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PubMed2002

Further evidence for the role of the dopamine D4 receptor (DRD4) gene in attachment disorganization: interaction of the exon III 48-bp repeat and the -521 C/T promoter polymorphisms.

In non-clinical low-risk populations 15% of infants show disorganized attachment behavior(1,2) with their caregivers in the Strange Situation,(3) a mildly stressful laboratory procedure testing infants' ability to cope with separation anxiety. Disorganization of early attachment has been primarily ascribed to inadequate parenting,(2,4,5) and has been associated with childhood behavior problems(6,7)and adolescent psychopathological tendencies.(5) We have recently reported an association between the DRD4 exon III 48 basepair repeat polymorphism and disorganization of infants' attachment behavior towards their mother in a low-social-risk group of 1-year-old infants:(8) the risk for disorganized attachment among infants carrying the 7-repeat allele was fourfold. Here we report further evidence for the involvement of the dopamine D4 receptor gene in attachment disorganization. The same group of infants was genotyped for the functional -521 C/T single nucleotide polymorphism (SNP) in the upstream regulatory region of the DRD4 gene(9) in order to test the association with attachment disorganization both alone and in interaction with the DRD4 exon III 7-repeat allele. While the -521 C/T genotype itself had no effect on attachment status (chi(2) = 0.41, df = 2, P = 0.82), there was an interaction between the structural 48-bp repeat polymorphism and the -521 C/T promoter polymorphism: the association between disorganized attachment and the 7-repeat allele was enhanced in the presence of the -521 T allele (chi(2) = 6.61 and 6.67, df = 1, P < 0.025 for CT and TT genotypes, respectively). In the presence of both risk alleles the odds ratio for disorganized attachment increased tenfold. This result supports our previous postulation that the DRD4 gene plays a role in the development of attachment behavior in low-risk, non-clinical populations.

Alleles↗
PubMed2005

High glucose-induced apoptosis in human vascular endothelial cells is mediated through NF-kappaB and c-Jun NH2-terminal kinase pathway and prevented by PI3K/Akt/eNOS pathway.

Our previous studies demonstrated that high glucose-induced apoptosis in human umbilical vein endothelial cells (HUVECs) is mediated by sequential activation of c-Jun N-terminal kinase (JNK) and caspase, and prevented by exogenous nitric oxide (NO). In this study we further elucidated the roles of the transcriptional factor NF-kappaB, phosphatidylinositol 3'-kinase (PI3K), Akt and endothelial nitric oxide synthase (eNOS) in the apoptosis of HUVECs induced by high glucose. The results showed that high glucose-induced apoptosis was significantly enhanced by PI3K inhibitors (wortmannin and LY294002), NOS inhibitor (NG-nitro-arginine methyl ester) and eNOS antisense oligonucleotide. In contrast, apoptosis was markedly reduced by NF-kappaB inhibitor (pyrrolidine dithiocarbamate, PDTC), NF-kappaB antisense oligonucleotide, NO donor (sodium nitroprusside, SNP), and overexpression of Akt. The high glucose-induced NF-kappaB activation and transient Akt phosphorylation were prevented by the presence of vitamin C. Moreover, high glucose-induced increase in eNOS expression was attenuated by PI3K inhibitors and the negative mutant of PI3K. The activity of JNK induced by high glucose was suppressed by NF-kappaB-specific antisense oligonucleotide. Taken together our results demonstrated that high glucose-induced HUVECs apoptosis is through NF-kappaB-dependent JNK activation and reactive oxygen species (ROS)-dependent Akt dephosphorylation. Activation of the ROS/PI3K/Akt/eNOS signaling pathway in early phase exerts protective effects against the induction of apoptosis by high glucose.

Androstadienes↗
PubMed2005

ABCA2 is a strong genetic risk factor for early-onset Alzheimer's disease.

Recent epidemiological, biological and genetic data indicate a relationship between cholesterol and Alzheimer's disease (AD) including the association of polymorphisms of ABCA1 (a gene that is known to participate in cholesterol and phospholipid transport) with AD prevalence. Based on these data, we postulated that genetic variation in the related and brain-specific ABCA2 gene leads to increase risk of AD. A large case-control study was conducted where the sample was randomly divided into a hypothesis-testing sample (230 cases/286 controls) and a validation sample (210 cases/233 controls). Among the 45 SNPs we tested, one synonymous SNP (rs908832) was found significantly associated with AD in both samples. Additional analyses performed on the whole sample showed a very strong association between this marker and early-onset AD (OR = 3.82, 95% C.I. = [2.00 - 7.30], P = 5 x 10(-5)). Further research is needed to understand the functional role of this polymorphism. However, together with the reported associations of AD with APOE, CYP46A1 and ABCA1, the present result adds a very significant support for the role of cholesterol and phospholipid homeostasis in AD and a rationale for testing novel cholesterol homeostasis-related therapeutic strategies in AD.

ATP-Binding Cassette Transporters↗
PubMed2005

[How about the uncertainty in the haplotypes in the population-based KORA studies?].

In the KORA surveys, numerous candidate genes in the context of type 2 diabetes, myocardial infarction, atherosclerosis or obesity are under investigation. Current focus is on genotyping single nucleotide polymorphism (SNPs). Haplotypes are also of increasing interest: haplotypes are combinations of alleles within a certain section of one chromosome. Analysing haplotypes in genetic association studies is often more efficient than studying the SNPs separately. A statistical problem in this context is the reconstruction of the phase: genotyping the SNPs determines the alleles of an individual at one particular locus of the DNA, but does not reveal which allele is located on which one of the two chromosomes. This information is required when talking about haplotypes. There are statistical approaches to identify the most likely two haplotypes of an individual given the genotypes. However, a certain error in prognosis is unavoidable. There are also errors in the genotypes. These errors are assumed to be small for one SNP but can accumulate over the SNPs involved in one haplotype and thus can induce further uncertainty in the haplotype. It is therefore the aim of our project to quantify the uncertainties in the haplotypes particularly for genes investigated in the KORA surveys. We conduct computer simulations based on the haplotypes and their frequencies observed in the KORA individuals and compare the results with simulations based on mathematical modelling of the evolutionary process ("coalescent models"). The uncertainties in the haplotypes have an impact on the search for association between genes and disease: an association may not be detected as the haplotype uncertainty obscures the haplotype frequency differences between cases and controls. It is a further aim of our project to elucidate the extent of this problem and to develop strategies for reducing it.

Adult↗
PubMed2004

Role of a KCNH2 polymorphism (R1047 L) in dofetilide-induced Torsades de Pointes.

Various drugs are reported to prolong the QT-interval on the surface ECG, thereby increasing the risk of developing a potentially fatal arrhythmia known as Torsades de Pointes (TdP). TdP case reports for these drugs have often been associated with risk factors such as overdosing, concomitant drugs and/or existing pathophysiological conditions. A few cases appear to be devoid of these factors. To determine what role genetic variation in the hERG gene plays in drug-induced arrhythmias, we screened DNA samples collected from 105 atrial-fibrillation patients treated with dofetilide for polymorphisms, seven of whom developed TdP. An uncommon missense change, R1047L, was identified in two of seven patients who experienced TdP as compared with five of 98 individuals who were free of TdP. Included in the affected individuals was the only subject homozygous for this SNP. Cellular electrophysiological studies revealed a 10-mV positive shift in the steady-state activation curve of the 1047L hERG channel stably expressed in HEK-293 cells as compared with the wild-type (WT) channel. The activation and inactivation kinetics of the 1047L current were significantly slower than the WT (P < 0.05) at given membrane potentials. A computer simulation using a rabbit ventricular myocyte model indicated that same extent of changes in the I(Kr) channel may result in an approximately 15% prolongation in the action potential duration. Our study suggests that 1047L leads to a functional impairment of the hERG channel, which may contribute to the higher incidence of TdP in 1047L carriers when challenged with a channel blocker.

Animals↗
PubMed2001

Regulation of intracellular localization of human MTH1, OGG1, and MYH proteins for repair of oxidative DNA damage.

In mammalian cells, more than one genome has to be maintained throughout the entire life of the cell, one in the nucleus and the other in mitochondria. It seems likely that the genomes in mitochondria are highly exposed to reactive oxygen species (ROS) as a result of their respiratory function. Human MTH1 (hMTH1) protein hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP, 8-oxo-dATP, and 2-hydroxy (OH)-dATP, thus suggesting that these oxidized nucleotides are deleterious for cells. Here, we report that a single-nucleotide polymorphism (SNP) in the human MTH1 gene alters splicing patterns of hMTH1 transcripts, and that a novel hMTH1 polypeptide with an additional mitochondrial targeting signal is produced from the altered hMTH1 mRNAs; thus, intracellular location of hMTH1 is likely to be affected by a SNP. These observations strongly suggest that errors caused by oxidized nucleotides in mitochondria have to be avoided in order to maintain the mitochondrial genome, as well as the nuclear genome, in human cells. Based on these observations, we further characterized expression and intracellular localization of 8-oxoG DNA glycosylase (hOGG1) and 2-OH-A/adenine DNA glycosylase (hMYH) in human cells. These two enzymes initiate base excision repair reactions for oxidized bases in DNA generated by direct oxidation of DNA or by incorporation of oxidized nucleotides. We describe the detection of the authentic hOGG1 and hMYH proteins in mitochondria, as well as nuclei in human cells, and how their intracellular localization is regulated by alternative splicing of each transcript.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Polymorphisms in exon 3 of the proopiomelanocortin gene in relation to serum leptin, salivary cortisol, and obesity in Swedish men.

The objective of the current study was to examine the potential impact of a cryptic trinucleotide repeat polymorphism in exon 3 of proopiomelanocortin (POMC) on serum leptin levels and salivary cortisol, as well as obesity and estimates of insulin, glucose, and lipid metabolism in 284 unrelated Swedish men born in 1944. Moreover, we examined if a single nucleotide polymorphism (SNP) (C-->T) in exon 3 was associated with these characteristics. The amplification of the microsatellite locus yielded a 155-bp fragment and a fragment with one additional copy of the 9-bp repeat unit GGCAGCAGC (164 bp). The allelic frequencies were 0.96 and 0.04, respectively. Tests for differences in phenotype showed that subjects with the longer polymerase chain reaction (PCR) repeat product (n = 21) had significantly higher serum leptin concentrations (P =.024) compared with subjects with the shorter PCR product (n = 230). Salivary cortisol levels, as well as obesity and its related metabolic perturbations, were the same across the POMC genotypes. In conclusion, a microsatellite polymorphism in exon 3 of POMC is associated with elevated serum leptin levels. This association might reflect variations in melanocortin expression and/or activity, because exon 3 contains, among others, the coding sequences for melanocortins.

Alleles↗
PubMed2006

The promoter region of the MDR1 gene is largely invariant, but different single nucleotide polymorphism haplotypes affect MDR1 promoter activity differently in different cell lines.

The MDR1 multidrug transporter represents one of the better characterized drug transporters that play an important role in protecting the body against xenobiotic insults. Single nucleotide polymorphisms (SNPs) and SNP haplotypes within this gene have been variously associated with differences in MDR1 expression/function, drug response as well as disease susceptibility. Nonetheless, the effect of polymorphisms at the MDR1 promoter region on its promoter activity remains less characterized. Through the examination of approximately 1.5 kilobases of MDR1 promoter region from five populations, including the Chinese, Malays, Indians, European Americans, and African Americans, we identified eight low-frequency SNPs, of which only two were polymorphic in at least four of the five populations examined. The other SNPs are mainly population-specific, the majority of which occur only in the African-American population. Recapitulation of the various combinations of SNP haplotypes in vitro in promoter-reporter assays revealed a few notable trends. The African and European American-specific haplotypes tended to result in enhanced MDR1 promoter activity only in the human embryonic kidney (HEK) 293 cell line. Haplotype GCTAACC, which occurs at variable frequencies in all the populations examined, with Asians having much lower frequencies (<2%) compared with the European Americans/African Americans (>4%), affected MDR1 promoter activity differently in different cell lines. Compared with the commonest haplotype, GCTA-ACC haplotype resulted in a significant decrease in MDR1 promoter activity in HeLa cells (P < 0.05) but a significant increase in the same promoter activity in HEK293 cells (P < 0.05). These results suggest that the MDR1 promoter region is largely invariant but that different haplotypes have differential effects on the MDR1 promoter activity in different cell lines.

Black or African American↗
PubMed2003

[Preliminary study on the association of chemokine RANTES gene polymorphisms with HIV-1 infection in Chinese Han population].

OBJECTIVE: To detect the single nucleotide polymorphism (SNP) of chemokine regulated upon activation, normal T cell expressed and secreted (RANTES) promoter and first intron of asymptomatic, human immunodeficiency virus 1 (HIV-1) infected individuals of in Han Chinese and evaluate the influence on HIV-1 infection by variants. METHODS: Case-control study was adopted, Genotypes of RANTES promoter -403 and -28 from 538 samples and RANTES first intron In1.1 from 300 samples of Han Chinese were detected by DNA sequencing or by polymerase chain reaction-restriction fragment length polymorphism. RESULTS: There were six genotypes of RANTES promoter -403 and -28 found in Han Chinese group. The distribution of genotypes was AC/AC 12.4%, AC/AG 3.5%, AC/GC 29.2%, AG/GC 10.9%, GC/GC 42.1%, AG/AG 1.5%. The haplotypes was GC 62.7%, AC 28.7%, AG 8.6%. Compared with AC/AC, Odd ratio (OR) of RANTES genotypes AC/AG, AC/GC, AG/GC, GC/GC was associated with weaker reduced susceptibility to HIV-1 infection. However, there were no significant contents of the allele frequencies between people living with HIV-1 and healthy individuals. The distribution of RANTES In1.1 alleles were T/T 71.0%, C/T 19.9%, C/C 9.1% and haplotypes were RANTES In1.1T 81%, In1.1C 19%, respectively; There were significant differences of RANTES In1.1 between people with HIV-1 infection and healthy individuals in males. The In1.1C-bearing genotypes would increase susceptibility to HIV-1 infection but no significant differences in females were found. Strong linkage disequilibrium was observed between all of the three RANTES SNPs. CONCLUSION: The two -403A/G, -28C/G variants in RANTES promoter region and intron In1.1 T/C mutation genotype were found to be associated with the genetic susceptibility to HIV-1 infection among the Han Chinese. However, the In1.1C allele or its haplotypes in RANTES intron 1 displayed a stronger dominant association with HIV-1 infection in males.

Adolescent↗
PubMed2001

High-throughput multiplex SNP genotyping with MALDI-TOF mass spectrometry: practice, problems and promise.

Single nucleotide polymorphisms (SNPs) are currently being identified and mapped at a remarkable pace, providing a rich genetic resource with vast potential for disease gene discovery, pharmacogenetics, and understanding the origins of modern humans. High-throughput, cost effective genotyping methods are essential in order to make the most advantageous and immediate use of these SNP data. We have incorporated the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) in our laboratory as a tool for differentiating genotypes based on the mass of the variant DNA sequence, and have utilized this method for production scale SNP genotyping. We have combined a 4 microl PCR amplification reaction using 3 ng of genomic DNA with a secondary enzymatic reaction (mini-sequencing) containing oligonucleotide primers that anneal immediately upstream of the polymorphic site, dideoxynucleotides, and a thermostable polymerase used to extend the PCR product by a single base pair. Mass spectrometry (MS) analysis of mini-sequencing reactions was performed using a MALDI-TOF instrument (Voyager-DE, Perseptive Biosystems, Framingham, MA). We performed both single and multiplex PCR and mini-sequencing reactions, and genotyped seven different variant sites in a random sample of 989 individuals. Genotypes generated with MS methods were compared with genotypes produced using a 5' exonuclease fluorescence-based assay (Taqman, Applied Biosystems, Foster City, CA) and a gel-based genotyping protocol. Because multiple polymorphisms can be detected in a single reaction, the MS technique provides a cost-effective and efficient method for high-throughput genotyping.

Alleles↗
PubMed2004

Characterization of porcine leptin receptor polymorphisms and their association with reproduction and production traits.

Fatness in pigs is of prime economic importance due to market incentives for production of lean pork and elevated fatness increasing the feed costs. Leptin (LEP) action, mediated through its specific receptors (LEPR), was reported to be involved in the regulation of fatness via feed intake, energy expenditure, and whole-body energy balance in pigs. In this study, we have designed 17 primer sets based on the human and mouse LEPR sequences and successfully amplified coding regions of 15 porcine LEPR exon fragments by polymerase chain reactions (PCR). Four single nucleotide polymorphisms (SNP) of Intron 2, Exons 2, 6, and 18 were found in Landrace, Yorkshire, and Duroc by mutagenetically separated-PCR (MS-PCR) and PCR-restriction fragment length polymorphisms (PCR-RFLP). Chi-square statistics was used to calculate homogeneity of genotypic frequencies of 4 gene polymorphisms for three breeds of animals. Effects of Intron 2, Exon 2, and Exon 18 polymorphisms on the reproduction trait such as litter sizes of sows were evident (p < 0.05) in Duroc and Yorkshire. There was no (p > 0.05) significant influence on the production trait of average daily gain due to four candidate gene polymorphisms in three porcine breeds. However, effects of Exon 6 and 18 polymorphisms on the production trait of backfat thickness were significant (p < 0.05) in Landrace and Yorkshire, respectively. Effects of Exon 18 polymorphisms on feed efficiency were also evident (p < 0.05) in Duroc.

Animals↗
PubMed2004

Catalog of 300 SNPs in 23 genes encoding G-protein coupled receptors.

We previously published a series of detailed maps of single nucleotide polymorphisms (SNPs) in the genomic regions of 209 gene loci encoding drug metabolizing enzymes, transporters, receptors, and other potential drug targets. In addition to the maps reported earlier, we provide here high-resolution SNP maps of 23 genes encoding G-protein coupled receptors in the Japanese population. A total of 300 SNPs were identified through screening of these loci; 83 in four adenosine receptor family genes, 45 in three adrenergic receptor family genes, 22 in three EDG receptor family genes, 29 in three melanocortin receptor family genes, 22 in two somatostatin receptor family genes, 21 in five anonymous G protein-coupled receptor family genes, and 78 in the others (AVPR1B, OXTR, and TNFRSF1A). We also discovered a total of 33 genetic variations of other types. Of the 300 SNPs, 132 (44%) appeared to be novel on the basis of comparisons with the dbSNP database of the National Center for Biotechnology Information (US) or with previous publications. The maps constructed in this study will serve as an additional resource for studies of complex genetic diseases and drug-response phenotypes to be mapped by linkage-disequilibrium association analyses.

Catalogs as Topic↗
PubMed2006

Haplotypes in cathechol-O-methyltransferase gene confer increased risk for psychosis in Alzheimer disease.

BACKGROUND: The gene encoding catechol-O-methyltransferase (COMT) has been suggested as a candidate for Alzheimer-related psychosis (AD-P) susceptibility, and an association between AD-P and a functional valine to methionine polymorphism has been reported. OBJECTIVE: The aim of this study was to assess the genetic contribution of other COMT variants to the risk of AD-P. METHODS: Two hundred and forty-six AD patients underwent clinical and neuropsychological examination as well as an evaluation of behavioural and psychiatric disturbances. They were subsequently divided into two subgroups according to the presence (AD-P) or the absence (AD-nP) of psychotic symptoms. Four single-nucleotide polymorphisms (SNPs) within COMT gene were evaluated, i.e. rs737865, rs737864, intron 1 C2754delC, and the well-known valine/methionine variant (rs4680). Analyses were performed on the single locus and pairwise disequilibrium of loci, and multi-locus haplotype. RESULTS: The individual SNP analysis confirmed an association for the valine/methionine variant with AD-P. Haplotype analyses revealed that the alleles at four loci (rs737865, rs737864, intron 1 C2754delC, rs4680) interacted to create the risk of psychosis in AD, as A-C-C-G haplotype (OR=2.08, 95% CI=1.02-4.27, P=0.044) and G-C-delC-G haplotype (OR=2.54, 95% CI=1.32-4.90, P=0.006) in respect to the most common and not-at-risk A-C-C-A haplotype which was significantly overrepresented in AD-P. CONCLUSIONS: The present findings provide evidence of COMT genetic variations' role in the susceptibility to AD-related psychosis. The observation of a haplotype effect of different polymorphisms within the COMT gene puts emphasis on the usefulness of haplotype analysis in better defining individualized genetic risk profiles in AD.

Aged↗
PubMed2004

A novel promoter polymorphism in the gene encoding complement component 5 receptor 1 on chromosome 19q13.3 is not associated with asthma and atopy in three independent populations.

BACKGROUND: The inflammatory functions of complement component 5 (C5) are mediated by its receptor, C5R1, which is expressed on bronchial, epithelial, vascular endothelial and smooth muscle cells. A susceptibility locus for murine allergen-induced airway hyper-responsiveness was identified in a region syntenic to human chromosome 19q13, where linkage to asthma has been demonstrated and where the gene encoding C5R1 is localized. OBJECTIVE: The aim of this study was to screen for novel polymorphisms in the C5R1 gene and to determine whether any identified polymorphisms are associated with asthma and/or atopy and whether they are functional. METHODS: Single-nucleotide polymorphism (SNP) detection in the gene encoding C5R1 was performed by direct sequencing. Genotyping was performed in three populations characterized for asthma and/or atopy: (1) 823 German children from The Multicenter Allergy Study; (2) 146 individuals from Tangier Island, Virginia, a Caucasian isolate; and (3) asthma case-parent trios selected from 134 families (N=783) in Barbados. Functional studies were performed to evaluate differences between the wild-type and the variant alleles. RESULTS: We identified a novel SNP in the promoter region of C5R1 at position -245 (T/C). Frequency of the -245C allele was similar in the German (31.5%) and Tangier Island (36.3%) populations, but higher in the Afro-Caribbean population (53.0%; P=0.0039 to <0.0001). We observed no significant associations between the -245 polymorphism and asthma or atopy phenotypes. Upon examination of the functional consequences of the -245T/C polymorphism, we did not observe any change in promoter activity. CONCLUSION: This new marker may provide a valuable tool to assess the risk for C5a-associated disorders, but it does not appear to be associated with asthma and/or atopy.

Asthma↗
PubMed2004

Polymorphisms of renin-angiotensin system genes with high-altitude pulmonary edema in Japanese subjects.

STUDY OBJECTIVES: The renin-angiotensin system (RAS), including angiotensin-converting enzyme (ACE) and angiotensin II type 1 receptor (AT(1)R), plays an important role in the pathogenesis of pulmonary hypertension, which is suggested to be critical in the development of high-altitude pulmonary edema (HAPE). Investigating the associations of the polymorphisms in the genes of RAS with HAPE is to elucidate the genetic background underlying this disease. DESIGN: A cross-sectional, case-control study. SETTING: Shinshu University Hospital, Matsumoto, Japan. PARTICIPANTS: Forty-nine HAPE-susceptible (HAPE-s) subjects with a history of HAPE, and 55 healthy climbers with HAPE resistance (HAPE-r). INTERVENTIONS: Twenty-one of 49 HAPE-s subjects underwent right cardiac catheterization. MEASUREMENTS AND RESULTS: The insertion/deletion polymorphism in the ACE gene (ACE-I/D) was investigated by polymerase chain reaction (PCR). There was no significant difference of the distribution of the ACE-I/D polymorphism between the HAPE-s and HAPE-r groups. The A(1166)C and G(1517)T single-nucleotide polymorphisms (SNPs) in AT(1)R gene were investigated by the PCR following digested by corresponding restricted endonuclease enzymes. The distribution of the G(1517)T SNP was significantly different between the two groups (p = 0.012). The pulmonary hemodynamics of the 21 HAPE-s subjects were retrospectively examined. The pulmonary artery pressure (PAP), pulmonary vascular resistance (PVR), and PVR index (PVRI) were all significantly increased on hospital admission. Moreover, the PVR and PVRI were significantly higher in the HAPE-s subjects with D positivity than in the HAPE-s subjects with I positivity (PVR, p = 0.015; PVRI, p = 0.028), while the PAP did not show any significant difference between the two subgroups. CONCLUSIONS: The ACE-I/D polymorphism is not associated with HAPE susceptibility in Japanese subjects. The AT(1)R gene polymorphisms may likely associate with HAPE susceptibility. The D allele of the ACE-I/D polymorphism probably contributes to the hyperresponsive PVR and PVRI to acute hypoxia.

Adult↗
PubMed2007

The G51S purine nucleoside phosphorylase polymorphism is associated with cognitive decline in Alzheimer's disease patients.

Alzheimer's disease (AD) is a polygenic and multifactorial complex disease, whose etiopathology is still unclear, however several genetic factors have shown to increase the risk of developing the disease. Purine nucleotides and nucleosides play an important role in the brain. Besides their role in neurotransmission and neuromodulation, they are involved in trophic factor release, apoptosis, and inflammatory responses. These mediators may also have a pivotal role in the control of neurodegenerative processes associated with AD. In this report the distribution of the exonic G/A single nucleotide polymorphism (SNP) in purine nucleoside phosphorylase (PNP) gene, resulting in the amino acid substitution serine to glycine at position 51 (G51S), was investigated in a large population of AD patients (n=321) and non-demented control (n=208). The PNP polymorphism distribution was not different between patients and controls. The polymorphism distribution was also analyzed in AD patients stratified according to differential progressive rate of cognitive decline during a 2-year follow-up. An increased representation of the PNP AA genotype was observed in AD patients with fast cognitive deterioration in comparison with that from patients with slow deterioration rate. Our findings suggest that the G51S PNP polymorphism is associated with a faster rate of cognitive decline in AD patients, highlighting the important role of purine metabolism in the progression of this neurodegenerative disorder.

Alleles↗
PubMed2003

FP-TDI SNP scoring by manual and statistical procedures: a study of error rates and types.

For technologies that are commonly used in ordinary laboratories such as fluorescence-polarization detection with template-directed, dye-terminator incorporation (FP-TDI), SNP genotype scoring is usually done manually. Here we study rates of errors and missing genotypes obtained with this procedure. We also introduce three statistical genotype scoring methods to examine whether they form a viable alternative. Data consisted of eight SNPs typed in about 1400 individuals from 268 pedigrees. The statistical procedures performed better on several internal criteria, such as the number of Mendelian errors, and showed much higher agreement with discrepant genotypes re-scored by two raters. The best results were obtained with the statistical procedure that incorporated information about regularities in the error structure of the FP-TDI data. We estimated that there were about 1.6% more errors if genotypes were scored manually. About 0.6% of these errors could be explained by data manipulation errors, leaving 1% as the result of possible incorrect scoring. There were 3.3% more missing genotypes in the manual scoring due to errors in data manipulation (1.7%) and conservative scoring (1.6%).

Algorithms↗
PubMed2001

The -174/-597 promoter polymorphisms in the interleukin-6 gene are not associated with susceptibility to multiple sclerosis.

Interleukin-6 (IL-6) has been implicated in the etiology of experimental autoimmune encephalomyelitis (EAE) in transgenic animals and contributes to neuropathology in humans. A single nucleotide polymorphism (SNP) at position -174 in the IL-6 gene promoter (IL-6pr) appears to influence IL-6 expression. Complete linkage disequilibrium was observed between the -174 and the -597 alleles. The aim of this study was to investigate the possible influence of -174/-597 IL-6pr polymorphisms on susceptibility to multiple sclerosis (MS). Genotyping of the -597 variant was performed by an RFLP method in 131 MS patients [88 relapsing-remitting (RR-MS), 43 secondary progressive (SP-MS)] and 157 healthy subjects. No differences were found between MS patients and controls with respect to the distribution of -597 IL-6pr genotypes. Neither was found when genotypes were analyzed according to the clinical course of the disease (RR-MS or SP-MS). Future studies focusing on complex transcriptional interactions between the IL-6pr and 3' flanking region polymorphic sites will be necessary to determine the IL-6 haplotype influence on susceptibility to MS.

Adult↗