Home About us Contact
|
Home About us Contact | ||
|
|
||
Screening Techniques (screening + techniques)
Selected AbstractsMultistage analysis strategies for genome-wide association studies: summary of group 3 contributions to Genetic Analysis Workshop 16GENETIC EPIDEMIOLOGY, Issue S1 2009Rosalind J. Neuman Abstract This contribution summarizes the work done by six independent teams of investigators to identify the genetic and non-genetic variants that work together or independently to predispose to disease. The theme addressed in these studies is multistage strategies in the context of genome-wide association studies (GWAS). The work performed comes from Group 3 of the Genetic Analysis Workshop 16 held in St. Louis, Missouri in September 2008. These six studies represent a diversity of multistage methods of which five are applied to the North American Rheumatoid Arthritis Consortium rheumatoid arthritis case-control data, and one method is applied to the low-density lipoprotein phenotype in the Framingham Heart Study simulated data. In the first stage of analyses, the majority of studies used a variety of screening techniques to reduce the noise of single-nucleotide polymorphisms purportedly not involved in the phenotype of interest. Three studies analyzed the data using penalized regression models, either LASSO or the elastic net. The main result was a reconfirmation of the involvement of variants in the HLA region on chromosome 6 with rheumatoid arthritis. The hope is that the intense computational methods highlighted in this group of papers will become useful tools in future GWAS. Genet. Epidemiol. 33 (Suppl. 1):S19,S23, 2009. © 2009 Wiley-Liss, Inc. [source] Low proportion of whole exon deletions causing phenylketonuria in Denmark and Germany,,HUMAN MUTATION, Issue 2 2007Lisbeth Birk Møller Abstract Phenylketonuria (PKU) is an autosomal recessive genetic disorder caused by mutations of the gene encoding phenylalanine hydroxylase (PAH). More than 500 different PAH mutations have been identified and about 90% of these are single base mutations. Although the identification rate of the PAH mutations is generally very high, some variants remain unidentified. A fraction of these mutations are the result of genomic deletions or duplications, which are not recognized with standard PCR-based methods. Here we present the results of exon deletion or duplication analysis in a total of 34 families, in which two mutations had not been identified using conventional diagnostic screening techniques. Using multiplex ligation-dependent probe amplification (MLPA), we found a deletion covering exon 1 and exon 2 (c.1-?_168+?del) in one patient, a deletion of exon 3 (c.169-?_352+?del) in four patients, and a deletion of exon 5 (c.442-?_509+?del) in two patients. A deletion was thus detected in about 20% (7/34) of the families tested. Out of a combined cohort of 570 independent PKU patients from Denmark and Germany, exon deletions were identified in a total of four patients. The estimated allelic frequency of exon deletions in PKU patients in these two populations is therefore below 0.5%. © 2007 Wiley-Liss, Inc. [source] An algorithm for thorough background subtraction from high-resolution LC/MS data: application for detection of glutathione-trapped reactive metabolitesJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 9 2008Haiying Zhang Abstract A control sample background-subtraction algorithm was developed for thorough subtraction of background and matrix-related signals in high-resolution, accurate mass liquid chromatography/mass spectrometry (LC/MS) data to reveal ions of interest in an analyte sample. This algorithm checked all ions in the control scans within a specified time window around the analyte scan for potential subtraction of ions found in that analyte scan. Applying this method, chromatographic fluctuations between runs were dealt with and background and matrix-related signals in the sample could be thoroughly subtracted. The effectiveness of this algorithm was demonstrated using four test compounds, clozapine, diclofenac, imipramine, and tacrine, to reveal glutathione (GSH)-trapped reactive metabolites after incubation with human liver microsomes supplemented with GSH (30 µM compound, 45-min incubation). Using this algorithm with a ± 1.0 min control scan time window, a ± 5 ppm mass error tolerance, and appropriate control samples, the GSH-trapped metabolites were revealed as the major peaks in the processed LC/MS profiles. Such profiles allowed for comprehensive and reliable identification of these metabolites without the need for any presumptions regarding their behavior or properties with respect to mass spectrometric detection. The algorithm was shown to provide superior results when compared to several commercially available background-subtraction algorithms. Many of the metabolites detected were doubly charged species which would be difficult to detect with traditional GSH adduct screening techniques, and thus, some of the adducts have not previously been reported in the literature. Copyright © 2008 John Wiley & Sons, Ltd. [source] Study of peptide,sugar non-covalent complexes by infrared atmospheric pressure matrix-assisted laser desorption/ionizationJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 7 2004Christopher E. Von Seggern Abstract Infrared atmospheric pressure matrix-assisted laser desorption/ionization quadrupole ion trap mass spectrometry was applied to the study of siglec binding to oligosaccharide ligands. Peptides were designed to mimic the binding sites of three members of the siglec family: sialoadhesin, MAG and CD22. These peptides were tested for their ability to complex with their carbohydrate ligands 3, -sialyllactose (3,SL) and 6, -sialyllactose (6,SL). All peptides demonstrated the ability to bind to the carbohydrates, with the peptide representing sialoadhesin maintaining its binding specificity for 3,SL in preference to 6,SL. This technique can be used to study other protein,sugar interactions and can be expanded to create high-throughput screening techniques. Copyright © 2004 John Wiley & Sons, Ltd. [source] Specific interaction between Sam68 and neuronal mRNAs: Implication for the activity-dependent biosynthesis of elongation factor eEF1AJOURNAL OF NEUROSCIENCE RESEARCH, Issue 1 2009Julien Grange Abstract In cultured hippocampal neurons and in adult brain, the splicing regulatory protein Sam68 is partially relocated to the somatodendritic domain and associates with dendritic polysomes. Transfer to the dendrites is activity-dependent. We have investigated the repertoire of neuronal mRNAs to which Sam68 binds in vivo. By using coimmunoprecipitation and microarray screening techniques, Sam68 was found to associate with a number of plasticity-related mRNA species, including Eef1a1, an activity-responsive mRNA coding for translation elongation factor eEF1A. In cortical neuronal cultures, translation of the Eef1a1 mRNA was strongly induced by neuronal depolarisation and correlated with enhanced association of Sam68 with polysomal mRNAs. The possible function of Sam68 in Eef1a1 mRNA utilization was studied by expressing a dominant-negative, cytoplasmic Sam68 mutant (GFP-Sam68,C) in cultured hippocampal neurons. The level of eEF1A was lower in neurons expressing GFP-Sam68,C than in control neurons, supporting the proposal that endogenous Sam68 may contribute to the translational efficiency of the Eef1a1 mRNA. These findings are discussed in the light of the complex, potentially crucial regulation of eEF1A biosynthesis during long-term synaptic change. © 2008 Wiley-Liss, Inc. [source] Rapid Screening Method of Cassava Cultivars for Resistance to Colletotrichum gloeosporioides f.sp. manihotisJOURNAL OF PHYTOPATHOLOGY, Issue 1 2002C. N. FOKUNANG An in vitro method for assessing cassava anthracnose disease (CAD) resistance was developed as a preliminary screen to a CAD-resistant breeding programme. Potato dextrose agar (PDA) media was amended by extracts from the stem cortex of 10 cassava cultivars (30001; 30572, 30211, 88/02549, 88/00695, 88/01336, 91/00344, 91/00313, 91/00684 and 91/00475), and assayed for efficacy of inhibition of the growth of Colletotrichum gloeosporioides f. sp. manihotis isolates (05FCN, 10FCN, 12FCN, and 18FCN). Morphological and physiological data indicated that there was a significant difference (P , 0.05), in mycelial growth, spore germination and sporulation among the four isolates on PDA amended with cassava stem extracts. Extracts from cassava cultivars 30211, 91/00684 and 91/00313 showed higher inhibition of germ tube development, mycelial growth and sporulation of the fungal isolates, whereas cultivars 88/02549 and 88/01336 showed the least inhibition. The 10 cultivars were further tested in both greenhouse and field conditions, under disease pressure for two planting seasons, to corroborate resistance to the fungus as observed in vitro. Greenhouse and field trials with the 10 cassava cultivars showed a significant difference (P , 0.05) in CAD resistance. Cultivars 88/02549 and 88/01336 were highly CAD-susceptible, as shown in the in vitro assays and confirmed in the greenhouse and field tests. The other eight cultivars were either resistant (30211, 91/00684), or moderately resistant (30572, 88/00695, 91/00475, 91/00344, 30001 and 91/00313) to CAD. The study shows that an in vitro screening assay of cassava for resistance to CAD could serve as a convenient preliminary screening technique to discriminate CAD-resistant from CAD-susceptible cassava cultivars. The in vitro screening method considerably reduces time and labour in comparison with the current screening techniques of cassava, which involve field planting, inoculation and evaluation. [source] An efficient use of the WATERGATE W5 sequence for observing a ligand binding with a protein receptorMAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2008Kazuo Furihata Abstract An efficient pulse sequence for observing a ligand binding with a receptor has been developed by incorporating the WATERGATE W5 sequence. In the conventional water ligand observed via gradient spectroscopy (WaterLOGSY) techniques, the water resonance is selectively excited using,e.g. the double-pulsed field gradient spin,echo (DPFGSE) sequence at the initial portion of pulse sequence. In the current version, the modified WATERGATE W5 sequence is incorporated at the initial portion of the pulse sequence, and the resonance at the water frequency can be selectively reserved by the modified WATERGATE W5 sequence. The efficiency of ligand-observed NMR screening techniques has been demonstrated using the human serum albumin (HSA),tryptophan complex. Copyright © 2008 John Wiley & Sons, Ltd. [source] Maternal age-specific fetal loss rates in Down syndrome pregnanciesPRENATAL DIAGNOSIS, Issue 6 2006George M. Savva Abstract Objectives Pregnancies affected by Down syndrome (DS) have a greater risk of spontaneous fetal loss than those that are unaffected. In this article, we investigate the relationship between maternal age and the risk of spontaneous fetal loss in DS pregnancies. Methods Fetal loss at different maternal ages were estimated by survival analysis using follow-up of 5177 prenatally diagnosed cases. The maternal age effect on loss rate was subsequently confirmed by a re-analysis of published comparisons of the maternal age-specific prevalence of DS at different gestational ages. Results The average fetal loss rate between the time of chorionic villus sampling (CVS) and term was 32% (95% CI: 26,38), increasing from 23% (95% CI: 16,31) for women aged 25 to 44% (33,56) for women aged 45. The average fetal loss rate between the time of amniocentesis and term was 25% (21,31), increasing from 19% (14,27) to 33% (26,45) across the same age range. Conclusion The fetal loss rate in DS pregnancies increases with maternal age, and this has consequences when estimating the live birth prevalence of DS in the presence of prenatal diagnosis and termination, and when assessing the performance of prenatal screening techniques. Copyright © 2006 John Wiley & Sons, Ltd. [source] Sequence variation at the human ABO locusANNALS OF HUMAN GENETICS, Issue 1 2002S. P. YIP The ABO blood group is the most important blood group system in transfusion medicine. Since the ABO gene was cloned and the molecular basis of the three major alleles delineated about 10 years ago, the gene has increasingly been examined by a variety of DNA-based genotyping methods and analysed in detail by DNA sequencing. A few coherent observations emerge from these studies. First, there is extensive sequence heterogeneity underlying the major ABO alleles that produce normal blood groups A, B, AB and O when in correct combination with other alleles. Second, there is also extensive heterogeneity underlying the molecular basis of various alleles producing ABO subgroups such as A2, Ax and B3. There are over 70 ABO alleles reported to date and these alleles highlight the extensive sequence variation in the coding region of the gene. A unifying system of nomenclature is proposed to name these alleles. Third, extensive sequence variation is also found in the non-coding region of the gene, including variation in minisatellite repeats in the 5, untranslated region (UTR), 21 single nucleotide polymorphisms (SNPs) in intron 6 and one SNP in the 3, UTR. The haplotypes of these variations reveal a specific relationship with the major ABO alleles. Fourth, excluding the common alleles, about half of the remaining alleles are due to new mutations and the other half can better be explained by intragenic recombination (both crossover and gene conversion) between common alleles. In particular, the recombination sites in hybrid alleles can be quite precisely defined through haplotype analysis of the SNPs in intron 6. This indicates that recombination is equally as important as point mutations in generating the genetic diversity of the ABO locus. Finally, a large number of ABO genotyping methods are available and are based on restriction analysis, allele specific amplification, mutation screening techniques or their combinations. [source] High-throughput screening techniques for rapid PEG-based precipitation of IgG4 mAb from clarified cell culture supernatantBIOTECHNOLOGY PROGRESS, Issue 3 2010Carol Knevelman Abstract Locating optimal protein precipitation conditions for complex biological feed materials is problematic. This article describes the application of a series of high-throughput platforms for the rapid identification and selection of conditions for the precipitation of an IgG4 monoclonal antibody (mAb) from a complex feedstock using only microliter quantities of material. The approach uses 96-microwell filter plates combined with high-throughput analytical methods and a method for well volume determination for product quantification. The low material, time and resource requirements facilitated the use of a full factorial Design of Experiments (DoE) for the rapid investigation into how critical parameters impact the IgG4 precipitation. To aid the DoE, a set of preliminary range-finding studies were conducted first. Data collected through this approach describing Polyethylene Glycol (PEG) precipitation of the IgG4 as a function of mAb concentration, precipitant concentration, and pH are presented. Response surface diagrams were used to explore interactions between parameters and to inform selection of the most favorable conditions for maximum yield and purification. PEG concentrations required for maximum yield and purity were dependant on the IgG4 concentration; however, concentrations of 14 to 20% w/v, pH 6.5, gave optimal levels of yield and purity. Application of the high-throughput approach enabled 1,155 conditions to be examined with less than 1 g of material. The level of insights gained over such a short time frame is indicative of the power of microwell experimentation in allowing the rapid identification of appropriate processing conditions for key bioprocess operations. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source] Photoscreening for diabetic retinopathy: a comparison of image quality between film photography and digital imagingCLINICAL & EXPERIMENTAL OPHTHALMOLOGY, Issue 4 2004Christina MC Klais MD Abstract Purpose:,Retinal images from patients attending an urban screening centre before and after the transition from film photography to digital image acquisition were analysed for quality of image. Methods:,A total of 1946 diabetic patients, aged 12,92 years (mean 55.6 ± 14.88 years), were included in this retrospective study of retinal screening techniques. Each imaging group was subdivided into age-matched groups. In all subjects pupils were pharmacologically dilated before photography. The images were reviewed by the same three experienced observers and graded at the time of screening from grade 1 (excellent quality) to grade 4 (unreadable). Results:,Of 938 patients in the film group, 31.3% had excellent images, 38.2% good, 22.7% poor and 7.8% were unreadable. Of the 1008 patients in the digital imaging group, 25.3% had excellent images, 46.3% good, 14.6% poor and 13.8% were unreadable. A significant difference was observed in patients over 65 years of age who exhibited a threefold increase in failure rate with digital imaging (33.7% v 11.3%)(P < 0.0001). Conclusion:,In this study population a statistically significant degradation of image quality was observed in those older than 65 years following transition to digital photography. This has implications for service provision planning. [source] | |||||||||||||