Automatic scoring and quality assessment using accuracy bounds for FP-TDI SNP genotyping data.

BACKGROUND: Human diversity, namely single nucleotide polymorphisms (SNPs), is becoming a focus of biomedical research. Despite the binary nature of SNP determination, the majority of genotyping assay data need a critical evaluation for genotype calling. We applied statistical models to improve the automated analysis of 2-dimensional SNP data. METHODS: We derived several quantities in the framework of Gaussian mixture models that provide figures of merit to objectively measure the data quality. The accuracy of individual observations is scored as the probability of belonging to a certain genotype cluster, while the assay quality is measured by the overlap between the genotype clusters. RESULTS: The approach was extensively tested with a dataset of 438 nonredundant SNP assays comprising >150,000 datapoints. The performance of our automatic scoring method was compared with manual assignments. The agreement for the overall assay quality is remarkably good, and individual observations were scored differently by man and machine in 2.6% of cases, when applying stringent probability threshold values. CONCLUSION: Our definition of bounds for the accuracy for complete assays in terms of misclassification probabilities goes beyond other proposed analysis methods. We expect the scoring method to minimise human intervention and provide a more objective error estimate in genotype calling.

Scattering spherical voids in nanocrystalline TiO2- enhancement of efficiency in dye-sensitized solar cells.

Spherical voids as light scattering centers in nanocrystalline TiO2 films were realized with polystyrene particles of diameter 400 nm, thus enhancing the photovoltaic performance by 25% on large areas, as well as providing an indication that these films can be used with electrolytes of higher viscosity.

Automated yeast two-hybrid screening for nuclear receptor-interacting proteins.

High throughput analysis of protein-protein interactions is an important sector of hypothesis-generating research. Using an improved and automated version of the yeast two-hybrid system, we completed a large interaction screening project with a focus on nuclear receptors and their cofactors. A total of 425 independent yeast two-hybrid cDNA library screens resulted in 6425 potential interacting protein fragments involved in 1613 different interaction pairs. We show that simple statistical parameters can be used to narrow down the data set to a high confidence set of 377 interaction pairs where validated interactions are enriched to 61% of all pairs. Within the high confidence set, there are 64 novel proteins potentially binding to nuclear receptors or their cofactors. We discuss several examples of high interest, and we expect that communication of this huge data set will help to complement our knowledge of the protein interaction repertoire of this family of transcription factors and instigate the characterization of the various novel candidate interactors.

SNP genotyping on a genome-wide amplified DOP-PCR template.

With the increasing demand for higher throughput single nucleotide polymorphism (SNP) genotyping, the quantity of genomic DNA often falls short of the number of assays required. We investigated the use of degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) to generate a template for our SNP genotyping methodology of fluorescence polarization template-directed dye-terminator incorporation detection. DOP-PCR employs a degenerate primer (5'-CCGACTCGAGNNNNNNATGTGG-3') to produce non-specific uniform amplification of DNA. This approach has been successfully applied to microsatellite genotyping. We compared genotyping of DOP-PCR-amplified genomic DNA to genomic DNA as a template. Results were analyzed with respect to feasibility, allele loss of alleles, genotyping accuracy and storage conditions in a high-throughput genotyping environment. DOP-PCR yielded overall satisfactory results, with a certain loss in accuracy and quality of the genotype assignments. Accuracy and quality of genotypes generated from the DOP-PCR template also depended on storage conditions. Adding carrier DNA to a final concentration of 10 ng/microl improved results. In conclusion, we have successfully used DOP-PCR to amplify our genomic DNA collection for subsequent SNP genotyping as a standard process.

Effects of grapefruit juice and smoking on verapamil concentrations in steady state.

OBJECTIVE: Human gut wall cytochrome P(450) (CYP)3A4 is inhibited by grapefruit juice (G), whereas smoking increases CYP1A2 activity. Both enzymes contribute to verapamil biotransformation. This study was performed to quantitatively assess the effect of these factors on verapamil pharmacokinetics in steady state. METHODS: Twenty-four young healthy volunteers of both sexes (12 smokers, 12 non-smokers) participated in this randomised crossover study. Prolonged release verapamil (120 mg, Isoptin KHK) was given bid for 7 days in two periods. During days 5-7, 1 l of either G or water was coadministered daily. On day 7, concentrations of verapamil and norverapamil enantiomers were determined during one dosing interval, and model independent pharmacokinetic parameters were estimated. PR intervals were monitored for pharmacodynamics. Statistical evaluation was done essentially using bioequivalence methods. RESULTS: G significantly increased ( R, S)-verapamil the area under the concentration-time curve at steady state (AUC(tau,ss)) by a mean of 1.45-fold [90% confidence interval (CI) 1.29, 1.63] and peak plasma concentration at steady state (C(max,ss)) by 1.63-fold (90% CI 1.38, 1.91). The increase in concentrations present for ( R)- and ( S)-enantiomers was slightly greater for verapamil than for norverapamil. Smokers had significantly lower AUC(tau,ss) and C(max,ss) values than non-smokers by (means) 0.61-fold to 0.85-fold for verapamil and norverapamil enantiomers, respectively. G effects were unrelated to naringenin pharmacokinetics. Prolongation of PR intervals by G coadministration was borderline significant; an increase above 350 ms occurred in two individuals during the G period. Significantly increased urinary 6-beta-hydroxycortisol excretion by G suggests induction of hepatic CYP3A. CONCLUSIONS: Patients on verapamil treatment should abstain from grapefruit juice. Smoking habits should be considered for verapamil dosing.