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PubMed1999

Systems properties of the Haemophilus influenzae Rd metabolic genotype.

Haemophilus influenzae Rd was the first free-living organism for which the complete genomic sequence was established. The annotated sequence and known biochemical information was used to define the H. influenzae Rd metabolic genotype. This genotype contains 488 metabolic reactions operating on 343 metabolites. The stoichiometric matrix was used to determine the systems characteristics of the metabolic genotype and to assess the metabolic capabilities of H. influenzae. The need to balance cofactor and biosynthetic precursor production during growth on mixed substrates led to the definition of six different optimal metabolic phenotypes arising from the same metabolic genotype, each with different constraining features. The effects of variations in the metabolic genotype were also studied, and it was shown that the H. influenzae Rd metabolic genotype contains redundant functions under defined conditions. We thus show that the synthesis of in silico metabolic genotypes from annotated genome sequences is possible and that systems analysis methods are available that can be used to analyze and interpret phenotypic behavior of such genotypes.

Cell Division↗
PubMed2003

Investigation on biovars and genotypes of Ureaplasma urealyticum in the cervix in a Chinese gynecologic check-up population and sex workers.

Ureaplasma urealyticum is a causative agent of non-gonococcal urethritis and is implicated in the pathogenesis of several other diseases. However, U. urealyticum is also frequently found in the normal genitourinary tract. To characterize the distribution pattern of biovars and genotypes in normal physical check-up women and in sex workers, cervical swabs taken from 261 physical check-up clients and 98 sex workers were cultured. Positive cultures were further biotyped and genotyped by PCR. The data indicate that a) U. urealyticum is more frequently isolated in sex workers than in physical check-up women (p < 0.001); b) infection with only one genotype (genotype 1, 3 or 6) of biovar 1 is frequently found in physical check-up women; c) biovar 2 infection and mixed infection caused by more than one genotype of biovar 1 are more prevalent in sex workers than in physical check-up women (p < 0.001 and p < 0.01, respectively); d) no difference in distribution of genotype 1, 3 and 6 of biovar 1 is found between sex workers and physical check-up women (p = 0.396); e) the PCR method described here is relatively simple, rapid and specific for the biotyping between biovar 1 and 2 and genotyping of genotypes 1, 3, 6, and 14 in biovar 1.

Adult↗
PubMed2000

A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data.

The identification of genes contributing to complex diseases and quantitative traits requires genetic data of high fidelity, because undetected errors and mutations can profoundly affect linkage information. The recent emphasis on the use of the sibling-pair design eliminates or decreases the likelihood of detection of genotyping errors and marker mutations through apparent Mendelian incompatibilities or close double recombinants. In this article, we describe a hidden Markov method for detecting genotyping errors and mutations in multilocus linkage data. Specifically, we calculate the posterior probability of genotyping error or mutation for each sibling-pair-marker combination, conditional on all marker data and an assumed genotype-error rate. The method is designed for use with sibling-pair data when parental genotypes are unavailable. Through Monte Carlo simulation, we explore the effects of map density, marker-allele frequencies, marker position, and genotype-error rate on the accuracy of our error-detection method. In addition, we examine the impact of genotyping errors and error detection and correction on multipoint linkage information. We illustrate that even moderate error rates can result in substantial loss of linkage information, given efforts to fine-map a putative disease locus. Although simulations suggest that our method detects </=50% of genotyping errors, it generally flags those errors that have the largest impact on linkage results. For high-resolution genetic maps, removal of the errors identified by our method restores most or nearly all the lost linkage information and can be accomplished without generating false evidence for linkage by removing incorrectly identified errors.

Alleles↗
PubMed2000

Intrauterine cytomegalovirus infection and glycoprotein B genotypes.

Cytomegalovirus (CMV) strains display polymorphisms for the gene encoding glycoprotein B (gB; gpUL55). Recent data suggest that the gB genotype may influence the outcome of acquired CMV infections. To determine whether the gB genotype also contributes to the outcome of intrauterine infection, CMV strains were studied from 56 infants with culture-confirmed intrauterine CMV infections who were born in Iowa or Texas. CMV gB genotypes were compared with the neonatal clinical features and neurodevelopmental outcomes. Fifty-three strains (95%) could be assigned a gB genotype. The overall distribution of genotypes was as follows: type 1, 50%; type 2, 18%; type 3, 23%; and type 4, 4%. Strains with the gB 3 genotype were more common among the Iowa infants (P=.082). The gB 3 genotype was more common among infants with asymptomatic infections (P=.004), but geographic location and ascertainment biases may have accounted for these differences. The gB genotypes did not correlate with the neurodevelopmental outcome of intrauterine infection.

Cytomegalovirus↗
PubMed2004

Effect of hepatitis C virus (HCV) genotype on HCV and HIV-1 disease.

The relationship between hepatitis C virus (HCV) genotype and HCV and human immunodeficiency virus (HIV) type 1 disease is not well defined. The present study analyzed data from a cohort of 207 HIV-1-infected and 126 HIV-1-uninfected children and adolescents with hemophilia who enrolled in the Hemophilia Growth and Development Study and were followed for 7 years. The mean HCV RNA level was higher in the participants in the HCV genotype 1 group than in the participants the HCV non-genotype 1 group, among both the HIV-1-infected (difference, +0.33 log(10) copies/mL; P=.038) and HIV-1-uninfected (difference, +0.59 log(10) copies/mL; P=.008) participants. Although HCV genotype was not associated with differences in HIV-1 RNA level, a significantly lower mean CD4(+) T cell count (difference, -127 cells/ microL; P=.026) and percentage of CD4(+) T cells (difference, -4.3%; P=.027) were observed in the participants in the HCV genotype 1 group, compared with those in the participants in the HCV non-genotype 1 group. In addition, the participants in the HCV genotype 1 group were at increased risk for progression to AIDS-related mortality (hazard ratio, 2.44; P=.037). The present study suggests that HCV infection and genotype may influence the natural history of HCV and HIV-1 disease.

Acquired Immunodeficiency Syndrome↗
PubMed2006

Liver enzyme elevation in hepatitis C virus (HCV)-HIV-coinfected patients prior to and after initiating HAART: role of HCV genotypes.

Transaminase elevation is frequently seen in hepatitis C virus (HCV)-HIV-coinfected patients receiving antiretroviral therapy (ART), representing an increase in the immune response against HCV and being one of the mechanisms proposed to be involved. There is a report claiming that HCV genotype 3 is an independent risk factor. Our objectives were to assess the incidence of liver toxicity in an HIV-HCV-coinfected population with relatively preserved cellular immunity, and the role of HCV genotypes in the elevation of liver enzymes, both at baseline and after initiating ART. All HIV(+) patients with positive anti-HCV serology and CD4(+) cell counts above 100/mm(3) who began triple ART were identified, and their HCV-RNA levels and HCV genotype were determined. Liver enzymes were determined at baseline and bimonthly during follow-up. Of anti-HCV patients 147 were included, 128 (87.1%) of whom had detectable plasma HCV-RNA. HCV-1 and HCV-4 genotypes were found to confer an increased probability of having at baseline transaminases within normal limits over the other genotypes. Severe transaminase elevations (grades 3 and 4) occurred in 5/124 patients (4.0%), all with high pre-HAART ALT and positive HCV-RNA levels. Multivariate analysis showed that patients with genotype HCV-3 had a 3.27 times higher risk of developing HAART-related transaminase elevations of any grade. In conclusion, subjects with the HCV-1 genotype more often had transaminases within normal limits at baseline. The incidence of severe transaminase elevation after initiating ART was very low (4%) in this HIV(+) population with relatively preserved cellular immunity. HCV genotype 3 was identified as a risk factor for the development of transaminase elevation of any grade.

Adult↗
PubMed2005

Influence of apolipoprotein E genotype on fat-soluble plasma antioxidants in Spanish children.

BACKGROUND: Apolipoprotein (apo) E is a major determinant of plasma lipid concentrations, which in turn influence the plasma concentrations of various fat-soluble vitamins. OBJECTIVE: We aimed to analyze the effect of APOE genotype on fat-soluble antioxidant concentrations in children. DESIGN: A total of 926 healthy boys and girls aged 6-8 y were selected from 4 cities in Spain. APOE genotyping was carried out, and plasma concentrations of lipids, apolipoproteins, and lipid-soluble antioxidants were measured. RESULTS: Plasma lipid concentrations were strongly influenced by APOE genotype. The mean plasma concentration of alpha-tocopherol was 21.3 micromol/L, which is one of the highest values ever reported for a population of children. Although plasma concentrations of alpha-tocopherol, gamma-tocopherol, lycopene, and alpha-carotene varied significantly between subjects with different APOE genotypes, most of these differences disappeared after adjustment for lipoprotein-related covariates. Nevertheless, tocopherol concentrations remained elevated in individuals with the E2/2 genotype. Multivariate regression analysis showed interactions of APOE genotype with triacylglycerol and apo B in determining alpha-tocopherol concentrations. When subjects were stratified according to major apo E groups, apo B appeared to be the most important predictor of alpha-tocopherol concentrations in all groups, whereas triacylglycerol was identified only in carriers of the E2 allele. CONCLUSIONS: The association between APOE genotype and lipophilic antioxidant concentrations is dependent mainly on the effect of the polymorphism on lipoprotein concentrations. However, triacylglycerol plays a role in determining the variability of alpha-tocopherol concentrations in E2 carriers only. This suggests that the alpha-tocopherol content in each lipoprotein class varies according to APOE genotype.

Analysis of Variance↗
PubMed1999

Hepatitis C virus genotypes and quantification of serum hepatitis C RNA in liver transplant recipients. Relationship with histologic outcome of recurrent hepatitis C.

The reasons for wide variations in the severity of recurrent hepatitis C after liver transplantation are unclear. We studied liver transplant recipients to assess the effect of hepatitis C virus (HCV) genotype and HCV RNA quantification on histologic progression of recurrent hepatitis C after transplantation. Twenty-five patients underwent transplantation for HCV cirrhosis and were followed up with virologic and histologic assessments for a mean of 51 months. HCV genotype was determined by line probe assay. HCV RNA was quantitated in serum samples by nested polymerase chain reaction. The HCV genotype 1 was detected in 17 patients and other genotypes in 8. Acute lobular hepatitis developed in 17 patients 162 days posttransplantation on average. Long-term biopsy specimens (mean, 51 months after the date of liver transplantation; range, 24-86 months) showed chronic hepatitis in 19 patients (mild, 5; moderate, 9; and severe, 5, 2 with extensive scarring). The serum alanine aminotransferase level was correlated with hepatocyte necrosis (piecemeal and lobular) but not with portal inflammation or fibrosis. Patients infected with genotype 1 had a higher Knodell score, and the 5 patients with severe hepatitis C all were infected with genotype 1. HCV RNA levels were significantly higher in patients with genotype 1 than in patients with other genotypes, as were the severity of histologic recurrence and levels of viral replication.

Adult↗
PubMed2002

The development of potential screens based on shoot calcium and iron concentrations for the evaluation of tolerance in Egyptian genotypes of white lupin (Lupinus albus L.) to limed soils.

European cultivars of white lupin (Lupinus albus L.) grow poorly in limed or calcareous soils. However, Egyptian genotypes are grown successfully in highly calcareous soil and show no stress symptoms. To examine their physiological responses to alkaline soil and develop potential screens for tolerance, three experiments were conducted in limed and non-limed (neutral pH) soil. Measurements included net CO2 uptake, and the partitioning of Fe2+ and Fe3+ and soluble and insoluble Ca in stem and leaf tissue. Intolerant plants showed clear symptoms of stress, whereas stress in the Egyptian genotypes and in L pilosus Murr. (a tolerant species) was less marked. Only the intolerant plants became chlorotic and this contributed to their reduced net CO2 uptake in the limed soil. In contrast, Egyptian genotypes and L pilosus showed no change in net CO2 uptake between the soils. The partitioning of Ca and Fe either resulted from the stress responses, or was itself a stress response. L pilosus and some Egyptian genotypes differed in soluble Ca concentrations compared with the intolerant cultivars, although no significant difference was apparent in the Ca partitioning of the Egyptian genotype Giza 1. In a limed soil, Giza 1 maintained its stem Fe3+ concentration at a level comparable with that of plants grown in non-limed soil, whereas stem [Fe3+] of an intolerant genotype increased. Gizal increased the percentage of plant Fe that was Fe2+ in its leaf tissue under these conditions; that of the intolerant genotype was reduced. The potential tolerance of the Egyptian genotypes through these mechanisms and the possibility of nutritional-based screens are discussed.

Adaptation, Physiological↗
PubMed2006

SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.

MOTIVATION: The technology to genotype single nucleotide polymorphisms (SNPs) at extremely high densities provides for hypothesis-free genome-wide scans for common polymorphisms associated with complex disease. However, we find that some errors introduced by commonly employed genotyping algorithms may lead to inflation of false associations between markers and phenotype. RESULTS: We have developed a novel SNP genotype calling program, SNiPer-High Density (SNiPer-HD), for highly accurate genotype calling across hundreds of thousands of SNPs. The program employs an expectation-maximization (EM) algorithm with parameters based on a training sample set. The algorithm choice allows for highly accurate genotyping for most SNPs. Also, we introduce a quality control metric for each assayed SNP, such that poor-behaving SNPs can be filtered using a metric correlating to genotype class separation in the calling algorithm. SNiPer-HD is superior to the standard dynamic modeling algorithm and is complementary and non-redundant to other algorithms, such as BRLMM. Implementing multiple algorithms together may provide highly accurate genotyping calls, without inflation of false positives due to systematically miss-called SNPs. A reliable and accurate set of SNP genotypes for increasingly dense panels will eliminate some false association signals and false negative signals, allowing for rapid identification of disease susceptibility loci for complex traits. AVAILABILITY: SNiPer-HD is available at TGen's website: http://www.tgen.org/neurogenomics/data.

Algorithms↗
PubMed2002

Influence of GSTM1 and GSTT1 genotypes on sister chromatid exchange induction by styrene in cultured human lymphocytes.

Glutathione S-transferases M1 (GSTM1) and T1 (GSTT1) are polymorphically expressed in humans; about 47% and 13% of Finns lack the GSTM1 and GSTT1 activity due to homozygous deletion of the respective genes (null genotypes). We previously observed that GSTT1 null genotype was associated with increased induction of sister chromatid exchanges (SCEs) by a metabolite of styrene, styrene-7,8-oxide, in human lymphocyte cultures, while GSTM1 genotype had no effect. In the present study, we examined the potential effect of these genotypes on SCE induction by the parent compound styrene. Seventy-two hour whole-blood lymphocyte cultures from 24 healthy human donors, representing all different combinations of these genotypes, were examined. In agreement with our earlier findings, styrene was an efficient inducer of SCEs in cultures of all donors. In two separate experiments, the mean number of SCEs/cell induced by 1.5 mM styrene was 1.55 times (P = 0.011) or 1.34 times (P = 0.015) higher in subjects lacking both GSTM1 and GSTT1 than in subjects having both genes. Donors null for only one of the genes showed intermediate SCE induction by styrene. At 0.5 mM styrene, no clear differences in SCE rates among the genotypes were seen. Our results suggest that the concurrent lack of the GSTM1 and GSTT1 genes increases the genotoxic effects of styrene in human cells. The discrepant findings obtained for the importance of GSTM1 genotype in modulating the genotoxic effects induced by styrene-7,8-oxide and styrene may reflect a difference between a direct treatment with styrene-7,8-oxide and its formation from styrene in the cells. Although glutathione conjugation is a minor route in styrene detoxification in human liver in vivo, individual sensitivity associated with GSTM1 and GSTT1 null genotypes may be important locally in blood circulation and in blood-forming organs.

Cells, Cultured↗
PubMed2004

Reduced nucleotide excision repair and GSTM1-null genotypes influence anti-B[a]PDE-DNA adduct levels in mononuclear white blood cells of highly PAH-exposed coke oven workers.

It is important to identify the potential genetic-susceptible factors that are able to modulate individual responses to exposure to carcinogenic polycyclic aromatic hydrocarbons (PAHs). In the present study we evaluated the influence of four polymorphisms of nucleotide excision repair (NER) genes [xeroderma pigmentosum-C (XPC)-PAT +/-, xeroderma pigmentosum-A (XPA) 5' non-coding region-A23G, XPD-exon 23 A35931C Lys751Gln, xeroderma pigmentosum-D (XPD)-exon 10 G23591A Asp312Asn] and that of glutathione S-transferase mu1 (GSTM1-active or -null) on benzo[a]pyrene diol epoxide (B[a]PDE)-DNA adduct levels from the lympho-monocyte fraction (LMF) of highly PAH benzo[a]pyrene (B[a]P)-exposed Polish coke oven workers (n = 67, 67% current smokers) with individual urinary post-shift excretion of 1-pyrenol exceeding the proposed biological exposure index (BEI) (2.28 micromol/mol creatinine). The bulky (+/-)-r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene (anti-B[a]PDE)-DNA adduct levels were detected by high-performance liquid chromatography (HPLC)/fluorescence analysis and genotypes by polymerase chain reaction. We found that workers with the low DNA repair capacity of XPC-PAT+/+ and XPA-A23A genotypes had significantly increased anti-B[a]PDE-DNA adduct levels (Mann-Whitney U-test, z = 2.24, P = 0.02 and z = 2.65, P = 0.01). Moreover, DNA adducts were also raised in workers without GSTM1 activity (GSTM1-null genotype) (Mann-Whitney U-test, z = 2.25, P = 0.0246). Workers with unfavourable XPC-PAT+/+ and XPA-A23A NER genotypes, alone (approximately 65% of workers) or combined with GSTM1-null genotype (approximately 75% of workers) were in the tertile with the highest adduct level, i.e. >4.11 adducts/10(8) nt (chi2 = 5.85, P = 0.0156 and chi2 = 5.40, P = 0.01). The increase in anti-B[a]PDE-DNA adduct levels (ln values) was significantly related in a multiple linear regression analysis to PAH exposure (i.e. urinary post-shift excretion of 1-pyrenol) (t = 2.61, P = 0.0115), lack of GSTM1 activity (t = 2.41, P = 0.0192) and to low DNA repair capacity of the XPC-PAT+/+ genotype (t = 2.34, P = 0.0226). The influence of the XPA-A23A genotype was not evident in this statistical analysis, and no associations with XPD polymorphisms, dietary habits or tobacco smoking were found. The modulation of anti-B[a]PDE-DNA adducts in the LMF by GSTM1-null and some low-activity NER genotypes may be considered as a potential genetic susceptibility factor capable of modulating individual responses to PAH (B[a]P) genotoxic exposure and the consequent risk of cancer in coke oven workers.

Benzopyrenes↗
PubMed2005

MGMT genotype modulates the associations between cigarette smoking, dietary antioxidants and breast cancer risk.

O(6)-methylguanine DNA methyl-transferase (MGMT) is the only known critical gene involved in cellular defense against alkylating agents in the DNA direct reversal repair (DRR) pathway. Three single nucleotide polymorphism (SNP) coding for non-conservative amino acid substitutions have been identified [C250T (Leu84Phe), A427G (Ile143Val) and A533G (Lys178Arg)]. To examine the importance of the DRR pathway in risk for breast cancer and the potential interaction with cigarette smoking and dietary antioxidants, we genotyped for these variants using biospecimens from the Long Island Breast Cancer Study Project. Genotyping was performed by a high throughput assay with fluorescence polarization and included 1067 cases and 1110 controls. Overall, there was no main effect between any variant genotype, haplotype or diplotype and breast cancer risk. Heavy smoking (>31 pack-year) significantly increased breast cancer risk for women with the codon 84 variant T-allele [odds ratio, OR = 3.0, 95% confidence interval (95% CI) = 1.4-6.2]. An inverse association between fruits and vegetables consumption and breast cancer risk was observed among women with the wild-type genotype for codon 84 (OR = 0.8, 95% CI = 0.6-0.9 for > or =35 servings of fruits and vegetables per week and CC genotype versus those with <35 servings per week and CC genotype). The association between fruits and vegetables consumption and reduced breast cancer risk was apparent among women with at least one variant allele for codon 143 (OR = 0.6, 95% CI = 0.5-0.9 for > or =35 servings of fruits and vegetables per week and AG or GG genotype versus those with <35 servings per week and AA genotype). Similar patterns were observed for dietary alpha-carotene and supplemental beta-carotene, but not for supplemental vitamins C and E. These data suggest that polymorphisms in MGMT may modulate the inverse association previously observed between fruits and vegetables consumption, dietary antioxidants and breast cancer risk, and support the importance of fruits and vegetables on breast cancer risk reduction.

Adult↗
PubMed1997

Alcohol dehydrogenase 3 genotype and risk of oral cavity and pharyngeal cancers.

BACKGROUND: The consumption of alcoholic beverages is a strong risk factor for cancers of the oral cavity and pharynx (oral cancers). Alcohol dehydrogenase type 3 (ADH3) metabolizes ethanol to acetaldehyde, a carcinogen. We evaluated whether individuals homozygous for the fast-metabolizing ADH3(1) allele (ADH3[1-1]) have a greater risk of developing oral cancer in the presence of alcoholic beverage consumption than those with the slow-metabolizing ADH3(2) allele (ADH3[1-2] and ADH3[2-2]). METHODS: As part of a population-based study of oral cancer conducted in Puerto Rico, the ADH3 genotypes of 137 patients with histologically confirmed oral cancer and of 146 control subjects (i.e., individuals with no history of oral cancer) were determined by molecular genetic analysis of oral epithelial cell samples. Risks were estimated by use of multiple logistic regression analyses. RESULTS: Compared with nondrinkers with the ADH3(1-1) genotype, consumers of at least 57 alcoholic drinks per week with the ADH3(1-1), ADH3(1-2), and ADH3(2-2) genotypes had 40.1-fold (95% confidence interval [CI] = 5.4-296.0), 7.0-fold (95% CI = 1.4-35.0), and 4.4-fold (95% CI = 0.6-33.0) increased risks of oral cancer, respectively; the risk associated with the ADH3(1-1) genotype, compared with the ADH3(1-2) and ADH3(2-2) genotypes combined, was 5.3 (95% CI = 1.0-28.8) among such drinkers. Considering all levels of alcohol consumption, the risk of oral cancer per additional alcoholic drink per week increased 3.6% (95% CI = 1.9%-5.4%) for subjects with the ADH3(1-1) genotype and 2.0% (95% CI = 0.9%-3.0%) for subjects with the ADH3(1-2) or ADH3(2-2) genotype (two-sided P = .04). CONCLUSIONS: The ADH3(1-1) genotype appears to substantially increase the risk of ethanol-related oral cancer, thus providing further evidence for the carcinogenicity of acetaldehyde.

Aged↗
PubMed2005

CYP2D6 genotype, antidepressant use, and tamoxifen metabolism during adjuvant breast cancer treatment.

BACKGROUND: The efficacy of tamoxifen therapy for the treatment of breast cancer varies widely among individuals. Plasma concentrations of the active tamoxifen metabolite endoxifen are associated with the cytochrome P450 (CYP) 2D6 genotype. We examined the effects of concomitant use of selective serotonin reuptake inhibitor antidepressants, which are CYP2D6 enzyme inhibitors commonly prescribed to treat hot flashes in women who take tamoxifen, and genotypes for genes that encode tamoxifen-metabolizing enzymes on plasma concentrations of tamoxifen and its metabolites. METHODS: Eighty patients with newly diagnosed with breast cancer who were beginning tamoxifen therapy (20 mg/day orally), 24 of whom were taking CYP2D6 inhibitors, were genotyped for common alleles of the CYP2D6, CYP2C9, CYP3A5, and sulfotransferase (SULT) 1A1 genes. Plasma concentrations of tamoxifen and its metabolites were measured after 1 and 4 months of tamoxifen therapy. Differences in plasma concentrations of tamoxifen and its metabolites between genotype groups were analyzed by the Wilcoxon rank sum test. All statistical tests were two-sided. RESULTS: Among all women, plasma endoxifen concentrations after 4 months of tamoxifen therapy were statistically significantly lower in subjects with a CYP2D6 homozygous variant genotype (20.0 nM, 95% confidence interval [CI] = 11.1 to 28.9 nM) or a heterozygous genotype (43.1 nM, 95% CI = 33.3 to 52.9 nM) than in those with a homozygous wild-type genotype (78.0 nM, 95%CI = 65.9 to 90.1 nM) (both P = .003). Among subjects who carried a homozygous wild-type genotype, the mean plasma endoxifen concentration for those who were using CYP2D6 inhibitors was 58% lower than that for those who were not (38.6 nM versus 91.4 nM, difference = -52.8 nM, 95% CI = -86.1 to -19.5 nM, P = .0025). The plasma endoxifen concentration was slightly reduced in women taking venlafaxine, a weak inhibitor of CYP2D6, whereas the plasma endoxifen concentration was reduced substantially in subjects who took paroxetine (a potent inhibitor of CYP2D6). Genetic variations of CYP2C9, CYP3A5, or SULT1A1 had no statistically significant associations with plasma concentrations of tamoxifen or its metabolites. CONCLUSION: Interactions between CYP2D6 polymorphisms and coadministered antidepressants and other drugs that are CYP2D6 inhibitors may be associated with altered tamoxifen activity.

Adult↗
PubMed2004

Genotypic variation of the response to cadmium toxicity in Pisum sativum L.

This work evaluates the (cor-)relations between selected biochemical responses to toxic Cd and the degree of Cd sensitivity in a set of pea genotypes. Ten genotypes were analysed that differ in their growth response to Cd when expressed as root or shoot tolerance indices (TIs). Concentrations of non-protein thiols (NPTs) and malondialdehyde (MDA), activity of chitinase, peroxidase (POX), and catalase significantly increased in all pea genotypes treated with Cd. Cd-sensitivity of genotypes was correlated with relative increases in MDA concentration as well as activities of chitinase and POX, suggesting similar Cd stress effects. Activities of ascorbate peroxidase (APX) decreased, but concentrations of glutathione (GSH) increased in the less Cd-sensitive genotypes. Differences in root and leaf contents of Cd revealed no correlation with TI, metabolic parameters, and enzyme activities in Cd-treated plants, respectively, except that shoot Cd concentration positively correlated with shoot chitinase activity. Toxic Cd levels inhibited uptake of nutrient elements such as P, K, S, Ca, Zn, Mn, and B by plants in an organ- and genotype-specific manner. Cd-sensitivity was significantly correlated with decreased root Zn concentrations. The results show both similarities, as well as distinct features, in Cd toxicity expression in genotypes of one species, suggesting that independent and multi-factorial reactions modulate Cd sensitivity on the low-tolerance level of plants. The study illustrates the biochemical basis of earlier detected genotypic variation in Cd response.

Ascorbate Peroxidases↗
PubMed2002

High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology.

The feasibility of large-scale genome-wide association studies of complex human disorders depends on the availability of accurate and efficient genotyping methods for single nucleotide polymorphisms (SNPs). We describe a new platform of the invader assay, a biplex assay, where both alleles are interrogated in a single reaction tube. The assay was evaluated on over 50 different SNPs, with over 20 SNPs genotyped in study cohorts of over 1500 individuals. We assessed the usefulness of the new platform in high-throughput genotyping and compared its accuracy to genotyping results obtained by the traditional monoplex invader assay, TaqMan genotyping and sequencing data. We present representative data for two SNPs in different genes (CD36 and protein tyrosine phosphatase 1beta) from a study cohort comprising over 1500 individuals with high or low-normal blood pressure. In this high-throughput application, the biplex invader assay is very accurate, with an error rate of <0.3% and a failure rate of 1.64%. The set-up of the assay is highly automated, facilitating the processing of large numbers of samples simultaneously. We present new analysis tools for the assignment of genotypes that further improve genotyping success. The biplex invader assay with its automated set-up and analysis offers a new efficient high-throughput genotyping platform that is suitable for association studies in large study cohorts.

Biotechnology↗
PubMed1995

Genotype distribution and transmission of hepatitis C virus (HCV) in French haemodialysed patients.

BACKGROUND: HCV genotyping was performed to identify the source of HCV infection in haemodialysed patients. METHODS: Specimens from 48 HCV-infected patients treated in the same dialysis unit were genotyped by line probe assay (LiPA). RESULTS: Thirty-seven patients (77%) were infected by genotype 1b. Only four of the 48 patients were never transfused and three of them had genotype 1b. In two of the three genotype 1b-infected patients, seroconversion was observed during the follow-up , suggesting a nosocomial HCV infection. Ten of the 44 transfused patients were infected with genotypes other than 1b. Blood products were very probably the source of infection in these patients. The 34 other patients (77.3%) were infected with genotype 1b and retrospective analysis failed to identify nosocomial and transfusional origin. Eight of the 11 patients with genotypes different from 1b were found in the 16 patients who were more than 55 years old. Only three of the eight originated from France. CONCLUSION: Blood transfusions and nosocomial infections were the main causes of HCV transmission in haemodialysed patients. Both screening of blood donors and aseptic measures in haemodialysis units may prevent HCV transmission.

Adult↗