| 1. |
- Almqvist, Catarina, et al.
(author)
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LifeGene - A large prospective population-based study of global relevance
- 2011
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In: European Journal of Epidemiology. - Stockholm : Springer Science and Business Media LLC. - 0393-2990 .- 1573-7284. ; 26:1, s. 67-77
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Journal article (peer-reviewed)abstract
- Studying gene-environment interactions requires that the amount and quality of the lifestyle data is comparable to what is available for the corresponding genomic data. Sweden has several crucial prerequisites for comprehensive longitudinal biomedical research, such as the personal identity number, the universally available national health care system, continuously updated population and health registries and a scientifically motivated population. LifeGene builds on these strengths to bridge the gap between basic research and clinical applications with particular attention to populations, through a unique design in a research-friendly setting. LifeGene is designed both as a prospective cohort study and an infrastructure with repeated contacts of study participants approximately every 5 years. Index persons aged 18-45 years old will be recruited and invited to include their household members (partner and any children). A comprehensive questionnaire addressing cutting-edge research questions will be administered through the web with short follow-ups annually. Biosamples and physical measurements will also be collected at baseline, and re-administered every 5 years thereafter. Event-based sampling will be a key feature of LifeGene. The household-based design will give the opportunity to involve young couples prior to and during pregnancy, allowing for the first study of children born into cohort with complete pre-and perinatal data from both the mother and father. Questions and sampling schemes will be tailored to the participants' age and life events. The target of LifeGene is to enrol 500,000 Swedes and follow them longitudinally for at least 20 years.
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| 2. |
- Chang, Ming, et al.
(author)
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CYP2C19*17 affects R-warfarin plasma clearance and warfarin INR/dose ratio in patients on stable warfarin maintenance therapy
- 2015
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In: European Journal of Clinical Pharmacology. - : Springer Science and Business Media LLC. - 0031-6970 .- 1432-1041. ; 71:4, s. 433-439
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Journal article (peer-reviewed)abstract
- We aimed to assess the influence of CYP2C19*17 on R-warfarin clearance as well as the effect of CYP2C19, CYP2C8, CYP2C9, and VKORC1 polymorphisms together with non-genetic factors on warfarin international normalized ratio (INR)/daily dose. One hundred fifty Caucasian Italian outpatients with data on steady-state plasma concentrations of S- and R-warfarin were genotyped for CYP2C19 (*2, *3, *4, *17), CYP2C9 (*2, *3), CYP2C8*3, and VKORC1*2. The statistical analysis was performed on the effect of genotypes/haplotypes, age, sex, and body weight on the clearance of warfarin enantiomers and dose-normalized INR. R-warfarin clearance was 32 % higher in carriers of CYP2C19*17 than in carriers of CYP2C19*2 (mean 2.5 mL/min, 95 % confidence interval (CI) 2.3-2.8 vs. 1.9 mL/min, 95 % CI 1.7-2.2; P (post hoc) = 0.01). Patients with CYP2C19*1/*1 genotype had an intermediate clearance (mean 2.1 mL/min, 95 % CI 1.8-2.4). The genotypes of VKORC1, CYP2C9, and CYP2C19, together with non-genetic factors (age, sex, and body weight) explained 52 % of the variability in warfarin INR/daily dose, of which CYP2C19 genotypes accounted for 7 %. This is the first study to include the gain-of-function CYP2C19*17 allele when assessing the impact of CYP2C19 polymorphisms on the clearance of warfarin enantiomers. CYP2C19 genotypes influenced the clearance of R-warfarin and contributed significantly to the variability in INR/daily dose, indirectly indicating a clinical relevance of R-warfarin.
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| 3. |
- Ghotbi, Roza, et al.
(author)
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Allele-specific expression and gene methylation in the control of CYP1A2 mRNA level in human livers
- 2009
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In: The Pharmacogenomics Journal. - : Springer Science and Business Media LLC. - 1470-269X .- 1473-1150. ; 9:3, s. 208-217
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Journal article (peer-reviewed)abstract
- The basis for interindividual variation in the CYP1A2 gene expression is not fully understood and the known genetic polymorphisms in the gene provide no explanation. We investigated whether the CYP1A2 gene expression is regulated by DNA methylation and displays allele-specific expression (ASE) using 65 human livers. Forty-eight percent of the livers displayed ASE not associated to the CYP1A2 mRNA levels. The extent of DNA methylation of a CpG island including 17 CpG sites, close to the translation start site, inversely correlated with hepatic CYP1A2 mRNA levels (P=0.018). The methylation of two separate core CpG sites was strongly associated with the CYP1A2 mRNA levels (P=0.005) and ASE phenotype (P=0.01), respectively. The CYP1A2 expression in hepatoma B16A2 cells was strongly induced by treatment with 5-aza-2'-deoxycytidine. In conclusion, the CYP1A2 gene expression is influenced by the extent of DNA methylation and displays ASE, mechanisms contributing to the large interindividual differences in CYP1A2 gene expression.
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| 4. |
- Malm, Linus, 1980-, et al.
(author)
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Metabolomic Quality Assessment of EDTA Plasma and Serum Samples
- 2016
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In: Biopreservation and Biobanking. - : Mary Ann Liebert Inc. - 1947-5535 .- 1947-5543. ; 14:5, s. 416-423
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Journal article (peer-reviewed)abstract
- Handling and processing of blood can significantly alter the molecular composition and consistency of biobank samples and can have a major impact on the identification of biomarkers. It is thus crucial to identify tools to determine the quality of samples to be used in biomarker discovery studies. In this study, a non-targeted gas chromatography/time-of-flight mass spectrometry (GC-TOFMS) metabolomic strategy was used with the aim of identifying quality markers for serum and plasma biobank collections lacking proper documentation of preanalytical handling. The effect of postcentrifugation delay was examined in serum stored in tubes with gel separation plugs and ethylenediaminetetraacetic acid (EDTA) plasma in tubes with or without gel separation plugs. The change in metabolic pattern was negligible in all sample types processed within 3 hours after centrifugation regardless of whether the samples were kept at 4 degrees C or 22 degrees C. After 8 and 24 hours postcentrifugation delay before aliquoting, there was a pronounced increase in the number of affected metabolites, as well as in the magnitude of the observed changes. No protective effect on the metabolites was observed in gel-separated EDTA plasma samples. In a separate series of experiments, lactate and glucose levels were determined in plasma to estimate the effect of precentrifugation delay. This separate experiment indicates that the lactate to glucose ratio may serve as a marker to identify samples with delayed time to centrifugation. Although our data from the untargeted GC-TOFMS analysis did not identify any specific markers, we conclude that plasma and serum metabolic profiles remain quite stable when plasma and serum are centrifuged and separated from the blood cells within 3 hours.
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| 5. |
- Qundos, Ulrika, et al.
(author)
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Profiling post-centrifugation delay of serum and plasma with antibody bead arrays
- 2013
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In: Journal of Proteomics. - : Elsevier BV. - 1874-3919 .- 1876-7737. ; 95:SI, s. 46-54
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Journal article (peer-reviewed)abstract
- Several biobanking initiatives have emerged to create extensive collections of specimen for biomedical studies and various analytical platforms. An affinity proteomic analysis with antibody suspension bead arrays was conducted to investigate the influence of the pre-analytical time and temperature conditions on blood derived samples. Serum and EDTA plasma prepared from 16 individuals was centrifuged and aliquots were kept either at 4. °C or in ambient temperature for 1. h and up to 36. h prior to first storage. Multiplexed protein profiles of post-centrifugation delay were generated in 384 biotinylated samples using 373 antibodies that targeted 343 unique proteins. Very few profiles were observed as significantly altered by the studied temperature and time intervals. Single binder and sandwich assays revealed decreasing levels of caldesmon 1 (CALD1) related to EDTA standard tubes and prolonged post-centrifugation delay of 36. h. Indications from changes in CALD1 levels require further confirmation in independent material, but the current data suggests that samples should preferentially be frozen during the day of collection when to be profiled with antibody arrays selected for this study. Biological significance: Affinity-based profiling of serum and plasma by microarray assays can provide unique opportunities for the discovery of biomarkers. It is though often not known how differences in sample handling after collection influence the downstream analysis. By profiling three types of blood preparations for alterations in protein profiles with respect to time and temperature post centrifugation, we addressed an important component in the analysis and of such specimen. We believe that this analysis adds valuable information to be considered when biobanking blood derived samples.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.
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| 6. |
- Rylander-Rudqvist, Tove, et al.
(author)
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Quality and quantity of saliva DNA obtained from the self-administrated oragene method - A pilot study on the cohort of Swedish men
- 2006
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In: Cancer Epidemiology, Biomarkers and Prevention. - Karolinska Inst, Inst Environm Med, Div Nutr Epidemiol, SE-17177 Stockholm, Sweden. Karolinska Inst, Dept Med Epidemiol & Biostat, KI Biobank, SE-17177 Stockholm, Sweden. : AMER ASSOC CANCER RESEARCH. - 1055-9965 .- 1538-7755. ; 15:9, s. 1742-1745
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Journal article (peer-reviewed)abstract
- Self-collection of saliva has the potential to provide molecular epidemiologic studies with DNA in a user-friendly way. We evaluated the new Oragene saliva collection method and requested saliva samples by mail from 611 men (ages 53-87 years). We obtained a response rate of, on average, 80% [varying from 89% (ages 67-71 years) to 71% (ages 77-87 years)]. DNA was extracted from 90 randomly selected samples, and its usefulness was evaluated with respect to quality, quantity, and whole-genome amplification (WGA). Visual inspection of DNA on agarose gels showed high molecular weight DNA (> 23 kb) and no degradation. Total DNA yield measured with PicoGreen ranged from 1.2 to 169.7 mu g, with a mean of 40.3 mu g (SD, 36.5 mu g) and a median of 29.4 mu g. Human DNA yield was estimated by real-time PCR of the human prothrombin gene to account for 68% (SD, 20%) of total DNA. We did WGA on 81 saliva DNA samples by using the GenomiPhi DNA kit and genotyped both saliva DNA and WGA DNA for 10 single-nucleotide polymorphisms randomly selected from the human genome. Overall genotyping success rate was 96% for saliva DNA and 95% for WGA DNA; 79% of saliva DNA samples and 79% of WGA DNA samples were successfully genotyped for all 10 single-nucleotide polymorphisms. For the 10 specific assays, the success rates ranged between 88% and 100%. Almost complete genotypic concordance (99.7%) was observed between saliva DNA and WGA DNA. In conclusion, Oragene saliva DNA in this study collected from men is of high quality and can be used as an alternative to blood DNA in molecular epidemiologic studies.
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| 7. |
- Shen, Qiujin, et al.
(author)
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Strong impact on plasma protein profiles by precentrifugation delay but not by repeated freeze-thaw cycles, as analyzed using multiplex proximity extension assays
- 2018
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In: Clinical Chemistry and Laboratory Medicine. - : WALTER DE GRUYTER GMBH. - 1434-6621 .- 1437-4331. ; 56:4, s. 582-594
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Journal article (peer-reviewed)abstract
- Background: A number of factors regarding blood collection, handling and storage may affect sample quality. The purpose of this study was to assess the impact on plasma protein profiles by delayed centrifugation and plasma separation and multiple freeze-thaw cycles.Methods: Blood samples drawn from 16 healthy individuals were collected into ethylenediaminetetraacetic acid tubes and kept either at 4 degrees C or 22 degrees C for 1-36 h prior to centrifugation. Plasma samples prepared 1 h after venipuncture were also subjected to two to eight cycles of freezing at -80 degrees C and thawing at 22 degrees C. Multiplex proximity extension assay, an antibody-based protein assay, was used to investigate the influence on plasma proteins.Results: Up to 36 h delay before blood centrifugation resulted in significant increases of 16 and 40 out of 139 detectable proteins in samples kept at 4 degrees C or 22 degrees C, respectively. Some increases became noticeable after 8 h delay at 4 degrees C but already after 1 h at 22 degrees C. For samples stored at 4 degrees C, epidermal growth factor (EGF), NF-kappa-B essential modulator, SRC, interleukin 16 and CD6 increased the most, whereas the five most significantly increased proteins after storage at 22 degrees C were CD40 antigen ligand (CD40-L), EGF, platelet-derived growth factor subunit B, C-X-C motif chemokine ligand 5 and matrix metallopeptidase 1 (MMP1). Only matrix metallopeptidase 7 (MMP7) decreased significantly over time and only after storage at 22 degrees C. No protein levels were found to be significantly affected by up to eight freeze-thaw cycles.Conclusions: Plasma should be prepared from blood after a limited precentrifugation delay at a refrigerated temperature. By contrast, the influence by several freeze-thaw cycles on detectable protein levels in plasma was negligible.
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| 8. |
- Simonsson, Ulrika S H, et al.
(author)
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Artemisinin autoinduction is caused by involvement of cytochrome P450 2B6 but not 2C9.
- 2003
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In: Clinical pharmacology and therapeutics. - 0009-9236 .- 1532-6535. ; 74:1, s. 32-43
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Journal article (peer-reviewed)abstract
- Our goal was to investigate whether artemisinin autoinduction is caused by an increase in cytochrome P450 (CYP) 2B6 or CYP2C9 activities, we evaluated the effects of multiple-dose artemisinin administration on S-mephenytoin N-demethylation in healthy subjects.
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| 9. |
- Tybring, Gunnel
(author)
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Enantioselective drug metabolism catalysed by the polymorphic CYP2D6 and CYP2C19 : a methodological investigation focused on mianserin, mephenytoin and omeprazole
- 1996
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Doctoral thesis (other academic/artistic)abstract
- The aim of this thesis was to develop enantioselective analytical methods and apply them to studies of oxidative metabolism of chiral drugs catalysed by the polymorphic cytochrome P450 CYP2D6 and CYP2C 19 enzymes. The work has been focused on mianserin, mephenytoin and omeprazole. The kinetics of mianserin were studied in 15 Swedish healthy volunteers after a single oral dose of 20 mg mianserin. A significant correlation was found between the metabolic ratio (MR) of debrisoquine and the area under the plasma concentration time curve (AUC~,2 h) for both mianserin and the main metabolite, desmethylmianserin. Further, chiral HPLC analysis showed that the elimination of S(+)-mianserin but not of R(-)-mianserin is catalysed by CYP2D6. The plasma concentrations of the enamtiomers of both mianserin and desmethylmianserin were studied in 66 Japanese depressed patients during mianserin treatment. A pronounced variation in plasma concentrations of the enantiomers was seen in patients treated with the same dose. In the majority of the samples, the plasma concentration of the more active S(+)-mianserin was higher than that of R(-)-mianserin. For desmethylmianserin, the R-enantiomer was the major form while the S-enantiomer was not detectable in most of the samples. The stereoselective metabolism of S,R-mephenytoin is widely used as a phenotyping test for CYP2CI9. An S-mephenytom conjugate is present in urine of extensive metabolisers (EM), but not of poor metabolisers (PM) of S-mephenytoin. This conjugate is easily hydrolysed back to S-mephenytoin, resulting in an increased urinary S/R ratio of mephenytoin. Earlier, two urine collections, (0-8 hour and 24-32 hour) were used, but this study shows that the two phenotypic groups can be separated in one single urine sample by estimating the S/R ratio before and after acid hydrolysis. The S-mephenytoin conjugate was isolated in urine from one EM and its structure was tentatively determined. The compound was isolated using several HPLC purifications. Gas chromatography, mass spectrometry and amino acid analysis showed that it is a cysteine conjugate of S-mephenytoin. The absolute structure is, however, unknown, but an S-N bond between cysteine and S-mephenytoin formed via an oxidative radical mechanism catalysed by CYP2C 19 is suggested. The use of omeprazole as a probe drug for CYP2C 19 was evaluated in 160 healthy Swedish volunteers. The MR expressed as the concentration ratio of omeprazole and hydroxyomeprazole in a plasma sample drawn 3 hours after intake of 20 mg omeprazole correlated with the urinary S/R ratio of mephenytoin. Furthermore, the phenotype determined with omeprazole agreed with the CYP2CI9 genotype with respect to the defect CYP2C19m~ and CYP2CI9m2 alleles. Enantioselective analysis of omeprazole and hydroxyomeprazole showed that the concentration of (+)-omeprazole was higher and it was eliminated at a lower rate than (-)-omeprazole in PMs while the opposite was seen jn EMs of S-mephenytoin. For hydroxyomeprazole, the (+)-enantiomer was present in much higher concentrations than the (-)-enamtiomer in EMs but not in PMs. This study shows that the CYP2CI9 catalysed hydroxylation of omeprazole is markedly stereoselective for the (+)-enantiomer. In conclusion, the studies presented in this thesis show that the variation in enzymatic activity as well as the marked enantioselectivity contribute to the pronounced variation in the rate of metabolism which is associated with pharmacogenetic polymorphisms.
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