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Search Results: 1 - 10 of 8324 matches for " Hans Binder "
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"Hook"-calibration of GeneChip-microarrays: Theory and algorithm
Hans Binder, Stephan Preibisch
Algorithms for Molecular Biology , 2008, DOI: 10.1186/1748-7188-3-12
Abstract: We present the so-called hook-calibration method which co-processes the log-difference (delta) and -sum (sigma) of the perfect match (PM) and mismatch (MM) probe-intensities. The MM probes are utilized as an internal reference which is subjected to the same hybridization law as the PM, however with modified characteristics. After sequence-specific affinity correction the method fits the Langmuir-adsorption model to the smoothed delta-versus-sigma plot. The geometrical dimensions of this so-called hook-curve characterize the particular hybridization in terms of simple geometric parameters which provide information about the mean non-specific background intensity, the saturation value, the mean PM/MM-sensitivity gain and the fraction of absent probes. This graphical summary spans a metrics system for expression estimates in natural units such as the mean binding constants and the occupancy of the probe spots. The method is single-chip based, i.e. it separately uses the intensities for each selected chip.The hook-method corrects the raw intensities for the non-specific background hybridization in a sequence-specific manner, for the potential saturation of the probe-spots with bound transcripts and for the sequence-specific binding of specific transcripts. The obtained chip characteristics in combination with the sensitivity corrected probe-intensity values provide expression estimates scaled in natural units which are given by the binding constants of the particular hybridization.The basic mechanism underlying the functioning of DNA microarrays is that of hybridization. Hybridization is defined as the binding between complementary single-stranded nucleic acids. In the case of microarrays one strand is anchored at the surface and the second one is dissolved in solution, referred to as probe and target, respectively. The experimental technique of detecting hybridized probes relies on the fluorescence intensity measurement to infer the transcript abundance specific for a
Estimating RNA-quality using GeneChip microarrays
Mario Fasold, Hans Binder
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-186
Abstract: Microarray intensity data contains information to estimate the RNA quality of the sample. We here study the interplay of the characteristics of RNA surface hybridization with the effects of partly truncated transcripts on probe intensity. The 3′/5′ intensity gradient, the basis of microarray RNA quality measures, is shown to depend on the degree of competitive binding of specific and of non-specific targets to a particular probe, on the degree of saturation of the probes with bound transcripts and on the distance of the probe from the 3′-end of the transcript. Increasing degrees of non-specific hybridization or of saturation reduce the 3′/5′ intensity gradient and if not taken into account, this leads to biased results in common quality measures for GeneChip arrays such as affyslope or the control probe intensity ratio. We also found that short probe sets near the 3′-end of the transcripts are prone to non-specific hybridization presumable because of inaccurate positional assignment and the existence of transcript isoforms with variable 3′ UTRs. Poor RNA quality is associated with a decreased amount of RNA material hybridized on the array paralleled by a decreased total signal level. Additionally, it causes a gene-specific loss of signal due to the positional bias of transcript abundance which requires an individual, gene-specific correction. We propose a new RNA quality measure that considers the hybridization mode. Graphical characteristics are introduced allowing assessment of RNA quality of each single array (‘tongs plot’ and ‘degradation hook’). Furthermore, we suggest a method to correct for effects of RNA degradation on microarray intensities.The presented RNA degradation measure has best correlation with the independent RNA integrity measure RIN, and therefore presents itself as a valuable tool for quality control and even for the study of RNA degradation. When RNA degradation effects are detected in microarray experiments, a correction of the induced bias i
Specific and non specific hybridization of oligonucleotide probes on microarrays
Hans Binder,Stephan Preibisch
Quantitative Biology , 2004, DOI: 10.1529/biophysj.104.055343
Abstract: Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the intended target is problematic because it adds a "chemical background" to the signal, which is not related to the expression degree of the target gene. The paper presents a molecular signature of specific and non specific hybridization with potential consequences for gene expression analysis. We analyzed the signal intensities of perfect match (PM) and mismatch (MM) probes of GeneChip microarrays to specify the effect of specific and non specific hybridization. We found that these events give rise to different relations between the PM and MM intensities as function of the middle base of the PMs, namely a triplet- (C>G=T>A>0) and a duplet-like (C=T>0>G=A) pattern of the PM-MM log-intensity difference upon binding of specific and non specific RNA fragments, respectively. The systematic behaviour of the intensity difference can be rationalized on the level of base pairings of DNA/RNA oligonucleotide duplexes in the middle of the probe sequence. Non-specific binding is characterized by the reversal of the central Watson Crick (WC) pairing for each PM/MM probe pair, whereas specific binding refers to the combination of a WC and a self complementary (SC) pairing in PM and MM probes, respectively. The intensity of complementary MM introduces a systematic source of variation which decreases the precision of expression measures based on the MM intensities.
Physico-chemical modelling of target depletion during hybridisation on oligonulceotide microarrays
Conrad J. Burden,Hans Binder
Quantitative Biology , 2009,
Abstract: The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridisation on oligonucleotide microarrays. Two possible regimes are identified: local depletion, in which depletion by a given probe feature only affects that particular probe, and global depletion, in which all features responding to a given target species are affected. Examples are given of two existing spike-in data sets experiencing measurable effects of target depletion. The first of these, from an experiment by Suzuki et al. using custom built arrays with a broad range of probe lengths and mismatch positions, is verified to exhibit local and not global depletion. The second dataset, the well known Affymetrix HGU133a latin square experiment is shown to be very well explained by a global depletion model. It is shown that microarray calibrations relying on Langmuir isotherm models which ignore depletion effects will significantly underestimate specific target concentrations. It is also shown that a combined analysis of perfect match and mismatch probe signals in terms of a simple graphical summary, namely the hook curve method, can discriminate between cases of local and global depletion.
Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays
Hans Binder,Mario Fasold,Torsten Glomb
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0007862
Abstract: Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates.
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures
Hans Binder, Knut Krohn, Stephan Preibisch
Algorithms for Molecular Biology , 2008, DOI: 10.1186/1748-7188-3-11
Abstract: In this publication we summarize the essential chip characteristics provided by this method, analyze special benchmark experiments to estimate transcript related expression measures and illustrate the potency of the method to detect and to quantify the quality of a particular hybridization. It is shown that our single-chip approach provides expression measures responding linearly on changes of the transcript concentration over three orders of magnitude. In addition, the method calculates a detection call judging the relation between the signal and the detection limit of the particular measurement. The performance of the method in the context of different chip generations and probe set assignments is illustrated. The hook method characterizes the RNA-quality in terms of the 3'/5'-amplification bias and the sample-specific calling rate. We show that the proper judgement of these effects requires the disentanglement of non-specific and specific hybridization which, otherwise, can lead to misinterpretations of expression changes. The consequences of modifying probe/target interactions by either changing the labelling protocol or by substituting RNA by DNA targets are demonstrated.The single-chip based hook-method provides accurate expression estimates and chip-summary characteristics using the natural metrics given by the hybridization reaction with the potency to develop new standards for microarray quality control and calibration.DNA microarray technology enables conducting experiments that measure RNA-transcript abundance (so called gene expression or expression degree) on a large scale of genomic sequences. The quality of the measurement systematically depends on experimental factors such as the performance of the measuring "device", e.g., on the chosen array-type, the design of the chip-platform and -generation and on the particular probe design, on one hand; and also on the quality of the sample, e.g. on the source of RNA and the used hybridization-pipeline includ
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
Mario Fasold, Peter F Stadler, Hans Binder
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-207
Abstract: Longer runs of three or more consecutive G along the probe sequence and in particular triple degenerated G at its solution end ((GGG)1-effect) are associated with exceptionally large probe intensities on GeneChip expression arrays. This intensity bias is related to non-specific hybridization and affects both perfect match and mismatch probes. The (GGG)1-effect tends to increase gradually for microarrays of later GeneChip generations. It was found for DNA/RNA as well as for DNA/DNA probe/target-hybridization chemistries. Amplification of sample RNA using T7-primers is associated with strong positive amplitudes of the G-bias whereas alternative amplification protocols using random primers give rise to much smaller and partly even negative amplitudes.We applied positional dependent sensitivity models to analyze the specifics of probe intensities in the context of all possible short sequence motifs of one to four adjacent nucleotides along the 25meric probe sequence. Most of the longer motifs are adequately described using a nearest-neighbor (NN) model. In contrast, runs of degenerated guanines require explicit consideration of next nearest neighbors (GGG terms). Preprocessing methods such as vsn, RMA, dChip, MAS5 and gcRMA only insufficiently remove the G-bias from data.Positional and motif dependent sensitivity models accounts for sequence effects of oligonucleotide probe intensities. We propose a positional dependent NN+GGG hybrid model to correct the intensity bias associated with probes containing poly-G motifs. It is implemented as a single-chip based calibration algorithm for GeneChips which can be applied in a pre-correction step prior to standard preprocessing.Fig. 1a shows the surface image of a hybridized Affymetrix GeneChip expression array. Its area of about 1.6 cm2 divides into a grid of nearly one million probe spots of size (11 × 11) μm2. Each of them is covered by a 'turf' of 25meric oligonucleotides attached to the chip surface. Their sequence is chose
Washing scaling of GeneChip microarray expression
Hans Binder, Knut Krohn, Conrad J Burden
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-291
Abstract: We conducted experiments on GeneChip microarrays with altered protocols for washing, scanning and staining to study the probe-level intensity changes as a function of the number of washing cycles. For calibration and analysis of the intensity data we make use of the 'hook' method which allows intensity contributions due to non-specific and specific hybridization of perfect match (PM) and mismatch (MM) probes to be disentangled in a sequence specific manner. On average, washing according to the standard protocol removes about 90% of the non-specific background and about 30-50% and less than 10% of the specific targets from the MM and PM, respectively. Analysis of the washing kinetics shows that the signal-to-noise ratio doubles roughly every ten stringent washing cycles. Washing can be characterized by time-dependent rate constants which reflect the heterogeneous character of target binding to microarray probes. We propose an empirical washing function which estimates the survival of probe bound targets. It depends on the intensity contribution due to specific and non-specific hybridization per probe which can be estimated for each probe using existing methods. The washing function allows probe intensities to be calibrated for the effect of washing. On a relative scale, proper calibration for washing markedly increases expression measures, especially in the limit of small and large values.Washing is among the factors which potentially distort expression measures. The proposed first-order correction method allows direct implementation in existing calibration algorithms for microarray data. We provide an experimental 'washing data set' which might be used by the community for developing amendments of the washing correction.Gene expression profiling using microarrays has become a standard technique for the large scale estimation of transcript abundance [1]. The method is based on the hybridization of RNA prepared from samples of interest with gene-specific oligonucleoti
Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays
Hans Binder,Stephan Preibisch,Toralf Kirsten
Quantitative Biology , 2005,
Abstract: The lack of specificity in microarray experiments due to non-specific hybridization raises a serious problem for the analysis of microarray data because the residual chemical background intensity is not related to the expression degree of the gene of interest. We analyzed the concentration dependence of the signal intensity of perfect match (PM) and mismatch (MM) probes in terms using a microscopic binding model using a combination of mean hybridization isotherms and single base related affinity terms. The signal intensities of the PM and MM probes and their difference are assessed with regard to their sensitivity, specificity and resolution for gene expression measures. The presented theory implies the refinement of existing algorithms of probe level analysis to correct microarray data for non-specific background intensities.
IGF2/H19 hypomethylation is tissue, cell, and CpG site dependent and not correlated with body asymmetry in adolescents with Silver-Russell syndrome
Kai Kannenberg, Karin Weber, Cathrin Binder, Christina Urban, Hans-Joachim Kirschner, Gerhard Binder
Clinical Epigenetics , 2012, DOI: 10.1186/1868-7083-4-15
Abstract: The ICR1 methylation status was analyzed in blood and in addition in buccal smear probes and cultured fibroblasts obtained from punch biopsies taken from the two body halves of 5 SRS patients and 3 controls. We found that the ICR1 hypomethylation in SRS patients was stronger in blood leukocytes and oral mucosa cells than in fibroblasts. ICR1 CpG sites were affected differently. The severity of hypomethylation was not correlated to body asymmetry. IGF2 expression and IGF-II secretion of fibroblasts were not correlated to the degree of ICR1 hypomethylation. SRS fibroblasts responded well to stimulation by recombinant human IGF-I or IGF-II, with proliferation rates comparable with controls. Clonal expansion of primary fibroblasts confirmed the complexity of the cellular mosaicism.We conclude that the ICR1 hypomethylation SRS is tissue, cell, and CpG site specific. The correlation of the ICR1 hypomethylation to IGF2 and H19 expression is not strict, may depend on the investigated tissue, and may become evident only in case of more severe methylation defects. The body asymmetry in juvenile SRS patients is not related to a corresponding ICR1 hypomethylation gradient, rendering more likely an intrauterine origin of asymmetry. Overall, it may be instrumental to consider not only the ICR1 methylation status as decisive for IGF2/H19 expression regulation.Silver-Russell syndrome (SRS; OMIM 180860) is a sporadically occurring, genetically and clinically heterogeneous disorder. It is diagnosed on the basis of the combination of intrauterine growth retardation, severe short stature, characteristic triangular face, relative macrocephaly, body asymmetry, underweight, and several minor abnormalities [1-3]. The relative limb length differences in asymmetric SRS patients are present at birth and stay stable during the growth process [4]. Short stature in SRS can be treated with pharmacological doses of recombinant growth hormone [5]. There is no apparent hormone deficiency. In contras
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