| 41. |
- Lahermo, P, et al.
(författare)
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A quality assessment survey of SNP genotyping laboratories
- 2006
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 27:7, s. 711-714
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- To survey the quality of SNP genotyping, a joint Nordic quality assessment (QA) round was organized between 11 laboratories in the Nordic and Baltic countries. The QA round involved blinded genotyping of 47 DNA samples for 18 or six randomly selected SNPs. The methods used by the participating laboratories included all major platforms for small- to medium-size SNP genotyping. The laboratories used their standard procedures for SNP assay design, genotyping, and quality control. Based on the joint results from all laboratories, a consensus genotype for each DNA sample and SNP was determined by the coordinator of the survey, and the results from each laboratory were compared to this genotype. The overall genotyping accuracy achieved in the survey was excellent. Six laboratories delivered genotype data that were in full agreement with the consensus genotype. The average accuracy per SNP varied from 99.1 to 100% between the laboratories, and it was frequently 100% for the majority of the assays for which SNP genotypes were reported. Lessons from the survey are that special attention should be given to the quality of the DNA samples prior to genotyping, and that a conservative approach for calling the genotypes should be used to achieve a high accuracy.
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| 42. |
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| 43. |
- Lindstrom, A., et al.
(författare)
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Pyrosequencing for detection of lamivudine-resistant hepatitis B virus
- 2004
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Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 42:10, s. 4788-4795
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Tidskriftsartikel (refereegranskat)abstract
- Chronic hepatitis B virus (HBV) infection can cause severe liver disease, including cirrhosis and hepatocellular carcinoma. Lamivudine is a relatively recent alternative to alpha interferon for the treatment of HBV infection, but unfortunately, resistance to lamivudine commonly develops during monotherapy. Lamivudine-resistant HBV mutants display specific mutations in the YMDD (tyrosine, methionine, aspartate, aspartate) motif of the viral polymerase (reverse transcriptase [rt]), which is the catalytic site of the enzyme, i.e., methionine 204 to isoleucine (rtM204I) or valine (rtM204V). The latter mutation is often accompanied by a compensatory leucine-to-methionine change at codon 180 (rtL180M). In the present study, a novel sequencing method, pyrosequencing, was applied to the detection of lamivudine resistance mutations and was compared with direct Sanger sequencing. The new pyrosequencing method had advantages in terms of throughput. Experiments with mixtures of wild-type and resistant viruses indicated that pyrosequencing can detect minor sequence variants in heterogeneous virus populations. The new pyrosequencing method was evaluated with a small number of patient samples, and the results showed that the method could be a useful tool for the detection of lamivudine resistance in the clinical setting.
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| 44. |
- Magnuson, Ann, et al.
(författare)
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High-valent Ruthenium-Manganese Complexes for Solar Energy Production.
- 2001
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Ingår i: PS2001 Proceedings.
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Konferensbidrag (refereegranskat)abstract
- We present progress in the development of artificial photosynthesis, as a means to harvesting and storage of solar energy. The plan is to compose molecular systems that combine known photochemistry with emerging functional model compounds. A photochemical device for solar energy conversion contains a photosensitizer, an electron acceptor system and a donor system that prevents charge recombination. Our goal is to utilize water as sacrificial electron donor, which will allow a net production of reducing equivalents, and the ultimate production of fuel. The only light-driven molecular catalyst for water oxidation exists in Photosystem II (PSII), which has a tetranuclear Mn-cluster in the active site. Here we present several Mn-compounds, that we have developed for the purpose of creating water-oxidizing catalysts. Our idea is to link Ru-tris(bipyridine) derivatives, which mimicks the function of the primary donor in PS II, with manganese complexes, mimicking the tetra-Mn cluster on the PSII donor side. We have constructed a number of heteronuclear complexes, containing a Ru-photosensitizer and various Mn-complexes. The compounds have been characterized with regards to their photophysical and photochemical properties, redox potentials and structure. The most promising compounds are capable of undergoing several electron transfers from the Mn-complex to the photosensitizer, leaving 3 to 4 oxidizing equivalents on the Mn. In the latest development, we have constructed ligands that stabilize higher oxidation states in Mn, in order to promote formation of Mn(V) which many believes is an intermediate in the water oxidation mechanism.
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| 45. |
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| 46. |
- Mercke Odeberg, Johanna, et al.
(författare)
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UGT1A polymorphisms in a Swedish cohort and a human diversity panel, and the relation to bilirubin plasma levels in males and females
- 2006
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Ingår i: European Journal of Clinical Pharmacology. - : Springer Science and Business Media LLC. - 0031-6970 .- 1432-1041. ; 62:10, s. 829-837
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The objective of this study was to investigate the prevalence of different polymorphisms and haplotypes associated with individual variations in pharmacokinetics and drug toxicity in the uridine-diphosphate glucuronosyl transferase (UGT) 1A gene in a Swedish cohort (248 healthy volunteers) and in 14 different ethnic groups. We also estimated UGT1A genotype-dependent glucuronidation efficiency using the endogenous substrate bilirubin as an indicator. Methods: Pyrosequencing-based genotyping assays were used to determine the different polymorphisms and haplotypes. Results: Haplotype analysis of the UGT1A1 (*1*28), UGT1A6 (*1*2), and UGT1A7(*1*2*3*4) allelic variants showed that three major haplotypes constituted 84% of the allelic variants in the cohort. We identified 15 haplotypes altogether from all groups, including previously undescribed haplotypes.Testing for the association of genotype and total bilirubin levels (nonfasting) in plasma disclosed that homozygous carriers of the TA allele, irrespective of haplotype combinations, had increased levels of bilirubin compared with noncarriers, but a gender-associated difference was observed. Conclusions: In a Swedish cohort, several genetic variants in the UGT1A gene are common, but prevalence in a population may differ because of ethnicity. A phenotype based on bilirubin levels has limitations in serving as an indicator of pharmacogenetic differences in glucuronidation due to the influence of gender. Because of possible substrate overlap regarding different UGT1A isoforms, determination of haplotypes of potential cis-acting polymorphisms in the UGT1A gene should be considered in pharmacogenetic association studies regarding drugs that undergo glucuronidation.
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| 47. |
- Myrberg, T, et al.
(författare)
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Structural properties of relaxed Ge buffer layers on Si(001) : effect of layer thickness and low temperature Si initial buffer
- 2004
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Ingår i: Journal of materials science. Materials in electronics. - : Springer Science Business Media. - 0957-4522 .- 1573-482X. ; 15:7, s. 411-417
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Tidskriftsartikel (refereegranskat)abstract
- We have used the strain sensitive tool two-dimensional reciprocal space mapping (2D-RSM) and high resolution rocking curves (HR-RC) to assess the effect of the layer thickness and the influence of low temperature Si buffer on the properties of fully relaxed Ge on Si (0 0 1). The samples were grown by chemical vapor deposition in an ASM commercial reactor. As complementary measurements we have employed secondary ion mass spectrometry (SIMS) for chemical analysis, cross sectional transmission electron microscopy for quality assessment, and finally atomic force microscopy (AFM) for investigating the surface roughness. The investigated samples have a thickness ranging from 0.25 to 5.0 mum. In addition and for a 5.0 mum thick Ge layer, an initial low temperature Si (LT-Si) template was grown before the Ge epitaxy. The results indicate that high quality fully relaxed Ge layers have been achieved using the adopted growth procedure. Most of the improvement in crystalline quality was observed for Ge layers with thickness up to 1.5 mum. Above this thickness the observed crystalline quality improvement was negligible. The LT-Si buffer observed to be disadvantageous for pure relaxed Ge growth.
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| 48. |
- Odeberg, Jacob, et al.
(författare)
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A cDNA RDA protocol using solid-phase technology suited for analysis in small tissue samples.
- 2000
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Ingår i: Biomolecular Engineering. - : Elsevier BV. - 1389-0344 .- 1878-559X. ; 17:1, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- cDNA representational difference analysis (cDNA RDA) is a PCR-based subtractive enrichment procedure for the cloning of differentially expressed genes. In this study, we have further developed the procedure to take advantage of solid-phase technology, and to facilitate the use of RDA when starting material is limited. Several parameters of the PCR-based generation of cDNA representations were investigated, and a solid-phase based purification step was introduced to simplify removal of digested adapter-ends and uncleaved fragments. The use of magnetic particles increased the speed of the method, and also eliminated the risk of carry-over contamination between iterative steps of subtraction and PCR amplification. The modified protocol was evaluated in monitoring differences in gene expression in (i) a rat system consisting of livers with and without growth hormone treatment, and in (ii) a human system consisting of normal colon and colon cancer.
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| 49. |
- Peluso, Marco, et al.
(författare)
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Bulky DNA adducts, 4-aminobiphenyl-haemoglobin adducts and diet in the European Prospective Investigation into Cancer and Nutrition (EPIC) prospective study
- 2008
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Ingår i: British Journal of Nutrition. - 1475-2662 .- 0007-1145. ; 100:3, s. 489-495
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Tidskriftsartikel (refereegranskat)abstract
- In contrast to some extensively examined food mutagens, for example, aflatoxins, N-nitrosamines and heterocyclic amines, some other food contaminants, in particular polycyclic aromatic hydrocarbons (PAH) and other aromatic compounds, have received less attention. Therefore, exploring the relationships between dietary habits and the levels of biomarkers related to exposure to aromatic compounds is highly relevant. We have investigated in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort the association between dietary items (food groups and nutrients) and aromatic DNA adducts and 4-aminobiphenyl-Hb adducts. Both types of adducts are biomarkers of carcinogen exposure and possibly of cancer risk, and were measured, respectively, in leucocytes and erythrocytes of 1086 (DNA adducts) and 190 (Hb adducts) non-smokers. An inverse. statistically significant, association has been found between DNA adduct levels and dietary fibre intake (P=0.02), vitamin E (P =0.04) and alcohol (P=0.03) but not with other nutrients or food groups. Also, an inverse association between fibre and fruit intake, and BMI and 4-aminobiphenyl-Hb adducts (P=0.03, 0.04, and 0.03 respectively) was observed. After multivariate regression analysis these inverse correlations remained statistically significant, except for the correlation adducts v. fruit intake. The present study suggests that fibre intake in the usual range can modify the level of DNA or Hb aromatic adducts, but Such role seems to be quantitatively modest. Fibres could reduce the formation of DNA adducts in different manners, by diluting potential food mutagens and carcinogens in the gastrointestinal tract, by speeding their transit through the colon and by binding carcinogenic substances.
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| 50. |
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