequency distributions between Bashkirs versus Russians and Tatars (chi2 = 12.328, df= 3,p = 0.008; chi2 = 9.218, df=3, p = 0.034, respectively for CYP1A1 gene and (chi2 = 18.779, df=3, p = 0.0001, chi = 14.326, df=3, p = 0.003, respectively for CYP1A2 gene). The (-2467)delT allele and CYP1A2*1D haplotype of CYPIA2 gene was associated with higher risk of COPD in Tatar ethnic group (OR = 1.83, 95% CI 1.24-2.71, chi2 = 9.48, p = 0.003 and chi2 = 9.733, p = 0.0027, Pcor = 0.008; OR = 3.908, 95% CI 1.56-10.19, respectively). On the other hand the CYP1A2*1A haplotype had protective effect (chi2 = 6.319, p = 0.0127, Pcor = 0.038; OR = 0.6012, 95% CI 0.402-0.898). But at the same time we did not find any differences in the genotypes and haplotypes frequency distributions of the CYP1A2 gene within the patients and healthy groups in Russian ethnic group. We also did not find any association of CYP1A1 gene with COPD in ethnic groups of Bashkortostan.     

Polymorphism of Apolipoproteine E in Relation with Alzheimer and Vascular Dementia

Summary 1. The epsilon 4 allele of the apolipoprotein E gene increases the risk of late onset familial and sporadic Alzheimer disease. Relation of epsilon 4 allele of the apolipoprotein E gene to various types of dementia and the onset of dementia were analyzed in the present study.2. The study comprised 139 patients (50 men and 89 women) with dementia, mean age 73.61 years (range 47–98). The diagnosis of dementia was made according to Diagnostic and Statistical Manual of Mental Disorders, and subtypes diagnoses were made according to NINCDS-ADRDA and NINDS-AIREN criteria. Minimental State Examination (MMSE) was used for the screening of dementia. Apolipoprotein E polymorphism was determined by the PCR-RFLP technique-polymerase chain reaction and subsequent digestion with specific restriction endonuclease. For statistical analyses chi-square test and the crude Gart′s odds ratio (OR) and 95% confidence intervals (CI) were used.3. From 139 dementia patients (MMSE ≤24 points) in 61 (45%) Alzheimer disease (AD) was present, in 44 patients (31%) vascular dementia (VD), and in 34 (24%) mixed dementia (MD) were revealed. In comparison with control group the presence of at least one ApoE-ɛ4 allele was significantly higher only in the group with AD (p < 0.001), (OR=2.76; 95%: 1.42–5.36). The frequency of ɛ4 allele carriers was significantly overrepresented in AD group compared with VD (χ²=5.94; p=0.0148). Differences between AD and MD or VD and MD were not confirmed.     

The investigation of allele and genotype frequencies of human C3 (rs2230199) in south Iranian population

The complement system is an important mediator of natural and acquired immunity. The complement system genes coding complement proteins have polymorphisms. Hereditary deficiencies of this system predispose to autoimmune conditions such as age-dependent macular degeneration or impairment of immunity against microorganisms. When different populations are compared, the frequency of complement polymorphism shows a very marked geographical distribution. The frequency of the functional polymorphism rs2230199 (Arg80Gly; C > G) in the C3 gene was determined in population from south of Iran (n = 200), using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). One hundred thirty-eight persons (69 %) were homozygous for C allele (CC or SS); fifty-six person (28 %) heterozygote GC (FS) and six people were homozygous for G allele (GG or FF) (3 %). The allele frequency was 82 % for C3S and 18 % for C3F. A distribution of C3C allele frequency in our population is different from the reports of Asians (100 %); Indians (90-98 %); African-American (93 %); Africans (99 %) and south Brazilian (97 %). However, this finding is similar with the findings Caucasian (80-82 %) ( http://www.ncbi.nlm.nih.gov/SNP ); Americans (80 %); Pushtoon, Hazaras, Osbek and Tajik ethnic groups in Afghanistan (88-90 %) and Tunisian population (84 %). Our study confirmed significant inter-ethnic differences in C3 (rs2230199) frequencies between south Iranians and other ethnic groups. The analysis of genetic variation in complement genes is a tool to provide new insights into the evolution of the human immune system.     

The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus

The dopamine D4 receptor gene (DRD4) has an expressed polymorphism in the third exon that may have functional relevance. The polymorphism exists at two levels. At the higher level there is an imperfect tandem repeat of 48 base pairs (bp) coding for 16 amino acids; alleles have been identified with 2 (32 amino acids) to 10 (160 amino acids) repeats. The imperfect nature of the repeats is responsible for a more subtle level of variation since alleles with the same number of repeats can differ in the exact sequences or in the order of the variants of the 48-bp unit. We have undertaken a global survey of this expressed polymorphism as one approach to understanding the evolutionary significance and origins of the polymorphism as well as understanding what selective forces, if any, may be operating at this locus. As the first step, we have determined the repeat number genotype of the DRD4 repeat polymorphism in 1,327 individuals from 36 different populations. The allele frequencies differ considerably among the different populations. The 4-repeat allele was the most prevalent (global mean allele frequency = 64.3%) and appeared in every population with a frequency ranging from 0.16 to 0.96. The 7-repeat allele was the second most common (global mean = 20.6%), appearing quite frequently in the Americas (mean frequency = 48.3%) but only occasionally in East and South Asia (mean frequency = 1.9%). The 2-repeat allele was the third most common (global mean frequency = 8.2%) and was quite frequent in East and South Asia (mean frequency = 18.1%) while uncommon in the Americas (mean frequency = 2.9%) and Africa (mean frequency = 1.7%). The universality of the polymorphism with only three common repeat-number alleles (4, 7, and 2) indicates that the polymorphism is ancient and arose before the global dispersion of modern humans. The diversity of actual allele frequencies for this expressed polymorphism among different populations emphasizes the importance of population considerations in the design and interpretation of any association studies carried out with this polymorphism. Received: 18 July 1995 / Revised: 18 December 1995     

Correlation of circulatory immunoglobulin levels with Mu opiate receptor allele

Opiates are known to induce immunosuppression in their users (addicts). Evidences supporting their role in suppressing a variety of immunological end points in addicts have been reported by several investigators. In the present study, we investigated the changes in serum immunoglobulin (Ig) levels and their correlation with Mu opiate receptor (MOR) genotypes. Eighty-seven users and forty-five non-users were recruited for the study. Genomic DNA, isolated from the peripheral blood, was used for genotyping for C17T and A118G polymorphism using PCR-RFLP method. The frequency of A and G alleles in non-users was 89% and 11% respectively, whereas in addicts, it was 67% and 33% respectively. Case control analysis between groups revealed that 118G allele was associated with opioid dependence [Chi square (chi2) = 13.56, odds ratio (OR) = 3.90, confidence interval 95% (CI 95%) = 1.80-8.67, p = 0.000231]. C17T polymorphism showed no association with opioid dependence [(chi2) = 0.9, OR = 2.49, CI 95% = 0.528-16.12, p = 0.343]. Mean Ig levels, both IgG (student's t-test = 2.2738, p = 0.007) and IgA (student's t-test = 2.848, p = 0.0051) differed between opiate users and nonusers. IgG and IgA levels were also significantly different in individuals with different MOR genotypes. Immunosuppression was observed in AA genotype-bearing individuals, while no suppression was seen in AG and GG genotypes bearing individuals. In case of C17T polymorphism, both CC and CT genotypes bearing individuals showed immunosuppression, as judged by circulating Ig levels.     

DNA Length Polymorphism of Tetranucleotide Repeat at the 5′ Side of the Myelin Basic Protein Gene in Russian Multiple Sclerosis Patients

The myelin basic protein gene (MBP) can confer the susceptibility to multiple sclerosis, because its protein product is the main protein component of myelin of the central nervous system and a potential autoimmune antigen in the disease. A possible association of multiple sclerosis with alleles and genotypes of a microsatellite repeat (TGGA) _n , located to the 5 side from the first exon of MBP in ethnic Russians (126 patients with definite multiple sclerosis and 142 healthy controls from Central Russia) was analyzed in a case–control study. Upon separation of the tetranucleotide repeat amplification products in 1.5% agarose gel, one can see two distinct bands that can be analyzed as two allele groups (A and B). The distribution of allele A and B group frequencies as well as phenotype frequency of alleles B and genotype frequency of A/A differs significantly in multiple sclerosis patients and healthy controls. Alleles A and genotype A/A are associated with multiple sclerosis. We also analyzed the association of multiple sclerosis with combined bearing of alleles and genotypes A and B of MBP and groups of alleles of the DRB1 gene of the major histocompatibility complex that correspond to serological specificities DR1-DR18. The comparison of subgroups of multiple sclerosis patients and healthy individuals, stratified according to HLA-DRB1 phenotypes, has shown a reliable increase in the phenotype frequency of allele B in healthy individuals and the genotype A/A frequency in patients, only among DR4- and DR5-positive individuals. No significant difference was found in the MBP allele and genotype distribution between multiple sclerosis patients and healthy individuals in combined groups of (DR4,DR5)-negative individuals, i.e., in the group of carriers of any phenotype except DR4 and DR5. Thus, MBP or some other nearby gene is involved in the multiple sclerosis development in Russians, predominantly (or exclusively) among DR4 and DR5 carriers. In this case, without stratification of analyzed individuals by the MBP alleles, multiple sclerosis is associated only with DR2(15), but not DR4 and DR5 alleles of DRB1. The results obtained are in favor of the genetic heterogeneity of multiple sclerosis, and suggest the possibility of epistatic interactions between the MBP and DRB1 genes.     

Difference in apolipoprotein E type 4 allele (APOE epsilon 4) among dentate and edentulous subjects

Objectives: To evaluate the frequency of apolipoprotein (APOE) alleles and determine whether APOE type 4 allele (?4) was associated with edentulousness even when certain factors were controlled. Background: The APOE are important in lipid homeostasis, and APOE ?4 has been found in many diseases and to have a negative impact on longevity. Tooth loss is more common in ill aged subjects with low income and education. Materials and methods: In a population‐based study involving 1860 subjects between 35 and 85 years 1321 dentate (mean age = 54; 54% women, 46% men) and 539 edentulous (mean age = 72; 62% women, 38% men) subjects were studied. Logistic regression was performed with dentate/edentulous as dependent variables and years of education, socio‐economic status, social network, stress level, handicap from birth, 23 various diseases and APOE ?4 as covariates. Thereafter, APOE ?4 frequencies were studied in 342 dentate and 336 edentulous subjects 50–85 years of age. The subjects were matched with regard to age, gender, years of education, living condition, stress level, handicap from birth and 23 various diseases. Results: APOE allele frequency in the total group was ?2 = 7.8%, ?3 = 76.4% and ?4 = 15.8%. Age, living condition, years of education and APOE ?4 were significant covariates in edentulous subjects (p ≤ 0.001). APOE ?4 in the matched groups revealed significant differences between the dentate group and the edentulous group (χ² = 5.68; p = 0.017). There was no group effect (F_(29,648) = 0.849; p < 0.696; Wilks’ lambda = 0.963). In the dentate group, the frequencies of APOE were: ?2 = 8.8%, ?3 = 77.9% and ?4 = 13.3%. Corresponding frequencies of APOE in the edentulous group were: ?2 = 6.6%, ?3 = 75.4% and ?4 = 18.0%. Conclusion: Despite matching both groups with regard to different background factors, the edentulous group had a higher frequency of APOE ?4 than the dentate group. Thus, genetic factors might contribute to greater risk in developing complex oral diseases leading to tooth loss or just be an indication that the subjects in our study carrying APOE ?4 are more fragile.     

MICA-A5.1 allele is associated with atypical forms of celiac disease in HLA-DQ2-negative patients

We selected 38 consecutive celiac disease (CD) patients (from a group of 316 consecutive CD patients) and 91 healthy blood donors, all of whom were HLA-DQ2 (DQA1*0501/DQB1*0201) negative, and investigated the presence of the classically associated alleles HLA-DQ8 and HLA-DRB4. We also studied the distribution of MICA transmembrane alleles in the two clinical forms of the disease. For this reason, these 38 DQ2-negative patients were subdivided into two groups: 18 typical CD patients and 20 atypical CD patients. No differences were found in the distribution of the DRB4 allele between DQ2-negative patients and controls. The HLA-DQ8 heterodimer (DQA1*03xx/DQB1*0302) was increased in CD patients (29%) compared with controls (10%), but no statistical differences were found. No differences were observed in the frequency of these alleles between either group of CD DQ2-negative patients. MICA-A5.1 was increased in atypical CD patients when compared with the typical forms of disease ( P(c)=0.03) and with healthy controls (P(c)=0.002). No other MICA allele was found to be significantly increased in the groups under study. The presence of MICA-A5.1 in atypical CD DQ2-negative patients may indicate a possible role of this allele in the development of CD.     

Allelic variants of the tumor necrosis factor superfamily as markers of the severity of the course of chronic obstructive lung disease and bronchiectatic disease

The distribution of allelic variants of genes of the TNF superfamily (TNFA and LTA) was studied in 172 patients with chronic obstructive pulmonary disease (COPD), bronchiectatic disease (n = 22), and in healthy individuals (n = 169). Analysis of the TNFA gene locus -308G-->A revealed no differences between the examined groups. Analysis of the LTA gene polymorphic locus +252A-->G showed that in patients with COPD, the frequency of the G allele was significantly higher than that in the control group (chi 2 = 3.98, p < 0.05). The presence of this allele in the genotype was correlated with the degree of COPD severity. Thus, in patients with stage II COPD, heterozygous AG genotype predominated (51.3%), whereas in patients with stage III COPD, the frequency of AG genotype was reduced to 32.7% at the expense of increased frequency of GG genotype (14.6%) (chi 2 = 6.78, p < 0.05; OR = 4.6, CI 1.37-15.96). The distribution of combined TNFA and LTA genotypes was also studied. In the group of COPD patients, the proportion of individuals with a combination of normal GG TNFA genotype and heterozygous AG LTA genotype was significantly higher (28.5% versus 18.4% in control; chi 2 = 4.14, p < 0.05; OR = 1.75, CI = 1.01-3.04). Genotype combinations were characterized at various clinical stages of COPD and bronchiectatic disease (BED). Thus, we have shown for the first time ever that LTA gene alleles and their combinations with the polymorphic variants of the TNFA gene are associated with predisposition to COPD and severity of this disease.     

Polymorphism in promoter regions of matrix metalloproteinases (MMP1, MMP9, and MMP12) in chronic obstructive pulmonary disease patients

Our studies have shown that the genotype and allele frequencies of polymorphisms G(-1607)GG of MMPI gene, C(-1562)T of MMP9 gene and A(-82)G of MMP12 gene do not significantly differ in the samples of chronic obstructive pulmonary disease (COPD) patients (N = 318) and healthy controls (N = 319) dwelling in Bashkortostan Republic. However, association of (-1562)T allele of the MMP9 gene with the severity of COPD disease progression has been revealed. In COPD patients at stage 4 of the disease, the frequency of allele T was significantly higher that in patients with the stages 2 and 3 (15.89% versus 8.38%; chi2 = 7.804, d.f. = 1, P = = 0.005; OR = 2.06 95% CI 1.22-3.49). The distribution of the genotype frequencies of C(-1562)T polymorphism of MMP9 gene significantly differed between the patients with various COPD severity (chi2 = 9.849, d.f. = 2, P = 0.007). The individuals with rare genotype TT were revealed only among patients with severe COPD form (3.97% versus 0%; chi2 = 4.78, P = 0.029, Pcor = 0.058). Analysis of this polymorphism in patients with early COPD onset (younger than 55 years old) has shown a significant increase in the allele Tfrequency in the group of patients with severe COPD (stage 4 according to GOLD) compared to the patients of the same age but with less severe COPD progression (chi2 = 5.26, d.f. = 1, P = 0.022). As the major clinical characteristics of stage 4 COPD is the development of pulmonary emphysema as well as bronchial walls deformation, we suggest that the increased expression of MMP9 gene caused by genetic polymorphism in the gene promoter is important in the early development of serious complications of the disease.     

磺酰脲类受体基因多态性与2型糖尿病的相关性研究

研 究磺酰脲类受体1（SUR1）基因外显子16-3c/t多态性在中国某南方汉族人群中是否为2型糖尿病的致病基因座。采用聚合酶链反应-限制酶酶切片段长度多态性（PCR-RFLP）方法对南方汉族46个2型糖尿病高发家系成员的SUR1基因外显子16的多态性进行分析。利用Mantel-Haenszel分层分析研究该基因座多态性与2型糖尿病的关系。在高发家系人群中,SUR1基因外显子16-3c/t多态性的基因型频率为：cc型29.3%、ct型507%、tt型20%,c等位基因频率为54.7%;患者组基因型频率为：cc型30.2% 、ct型53.8%、tt型16.0% ,c等位基因频率为57.1% ;未患病亲属组基因型频率为：cc型28.3% 、ct型47.2%、tt型24.5%,c等位基因频率为519%,两组间基因型和等位基因的差异经检验无统计学意义（分别为χ2=3.224,P=0.199;χ2=1.250,P=0264）。在性别、吸烟、饮酒、肥胖、高血压等混杂因素中的频率差异亦无显著性。c等位基因频率低于北方汉族人。在中国某南方汉族2型糖尿病高发家族人群中,未发现SUR1基因外显子16-3c/t多态性与2型糖尿病存在关联,该基因座可能不是该人群的致病基因。 Abstract:To study whether the 3c/t polymorphism of the sulfonylurea receptor 1 (SUR1) gene exon16 increased the risk of type 2 diabetes mellitus in type 2 diabetes mellitus pedigrees in Han population in south area of China.Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used in 46 type 2 diabetes mellitus pedigrees.The polymorphism in SUR1 was tested and analyzed by Mantel-Haenszel χ2 test.Frequencies of SUR1-3c/t polymorphism had no significant difference between type 2 diabetes mellitus and normal relatives（genotypes χ2=3.224,P=0.199;frequency of allele χ2=1.250,P=0.264）.In all subjects,type 2 diabetes mellitus and normal relatives,SUR1-3c/t genotypes were listed (cc:29.3%,30.2%,28.3%;ct:50.7%,53.8%,47.2%;tt:20%,16.0%,24.5% respectively).The frequencies of c were 54.7%,57.1% and 51.9% respectively.The frequency of c is lower than Han population in northern China.The results show that SUR1 exon16-3c/t polymorphism is not associated with type 2 diabetes mellitus in the population.     

The T-786C and C774T endothelial nitric oxide synthase gene polymorphisms independently affect the onset pattern of severe diabetic retinopathy.

Genetic factors could be implicated in the pathogenesis of severe diabetic retinopathy (DR). Recently, we reported a strong association between the eNOS4b/a endothelial nitric oxide synthase (eNOS) polymorphism and severe DR. To examine whether T-786C and C774T eNOS polymorphisms are involved in severe DR, 254 Caucasians with longstanding C-peptide-negative type 1 diabetes, 128 patients with absent/mild DR (control group), and 126 patients with preproliferative/proliferative DR (study group) were genotyped. The distribution of T-786C and C774T eNOS polymorphisms was in Hardy-Weinberg equilibrium and did not differ between the study and control groups. However, in case patients (n=126), T-786C and C774T polymorphisms influenced the onset pattern of severe DR (P=0.0169 and P=0.0257, respectively). The C-786C genotype was associated with early-onset severe DR (duration of diabetes: 15.2+/-5.9 vs. 19.4+/-6.3 years, P=0.0105), and the homozygous T774T genotype was associated with late-onset severe DR (24.3+/-7.0 vs. 18.4+/-6.2 years, P=0.0067). In the case of patients with high glycosylated hemoglobin levels (HbA1c >8%, n=88), the association between the T-786C polymorphism and early-onset severe DR was stronger (P=0.0068). Case patients carrying the C-786C genotype had higher HbA1c values (9.61+/-1.89%) than those carrying the T-786T genotype (8.93+/-1.47%, P=0.0173). Multivariate analysis showed that T-786C polymorphism was the best independent factor for onset pattern of severe DR (P<0.001). These findings, supported by previous associations between eNOS4b/a polymorphism and DR, suggest that T-786C and C774T eNOS polymorphisms affect the onset pattern of severe DR.     

Determination of allele frequency in pooled DNA: comparison of three PCR-based methods

Determination of allele frequency in pooled DNA samples is a powerful and efficient tool for large-scale association studies. In this study, we tested and compared three PCR-based methods for accuracy, reproducibility, cost, and convenience. The methods compared were: (i) real-time PCR with allele-specific primers, (ii) real-time PCR with allele-specific TaqMan probes, and (iii) quantitative sequencing. Allele frequencies of three single nucleotide polymorphisms in three different genes were estimated from pooled DNA. The pools were made of genomic DNA samples from 96 cases with basal cell carcinoma of the skin and 96 healthy controls with known genotypes. In this study, the allele frequency estimation made by real-time PCR with allele-specific primers had the smallest median deviation (MD) from the real allele frequency with 1.12% (absolute percentage points) and was also the cheapest method. However; this method required the most time for optimization and showed the highest variation between replicates (SD = 6.47%). Quantitative sequencing, the simplest method, was found to have intermediate accuracies (MD = 1.44%, SD = 4.2%). Real-time PCR with TaqMan probes, a convenient but very expensive method, had an MD of 1.47% and the lowest variation between replicates (SD = 3.18%).     

HLA-DR polymorphism in a Senegalese Mandenka population: DNA oligotyping and population genetics of DRB1 specificities.

HLA class II loci are useful markers in human population genetics, because they are extremely variable and because new molecular techniques allow large-scale analysis of DNA allele frequencies. Direct DNA typing by hybridization with sequence-specific oligonucleotide probes (HLA oligotyping) after enzymatic in vitro PCR amplification detects HLA allelic polymorphisms for all class II loci. A detailed HLA-DR oligotyping analysis of 191 individuals from a geographically, culturally, and genetically well-defined western African population, the Mandenkalu, reveals a high degree of polymorphism, with at least 24 alleles and a heterozygosity level of .884 for the DRB1 locus. The allele DRB1*1304, defined by DNA sequencing of the DRB1 first-domain exon, is the most frequent allele (27.1%). It accounts for an unusually high DR13 frequency, which is nevertheless within the neutral frequency range. The next most frequent specificities are DR11, DR3, and DR8. Among DRB3-encoded alleles, DR52b (DRB3*02) represents as much as 80.7% of all DR52 haplotypes. A survey of HLA-DR specificities in populations from different continents shows a significant positive correlation between genetic and geographic differentiation patterns. A homozygosity test for selective neutrality of DR specificities is not significant for the Mandenka population but is rejected for 20 of 24 populations. Observed high heterozygosity levels in tested populations are compatible with an overdominant model with a small selective advantage for heterozygotes.     

High Prevalence of Diabetic Retinopathy in Diabetic Patients Concomitant with Metabolic Syndrome

Objective

To evaluate the relationship between metabolic syndrome (MetS) and the prevalence of diabetic retinopathy (DR).

Research Design and Methods

We conducted a case-controlled study, with data obtained from 2,551 Chinese participants between 18–79 years of age (representing a population of 1,660,500 in a district of Beijing). 74 cases of DR were found following data assessment by two 45° digital retinal images. Subjects without DR (NDR group) selected from the remaining 2,477 subjects were matched 1:1 to the DR group by HbA1c. MetS was defined by incorporating diagnostic criteria of the American Heart Association/National Heart, Lung, and Blood Institute (AHA/NHLBI) and the International Diabetes Federation (IDF).

Results

There were no statistical differences between the DR group and NDR group in a number of biological or laboratory tests. However, the percentage of patients with DR increased vs. patients without DR with the number of MetS components from 1 to 5 (14.3% vs. 85.7%, 38.9% vs. 61.1%, 49.1% vs. 50.9%, 61.4% vs. 38.6% and 83.3% vs. 16.7%, respectively) (Pearson χ² = 9.938, P = 0.037). The trend to develop DR with MetS was significantly higher than that without MetS (NMetS) (χ² = 5.540, P = 0.019). MetS was an independent statistical indicator of the presence of DR after adjusting for age and sex [odds ratio (95% CI): 2.701(1.248–5.849), P = 0.012], which is still the case with an additional adjustment for WC, SBP, TC, HbA1c and duration of diabetes [odds ratio (95% CI): 2.948(1.134–7.664), P = 0.027].

Conclusion

DR is one of the diabetic microvascular complications. Apart from poor glycemic control, the concomitance of other metabolic factors can also influence DR. MetS, defined as a cluster of metabolic risk factors, is a strong and independent indicator of DR, even to the same extent as glycemic control.     

PCR/oligonucleotide probe typing of HLA class II alleles in a Filipino population reveals an unusual distribution of HLA haplotypes.

We have analyzed the distribution of HLA class II alleles and haplotypes in a Filipino population by PCR amplification of the DRB1, DQB1, and DPB1 second-exon sequences from buccal swabs obtained from 124 family members and 53 unrelated individuals. The amplified DNA was typed by using nonradioactive sequence-specific oligonucleotide probes. Twenty-two different DRB1 alleles, including the novel Filipino *1105, and 46 different DRB1/DQB1 haplotypes, including the unusual DRB1*0405-DQB1*0503, were identified. An unusually high frequency (f = .383) of DPB1*0101, a rare allele in other Asian populations, was also observed. In addition, an unusual distribution of DRB1 alleles and haplotypes was seen in this population, with DR2 (f = .415) and DRB1*1502-DQB1*0502 (f = .233) present at high frequencies. This distribution of DRB1 alleles differs from the typical HLA population distribution, in which the allele frequencies are more evenly balanced. The distribution of HLA class II alleles and haplotypes in this Filipino population is different from that of other Asian and Pacific groups: of those populations studied to date; the Indonesian population is the most similar. DRB1*1502-DQB1*0502 was in strong linkage disequilibrium (D'' = .41) with DPB1*0101 (f = .126, for the extended haplotype), which is consistent with selection for this DR, DQ, DP haplotype being responsible for the high frequency of these three class II alleles in this population.     

Abnormal segregation of prion protein octapeptide-repeat alleles in cattle

The study was conducted on full-families of Black-and-White cattle obtained as 25 AI sire families and 355 cows, as well as their progenies, mostly heifers at the age of 1-3 months. The sire group was composed by the casual qualification of 10 PRNP 6/6 and 15 PRNP 6/5 individuals on the basis of accessible young progenies. The randomly selected group of cows is characterised by a very high frequency of PRNP 6/6 (74.9%), followed by lower frequency of PRNP 6/5 (24.5%) and a very low frequency of PRNP 5/5 genotype (0.6%). The progenies represent all expected genotypes, such as: PRNP 6/6 (60.5%), PRNP 6/5 (35.8%) and PRNP 5/5 (3.7%), respectively. Taking into consideration the genotypes of parents and progenies, the segregation of PRNP 6 and PRNP 5 alleles was analysed. Results of the non-informative mating variant of male symbol PRNP 6/6 x female symbol PRNP 6/6 (n = 87) are affected by the PRNP 6/6 progeny genotype in all cases. Subsequently, the results of mating variants male symbol PRNP 6/6 x female symbol PRNP 6/5 (n = 29) and male symbol PRNP 6/5 female symbol PRNP 6/6 (n = 179) showed statistically non-significant differences in both above-mentioned alternations. The progeny group related from male symbol PRNP 6/5 x female symbol PRNP 6/5 parental mating obtained fully informative and most valuable results based on the presented research concept. In the common group of 58 calves, the genotype PRNP 6/6 is represented by 26 individuals (44.8%), PRNP 6/5 - by 19 individuals (32.8%) and PRNP 5/5 - by 13 individuals (22.4%). Therefore, the theoretical genotype rate (25% : 50% : 25%) is drastically deformed and the differentiation between the observed and expected numbers of animals is statistically highly significant (chi(2) = 12.72; 2 df.). These differences are affected by two times higher PRNP 6/6 homozygous (chi(2) = 9.12; 1 df.) and responsively by the low number of PRNP 6/5 heterozygous animals (chi(2) = 3.45; 1 df.). Further investigations are carried out to explain the genetic determination of abnormal PRNP octa-peptide repeat allele segregation, which suggests possible lethal cis-trans linkage effects.