Identifying differentially methylated genes using mixed effect and generalized least square models

<p>Abstract</p> <p>Background</p> <p>DNA methylation plays an important role in the process of tumorigenesis. Identifying differentially methylated genes or CpG islands (CGIs) associated with genes between two tumor subtypes is thus an important biological question. The methylation status of all CGIs in the whole genome can be assayed with differential methylation hybridization (DMH) microarrays. However, patient samples or cell lines are heterogeneous, so their methylation pattern may be very different. In addition, neighboring probes at each CGI are correlated. How these factors affect the analysis of DMH data is unknown.</p> <p>Results</p> <p>We propose a new method for identifying differentially methylated (DM) genes by identifying the associated DM CGI(s). At each CGI, we implement four different mixed effect and generalized least square models to identify DM genes between two groups. We compare four models with a simple least square regression model to study the impact of incorporating random effects and correlations.</p> <p>Conclusions</p> <p>We demonstrate that the inclusion (or exclusion) of random effects and the choice of correlation structures can significantly affect the results of the data analysis. We also assess the false discovery rate of different models using CGIs associated with housekeeping genes.</p

Identification of Type 1 Diabetes-Associated DNA Methylation Variable Positions That Precede Disease Diagnosis

Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is similar to 50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. We generated genome-wide DNA methylation profiles of purified CD14(+) monocytes (an immune effector cell type relevant to T1D pathogenesis) from 15 T1D-discordant MZ twin pairs. This identified 132 different CpG sites at which the direction of the intra-MZ pair DNA methylation difference significantly correlated with the diabetic state, i.e. T1D-associated methylation variable positions (T1D-MVPs). We confirmed these T1D-MVPs display statistically significant intra-MZ pair DNA methylation differences in the expected direction in an independent set of T1D-discordant MZ pairs (P = 0.035). Then, to establish the temporal origins of the T1D-MVPs, we generated two further genome-wide datasets and established that, when compared with controls, T1D-MVPs are enriched in singletons both before (P = 0.001) and at (P = 0.015) disease diagnosis, and also in singletons positive for diabetes-associated autoantibodies but disease-free even after 12 years follow-up (P = 0.0023). Combined, these results suggest that T1D-MVPs arise very early in the etiological process that leads to overt T1D. Our EWAS of T1D represents an important contribution toward understanding the etiological role of epigenetic variation in type 1 diabetes, and it is also the first systematic analysis of the temporal origins of disease-associated epigenetic variation for any human complex disease

Re-examining the Unified Theory of Acceptance and Use of Technology (UTAUT): Towards a Revised Theoretical Model

YesBased on a critical review of the Unified Theory of Acceptance and Use of Technology (UTAUT), this study first formalized an alternative theoretical model for explaining the acceptance and use of information system (IS) and information technology (IT) innovations. The revised theoretical model was then empirically examined using a combination of meta-analysis and structural equation modelling (MASEM) techniques. The meta-analysis was based on 1600 observations on 21 relationships coded from 162 prior studies on IS/IT acceptance and use. The SEM analysis showed that attitude: was central to behavioural intentions and usage behaviours, partially mediated the effects of exogenous constructs on behavioural intentions, and had a direct influence on usage behaviours. A number of implications for theory and practice are derived based on the findings

Global Health Governance and the Commercial Sector: A Documentary Analysis of Tobacco Company Strategies to Influence the WHO Framework Convention on Tobacco Control

Heide Weishaar and colleagues did an analysis of internal tobacco industry documents together with other data and describe the industry's strategic response to the proposed World Health Organization Framework Convention on Tobacco Control

Geographic variation in social organization of Galápagos mockingbirds: ecological correlates of group territoriality and cooperative breeding

To investigate ecological influences on cooperative social organization, I studied the four allopatric species of mockingbirds ( Nesomimus spp.) endemic to the Galápagos archipelago on four islands. On three small, low and arid islands (Genovesa, Champion and Española), mockingbird territories filled all terrestrial habitat, mean group size varied from 4.5 to 14.2 adults, maximum group size ranged from seven to 24 birds, and 70–100% of groups contained more than two birds. San Cristóbal is larger and higher, and it supports a broader range of habitats. At one highland and two coastal sites on this island, mockingbirds did not hold territories in all available habitats, group size averaged 2.2 adults, only 25% of groups were larger than two, and none included more than three adults. Adults dispersed into vacant habitat to establish new territories only on San Cristóbal. Helping behavior has not yet been observed on San Cristóbal, but it occurs on the other three islands. These results support the hypothesis that social groups and cooperative breeding are maintained where limited availability of preferred habitat constrains dispersal. The mechanism relaxing habitat saturation on San Cristóbal, however, remains undetermined. Predation by introduced rats and cats may reduce survival and indirectly reduce group size; these predators are absent from Genovesa, Champion and Española. Differences in food supplies could also affect interand intra-island variation in population density. Variation in social organization among arid coastal sites on the four islands, and similarity between climatically different sites on San Cristóbal, suggest that climatic conditions are less important as determinants of dispersal and breeding. Skews in adult sex ratios also fail to account for inter-island variation in sociality. Although they live in a climatically variable environment, territorial behavior and the physical limits of suitable habitat have an overriding influence on cooperative social organization in Galápagos mockingbirds.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46894/1/265_2004_Article_BF00302932.pd

Freeze-drying of proteins from a sucrose-glycine excipient system: Effect of formulation composition on the initial recovery of protein activity

The purpose of this study was to investigate the effect of sucrose-glycine excipient systems on the stability of selected model proteins during lyophilization. Recovery of protein activity after freeze-drying was examined for the model proteins lactate dehydrogenase and glucose 6-phosphate dehydrogenase in a sucrose-glycine-based excipient system in which the formulation composition was system-atically varied. In a sucrose-only excipient system, activity recovery of both model proteins is about 80% and is independent of sucrose concentration over a range from 1 to 40 mg/mL. When both sucrose and glycine are used and the ratio of the 2 excipients is varied, however, activity recovery decreases in a pattern that is consistent with the inhibition of activity recovery by glycine crystals, despite the presence of an adequate amount of sucrose to afford protection. Annealing of sucrose-glycine formulations causes a small but significant decrease in activity recovery relative to unannealed controls, whereas no annealing effect is observed with sucrose-only formulations. Addition of 0.01% polysorbate 80 to the formulation resulted in complete recovery of activity, irrespective of the sucroseglycine ratio or annealing. Addition of the same concentration of polysorbate 80 to the reconstitution medium caused an increase in activity recovery for each formulation, but the overall pattern remained unchanged. The data are consistent with an interfacial model for lyophilization-associated loss of protein activity involving denaturation at a solid/freeze-concentrate interface