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Results for “Genetic Variation”

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PubMed2002

Cryptogenic stroke in relation to genetic variation in clotting factors and other genetic polymorphisms among young men and women.

BACKGROUND AND PURPOSE: The purpose of the present study was to compare the prevalences of genetic polymorphisms in persons with cryptogenic stroke with those among stroke patients with evidence of large-artery occlusive disease or an unequivocal cardioembolic source (noncryptogenic stroke). METHODS: We compared the prevalences of genetic polymorphisms thought to be related to thrombi formation in young stroke patients with evidence of large-artery occlusive disease or an unequivocal cardioembolic source (noncryptogenic stroke; controls; n=79) with those in young stroke patients without such sources (cryptogenic stroke; cases; n=67). Common variations in the genes encoding factor V, prothrombin, angiotensin I-converting enzyme, 5,10-methylenetetrahydrofolate reductase, endothelial cell nitric oxide synthase, tissue plasminogen activator, plasminogen activator inhibitor-1, and fibrinogen were evaluated. We also compared the allele prevalence of these genes among all stroke patients with those among a large pool of historical controls assayed for these genes. RESULTS: None of these genetic polymorphisms was statistically significantly related to cryptogenic stroke. With respect to a comparison of all ischemic stroke with historical controls, only the prevalence of tissue plasminogen activator D allele among stroke subjects was statistically significantly higher than that of the historical controls (P=0.0014). CONCLUSIONS: These findings generally do not support the hypothesis that genes associated with a prothrombotic state are risk factors among a subgroup of young people with stroke of undetermined cause. Except for the D tissue plasminogen activator allele, the findings also indicated that these genetic factors are unrelated, or only weakly related, to all ischemic stroke.

Adult↗

PubMed2006

Genetic variation of human cytochrome p450 reductase as a potential biomarker for mitomycin C-induced cytotoxicity.

The importance of genetic variation in clinical response to various drugs is now well recognized. Identification of genetic biomarkers that can predict efficacy and toxicity of chemotherapeutic drugs in cancer patients holds great promise in treatment improvement and cost reduction. Mitomycin C (MMC) is a common anticancer drug used for the treatment of numerous types of tumors. Metabolism-mediated activation, by either one-electron or two-electron reduction, plays a critical role in the chemotherapeutic action of MMC. NADPH-cytochrome P450 (oxido)reductase (POR) is a major enzyme responsible for MMC activation through the one-electron reductive pathway, which leads to the production of semiquinone anion radicals and subsequent DNA damage in the cells. Recently, a total of six naturally occurring human POR variants with single amino acid changes (Y181D, A287P, R457H, V492E, C569Y, and V608F) have been identified. Although the catalytic efficiency of these variants in reduction of cytochrome c was reported to be altered, their capability in activating MMC, a direct substrate of POR, has not been examined. In the present study, we demonstrated that except for the C569Y variant, MMC-induced toxicity assayed as cell viability and proliferative capability was significantly decreased in the Flp-In Chinese hamster ovary cells stably expressing all the other POR variants in comparison with the cells expressing wild-type human POR. Cells expressing the V608F and Y181D variants had a complete loss of the capability to activate MMC. Our finding suggests that these functional POR genetic variations may serve as a potential biomarker to predict the chemotherapeutic response to MMC.

Animals↗

PubMed1998

Genetic variation in paraoxonase-2 is associated with variation in plasma lipoproteins in Canadian Oji-Cree.

We report studies of the association between genetic variation in PON2 and variation in plasma quantitative traits in a sample of 334 non-diabetic Oji-Cree. We detected associations between PON2 variation in codon 148 (Ala --> Gly) and variation in fasting plasma concentrations of total and low-density lipoprotein (LDL) cholesterol and apolipoprotein (apo) B. In particular, homozygotes for a PON2 allele that encoded A148 had significantly higher plasma total, LDL cholesterol and apo B than subjects having the other two genotypes (p < 0.01). Taken together, our results suggest that common genetic variation on chromosome 7q21.3-22.1 in PON2 is associated with significant variation of intermediate traits in plasma lipoprotein metabolism.

Adult↗

PubMed1995

Genetic variation in body temperature and its response to short-term acute heat stress in broilers.

Genetic variation in body temperature of broilers and its response to short-term acute (43.5 C for 45 min) heat stress was studied. Body temperatures before (T0) and after (T45) heat exposure were recorded and the changes in body temperature (T delta) were calculated for 5-wk-old chicks from 32 broiler sire families. The T0 data were utilized to rank the families as to their relative body temperature and used to conduct a one-generation divergent family selection program for high basal body temperature (H-BT) and low basal body temperature (L-BT). A control (C) line was established by random selection from the nonselected birds. There was little genetic variation in the base broiler population for body temperature, and one generation of selection for divergence in T0 did not result in differences. There were also no differences among lines in T45. Low realized heritability estimates of .09 and .17 were obtained for T0 in the L-BT and H-BT lines. Phenotypic correlations between body temperature and body weight were very low for all groups. Highly significant negative correlations were observed between T0 and T delta after heat exposure. The T0 fluctuated during the course of each day and between days. The adjustment of the data to eliminate this variation did not result in increased heritability estimates.

Animals↗

PubMed2007

Joint analysis of the influence of CYP11B1 and DGAT1 genetic variation on milk production, somatic cell score, conformation, reproduction, and productive lifespan in German Holstein cattle.

Recent publications indicate genetic variation in milk production traits on proximal BTA14, which cannot be explained solely with genetic variation in the DGAT1 gene. To elucidate these QTL effects, animals from a German Holstein granddaughter design (18 families, 1,291 sons) were genotyped for CYP11B1 (V30A) and DGAT1 (K232A) polymorphisms. Frequencies of alleles of maternal descent were estimated for CYP11B1(V) (0.776) and DGAT1(K) (0.549). Allele substitution effects (alpha/2) were first calculated for both alleles in separate models and then in a joint model. From the joint analysis, CYP11B1(V) effects on fat content (+0.04%) and protein content (+0.01%) were positive. Effects on milk yield (-82 kg), fat yield (-0.5 kg), and protein yield (-1.9 kg) were negative. Compared with the individual analysis, DGAT1(K) effects on fat content (+0.28%), protein content (+0.06%), and milk yield (-258 kg) were reduced; fat yield (+10.8 kg) was enhanced; and protein yield (-3.8 kg) was reduced. In the joint analysis, allele substitution effects of CYP11B1(V) and DGAT1(K) together explained more of the variation in milk production traits than DGAT1(K) alone. Further significant effects were found for CYP11B1(V) and DGAT1(K) among 6 reproduction traits and 14 conformational traits. These observations indicate a possible negative influence of DGAT1(K) on maternal nonreturn rate, and thus, on length of productive life.

Animals↗

PubMed2006

Genetic variations of the NR3C1 gene in children with sporadic nephrotic syndrome.

Previous studies have demonstrated that the genetic variations of glucocorticoid receptor gene (NR3C1) are associated with both familial steroid resistance and acquired steroid resistance in some diseases, such as Cushing's disease, leukemia, lupus nephritis, and female pseudohermaphroditism. In this study, we examined the genetic variations of NR3C1 in 35 children with sporadic steroid-resistant nephrotic syndrome (SRNS), and in 83 cases with sporadic steroid-sensitive NS (SSNS) using polymerase chain reaction, denaturing high-performance liquid chromatography and DNA sequencing, and analyzed possible associations between NR3C1 variants and steroid resistance in sporadic NS. No causative mutations were found; however, six previously identified and six novel polymorphisms, 1206C > T, 1374A > G, 2382C > T, 2193T > G, IVS7-68_-63delAAAAAA, and IVS8-9C > G, were detected. Two novel haplotypes, [1374A > G; IVS7-68_-63delAAAAAA; IVS8-9C > G; 2382C > T] and [1896C > T; 2166C > T; 2430T > C], of NR3C1 were also identified in sporadic NS and controls. The odds ratios (95% Confidence Interval) for the two novel NR3C1 haplotypes in the sporadic nephrotic children at risk of steroid resistance were 4.970 (0.889-27.788) and 2.194 (0.764-6.306), respectively, but the association between NR3C1 haplotypes and steroid resistance was not significant. Further studies on the possible association between the two novel NR3C1 haplotypes and steroid resistance in sporadic NS in larger cohorts are required.

Adolescent↗

PubMed2001

Genetic variation at minisatellite loci D1S7, D4S139, D5S110 and D17S79 among three population groups of eastern India.

Genetic variation at four minisatellite loci D1S7, D4S139, D5S110 and D17S79 in three predominant population groups of eastern India, namely Brahmin, Kayastha and Garo, are reported in this study. The Brahmin and Kayastha are of Indo-Caucasoid origin while the Garo community represents the Indo-Mongoloid ethnic group. The methodology employed comprised generation of HaeIII-restricted fragments of isolated DNA, Southern blotting, and hybridization using chemiluminescent probes MS1, pH30, LH1 and V1 for the four loci. All four loci were highly polymorphic in the population groups. Heterozygosity values for the four loci ranged between 0.68 and 0.95. Neither departure from Hardy Weinberg expectations nor evidence of any association across alleles among the selected loci was observed. The gene differentiation value among the loci is moderate (GST = 0.027). A neighbour-joining tree constructed on the basis of the generated data shows very low genetic distance between the Brahmin and Kayastha communities in relation to the Garo. Our results based on genetic distance analysis are consistent with results of earlier studies based on serological markers and linguistic as well as morphological affiliations of these populations and their Indo-Caucasoid and Indo-Mongoloid origin. The minisatellite loci studied here were found to be not only useful in showing significant genetic variation between the populations but also to be suitable for human identity testing among eastern Indian populations.

Asian People↗

PubMed2004

Genetic variation at NNRTI resistance-associated positions in patients infected with HIV-1 subtype C.

OBJECTIVE: Genetic differences between subtypes of HIV-1, even when not associated with key resistance mutations, are known to affect baseline susceptibility to specific antiretroviral drugs and resistance-development pathways. We studied the prevalence and patterns of non-nucleoside reverse transcriptase inhibitor (NNRTI)-associated mutations in HIV-1 subtype C-infected patients. METHOD: We analysed the genetic variation at sites associated with NNRTI and nucleoside reverse transcriptase inhibitor resistance in subtype C- versus B-infected patients, both drug-naive and -experienced. We extended the comparison to subtype B records from the Stanford database. RESULTS: A total of 150 subtype B and 341 subtype C-infected patients were studied. No significant differences were found in treatment and clinical parameters between the groups. In NNRTI-naive patients, changes in NNRTI positions were present in 9.3% of subtype B- versus 33.1% of subtype C-infected patients (P < 0.001). Differences were seen in both drug-naive (subtype B, 10.0% versus subtype C, 50.1%; P < 0.021) and drug-experienced NNRTI-naive patients (subtype B, 9.0% versus subtype C, 23.8%; P < 0.001). In NNRTI experienced patients, the number of A98G/S changes was significantly higher in subtype C patients treated with either efavirenz or nevirapine (P < 0.0001), and V106M was higher in efavirenz-treated subtype C-infected patients (P < 0.0001). The average mutation rates were 1.26 and 1.67 per patient for subtypes B and C, respectively (P = 0.036). The frequency of nucleoside associated mutations, but not M184V, in treated patients was significantly higher in subgroup B-infected patients (P = 0.028). CONCLUSION: Collectively, these data indicate that genetic variation at NNRTI resistance-associated positions such as V106M and A98S is substantially greater in subtype C-infected patients than in subtype B-infected patients. The natural structure of each subtype probably affects the frequency and pattern of drug resistance mutations selected under treatment.

Adult↗

PubMed1996

Genetic variation in Sri Lanka.

A population genetic study was designed to analyze genetic composition and population structure of the five main population groups (Sinhalese, Tamils, Moors, Burghers, and Malays) of Sri Lanka. Twentyseven polymorphic and three monomorphic loci were examined in all five populations. Several genetic markers, including subtype variation of HP, TF, PI, GC, ORM, and PGM1, were analyzed for the first time and helped to clarify the range of genetic variation for Sri Lankan populations. Many genetic systems (Rh, JK, ACP, ESD, HP, C3, TF, and GC) showed a high level of variation among the populations of Sri Lanka. However, at the individual level the Burgher population (a hybrid group between the Dutch and Portuguese and the local Sinhalese) showed European features, but its gene frequencies were either intermediate to its parental populations or more similar to the local Sinhalese. In the F statistic analysis all populations showed positive FIS values, ranging from 0.0305 in the Burghers to 0.1084 in the Malays; however, for a large number of loci the FIS values for the Burghers were negative, indicating the possible hybrid nature of this population. In genetic affinity studies the Burghers, Moors, and Malays showed a greater degree of isolation, but compared with the possible populations of their origin, the five populations of Sri Lanka tended to show some degree of affinity to each other. Our analysis therefore suggests that there is little evidence of disruptive selection; however, restricted gene flow favors the change of allele frequency toward the local Sinhalese and Tamil populations.

Ethnicity↗

PubMed2003

Genetic variation within and among infrapopulations of the marine digenetic trematode Lecithochirium fusiforme.

Allozyme markers were used to study genetic variation in Lecithochirium fusiforme within a natural population of Conger conger. Six of 16 enzyme-coding loci studied were found to be polymorphic. These loci were surveyed in 12 infrapopulations of adult flukes. High levels of genetic variation were detected (P = 0.375); Ho = 0.048; He = 0.085). However, the population did not conform to Hardy-Weinberg expectations, as it showed a significant deficit of heterozygotes. L. fusiforme also exhibited low differentiation between infrapopulations (FST = 0.064). Despite significant linkage disequilibrium at Pgm-1 and Pgm-2 (P < 0.05), mating system does not appear to be the principal reason for the deficit of heterozygotes detected, because some polymorphic loci were in Hardy-Weinberg equilibrium. Association between FIS and FST statistics suggests the existence of the Wahlund effect. However, all infrapopulations showed a strong deficit of heterozygotes for most polymorphic loci (FIS = 0.409). Detection of significant genetic differentiation among temporal samples and the existence of paratenic hosts in the life-cycle suggests the Wahlund effect, caused by the mixture of genetically distinct temporal samples in the infrapopulations. Occasional temporal gene flow also might explain the high estimated genetic polymorphism.

Animals↗

PubMed2006

Genetic variation and phylogeography of the swordtail fish Xiphophorus cortezi (Cyprinodontiformes, Poeciliidae).

Swordtail fish have been studied extensively in relation to diverse aspects of biology; however, little attention has been paid to the patterns of genetic variation within and among populations of swordtails. In this study, we sequenced the mtDNA control region from 65 individuals and 10 populations of Xiphophorus cortezi to investigate the genetic variation within and among populations, including tests for correlations between genetic and geographic distances and tests for species monophyly. We found low gene and nucleotide diversity within populations and high degrees of genetic differentiation among populations. Significant and positive correlations between genetic distance and both river and straight-line geographic distance indicate that genetic differentiation among X. cortezi populations can be explained, to some extent, by an isolation-by-distance model and provide evidence of stream capture. Phylogenetic analyses suggest that X. cortezi is paraphyletic relative to X. malinche, raising questions concerning the status of these taxa as separate species.

Animals↗

PubMed1994

Genetic variation in parameters reflecting immune competence of swine.

Genetic variation in total and differential white blood cell (WBC) counts, phagocytic capacity of polymorphonuclear leukocytes (PMNL), virus induced interferon-alpha (IFN-alpha) production, mitogen induced proliferation and interleukin 2 (IL-2) production of mononuclear cells (MNC) in vitro was studied in blood collected from 124 Yorkshire piglets, aged 8 weeks. The piglets were the offspring from 12 sires and 31 dams. Data from an earlier experiment, including 96 piglets of seven sires and 24 dams, were added when estimating heritabilities for Con A induced proliferation and IL-2 production. The highest heritability (h2 = 0.87 +/- 0.41) was estimated for the total number of PMNL. Medium high heritabilities (h2 = 0.3-0.4) were estimated for the phagocytic capacity of PMNL, Con A induced proliferation and IL-2 production and the total number of WBC, while the heritability estimates were lower (h2 = 0.00-0.08 +/- 0.12) for the total number of lymphocytes, serum concentrations of Ig and IFN-alpha production. Pronounced differences between litters from various dams were found for total number of lymphocytes, IFN-alpha production, Con A induced proliferation and IL-2 production. The Con A induced proliferation was positively correlated (r = 0.48, P < 0.001) with the IL-2 production and both these parameters were correlated (r = 0.44 and 0.37, respectively, P < 0.001) to the virus induced IFN-alpha production. Despite these positive correlations, no parental offspring group was uniformly superior across all traits measured. However, the heritabilities estimated for the immune parameters are sufficiently high to be used as genetic markers in selection for general immune competence of swine.

Animals↗

PubMed2007

Comprehensive evaluation of genetic variation in the IGF1 gene and risk of prostate cancer.

Insulin-like growth factor-I (IGF1) stimulates cell proliferation, decreases apoptosis, and has been implicated in cancer development. Epidemiological studies have shown elevated levels of circulating IGF1 to be associated with increased risk of prostate cancer. To what extent genetic variation in the IGF1 gene is related to prostate cancer risk is largely unknown. We performed a comprehensive haplotype tagging (HT) assessment of single nucleotide polymorphisms (SNPs) representing the common haplotype variation in the IGF1 gene. We genotyped 10 SNPs (9 haplotype tagging SNPs (htSNPs)) within Cancer Prostate in Sweden (CAPS), a case-control study of 2,863 cases and 1,737 controls, in order to investigate if genetic variation in the IGF1 gene is associated with prostate cancer risk. Three haplotype blocks were identified across the IGF1 gene and 9 SNPs were selected as haplotype tagging SNPs. Common haplotypes in the block covering the 3' region of the IGF1 gene showed significant global association with prostate cancer risk (p = 0.004), with one particular haplotype giving an odds ratio of 1.46 (95% CI = 1.15-1.84, p = 0.002). This haplotype had a prevalence of 5% in the study population. Our results indicate that common variation in the IGF1 gene, particularly in the 3' region, may affect prostate cancer risk. Further studies on genetic variations in the IGF1 gene in relation to prostate cancer risk as well as to circulating levels of IGF1 are needed to confirm this novel finding.

Case-Control Studies↗

PubMed1991

Genetic variation in Con A-induced production of interleukin 2 by porcine peripheral blood mononuclear cells.

Genetic variation in concanavalin A (Con A)-induced proliferation and interleukin 2 (IL-2) production by peripheral blood mononuclear cells (PBMC) was studied in blood collected from 96 piglets, aged 7 weeks. The piglets were the offspring of seven sires and 24 dams. Pronounced differences between litters from various dams were observed in the immune parameters measured. Also, large individual differences in the magnitudes of Con A-induced proliferation and IL-2 production were seen for PBMC collected from individual pigs within each litter. Both the time course and magnitude of IL-2 activity showed genetic variation, as results from the offspring of the seven sires differed significantly. However, only the time course, not the magnitude, of proliferation differed among the offspring groups. It was possible to establish a rank order for the sires based on the IL-2 production of PBMC by their offspring. As IL-2 has a key role in regulating the immune response, mitogen-induced IL-2 activity seems to be a good candidate as a general marker for cell-mediated immunity in pigs.

Animals↗

PubMed2006

Genetic variation and covariation for resistance and tolerance to Cucumber mosaic virus in Mimulus guttatus (Phrymaceae): a test for costs and constraints.

Genetic variation for resistance and tolerance to pathogens may be maintained by costs represented as genetic tradeoffs between these traits and fitness. The evolution of resistance and tolerance also may be constrained by negative genetic correlations between these defense systems. Using a complete diallel, we measured genetic variation and covariation for and among performance, resistance, and tolerance traits in Mimulus guttatus challenged with a generalist pathogen, Cucumber mosaic virus (CMV). Viral coat protein was detected by enzyme-linked immunosorbent assay (ELISA) in all inoculated plants, indicating that all plants were susceptible to infection, although the ELISA absorbance varied quantitatively across plants. Plants inoculated with CMV had significantly reduced aboveground biomass and flower production relative to controls, although date of first flower was unaffected by infection. All three of these performance traits showed moderate to high narrow-sense heritability (h2 = 0.32-0.62) in both inoculated and control plants. We found phenotypic variation for both tolerance of and resistance to our strain of CMV, but both displayed very low narrow-sense heritability (h2 < 0.03). We found no evidence of a trade-off between resistance and tolerance. We also found no evidence for a cost of resistance or tolerance. In fact, a significant genetic correlation suggested that plants that were large when healthy had the greatest tolerance when infected. Significant, positive genetic correlations found between performance of uninfected and infected plants suggested that selection would likely favor the same M. guttatus genotypes whether CMV is present or not.

Biological Evolution↗

PubMed2001

Geographical patterns of genetic variation in two species of Stylosanthes Sw. using amplified fragment length polymorphism.

Understanding the extent and distribution of genetic diversity within a species is essential for the development of effective conservation strategies. The objective of this study was to assess genetic variation using amplified fragment length polymorphisms (AFLP) in two species of the tropical legume genus Stylosanthes Sw. Annual, S. humilis (2n = 20) and perennial, S. viscosa (2n = 20) are found throughout tropical America, and are sympatric for much of their range of distribution. One hundred and eleven accessions, covering a wide geographical range, were selected for AFLP analysis. Binary data matrices derived from DNA banding patterns were analysed using the software programs NTSYS-PC and ARLEQUIN. Several accessions were found to be misidentified. Of the S. humilis accessions, the overall average similarity value was (0.72) slightly higher than the value obtained for S. viscosa (0.67). Cluster analysis and principal coordinate analysis grouped accessions from both species by geographical origin, with a few exceptions. Analysis of molecular variance (AMOVA) in S. humilis revealed 59.4% of the variation among groups formed from the cluster analysis. This was highly significant (P < 0.001). For S. viscosa AMOVA also revealed more variation among than within groups (66.5%). This was also highly significant (P < 0.001). The majority of accessions of both species conserved ex situ are of Brazilian and Venezuelan origin. This study has identified areas in Central America and Mexico for which novel genetic variation may be found and where conservation activities should be focused.

Evolution, Molecular↗

PubMed2006

Genetic variation in the visfatin gene (PBEF1) and its relation to glucose metabolism and fat-depot-specific messenger ribonucleic acid expression in humans.

CONTEXT AND OBJECTIVE: Visfatin is a peptide suggested to play a role in glucose homeostasis. In the present study, we investigated the role of genetic variation in the visfatin gene in the pathophysiology of obesity/type 2 diabetes mellitus (T2DM). DESIGN: The visfatin gene (PBEF1) was sequenced in DNA samples from 24 nonrelated Caucasian subjects. Identified genetic variants were used for association analyses of T2DM in a case-control study (503 diabetic subjects and 476 healthy controls) and T2DM-related traits in 626 nondiabetic subjects. The effect of genetic variation in the visfatin gene on its mRNA expression in a subgroup of 157 nondiabetic subjects with measurements of visfatin mRNA expression in visceral and sc fat depots was also analyzed. RESULTS: Seven single-nucleotide polymorphisms (SNPs) and one insertion/deletion were identified. Three SNPs (rs9770242, -948G-->T, rs4730153) that were representatives of their linkage disequilibrium groups were genotyped in Caucasians from Germany with a wide range of body fat distribution and insulin sensitivity for association analyses. No association of T2DM with any of the genotyped SNPs or their haplotypes was found. However, the ratio of visceral/sc visfatin mRNA expression was associated with all three genetic polymorphisms (P < 0.05). Moreover, the -948G-->T variant was associated with 2-h plasma glucose and fasting insulin concentrations (P < 0.05) in nondiabetic subjects. CONCLUSIONS: In conclusion, our data suggest that genetic variation in the visfatin gene may have a minor effect on visceral and sc visfatin mRNA expression profiles but does not play a major role in the development of obesity or T2DM.

Adipose Tissue↗

PubMed2000

Comparing sensory experiences across individuals: recent psychophysical advances illuminate genetic variation in taste perception.

Modern psychophysics has traveled considerably beyond the threshold measures that dominated sensory studies in the first half of this century. Current methods capture the range of perceived intensity from threshold to maximum and promise to provide increasingly accurate comparisons of perceived intensities across individuals. The application of new psychophysical tools to genetic variation in taste allowed us to discover supertasters, individuals who live in particularly intense taste worlds. Because of the anatomy of the taste system, supertasters feel more burn from oral irritants like chili peppers, more creaminess/ viscosity from fats and thickeners in food and may also experience more intense oral pain. Not surprisingly, these sensory differences influence food choices and thus health. A discussion of the milestones on the road to understanding genetic variation in taste must include discussion of some potholes as well. Often our failures have been as instructive as our successes in the effort to evaluate the impact of genetic variation in taste.

Genetic Variation↗