Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors

<p>Abstract</p> <p>Background</p> <p>Microarray Comparative Genomic Hybridization (array CGH) provides a means to examine DNA copy number aberrations. Various platforms, brands and underlying technologies are available, facing the user with many choices regarding platform sensitivity and number, localization, and density distribution of probes.</p> <p>Results</p> <p>We evaluate three different platforms presenting different nature and arrangement of the probes: The Agilent Human Genome CGH Microarray 44 k, the ROMA/NimbleGen Representational Oligonucleotide Microarray 82 k, and the Illumina Human-1 Genotyping 109 k BeadChip, with Agilent being gene oriented, ROMA/NimbleGen being genome oriented, and Illumina being genotyping oriented. We investigated copy number changes in 20 human breast tumor samples representing different gene expression subclasses, using a suite of graphical and statistical methods designed to work across platforms. Despite substantial differences in the composition and spatial distribution of probes, the comparison revealed high overall concordance. Notably however, some short amplifications and deletions of potential biological importance were not detected by all platforms. Both correlation and cluster analysis indicate a somewhat higher similarity between ROMA/NimbleGen and Illumina than between Agilent and the other two platforms. The programs developed for the analysis are available from <url>http://www.ifi.uio.no/bioinf/Projects/</url>.</p> <p>Conclusion</p> <p>We conclude that platforms based on different technology principles reveal similar aberration patterns, although we observed some unique amplification or deletion peaks at various locations, only detected by one of the platforms. The correct platform choice for a particular study is dependent on whether the appointed research intention is gene, genome, or genotype oriented.</p

RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls

<p>Abstract</p> <p>Background</p> <p>RNA from exosomes and other microvesicles contain transcripts of tumour origin. In this study we sought to identify biomarkers of glioblastoma multiforme in microvesicle RNA from serum of affected patients.</p> <p>Methods</p> <p>Microvesicle RNA from serum from patients with de-novo primary glioblastoma multiforme (N = 9) and normal controls (N = 7) were analyzed by microarray analysis. Samples were collected according to protocols approved by the Institutional Review Board. Differential expressions were validated by qRT-PCR in a separate set of samples (N = 10 in both groups).</p> <p>Results</p> <p>Expression profiles of microvesicle RNA correctly separated individuals in two groups by unsupervised clustering. The most significant differences pertained to down-regulated genes (121 genes > 2-fold down) in the glioblastoma multiforme patient microvesicle RNA, validated by qRT-PCR on several genes. Overall, yields of microvesicle RNA from patients was higher than from normal controls, but the additional RNA was primarily of size < 500 nt. Gene ontology of the down-regulated genes indicated these are coding for ribosomal proteins and genes related to ribosome production.</p> <p>Conclusions</p> <p>Serum microvesicle RNA from patients with glioblastoma multiforme has significantly down-regulated levels of RNAs coding for ribosome production, compared to normal healthy controls, but a large overabundance of RNA of unknown origin with size < 500 nt.</p

Mining for genotype-phenotype relations in Saccharomyces using partial least squares

<p>Abstract</p> <p>Background</p> <p>Multivariate approaches are important due to their versatility and applications in many fields as it provides decisive advantages over univariate analysis in many ways. Genome wide association studies are rapidly emerging, but approaches in hand pay less attention to multivariate relation between genotype and phenotype. We introduce a methodology based on a BLAST approach for extracting information from genomic sequences and Soft- Thresholding Partial Least Squares (ST-PLS) for mapping genotype-phenotype relations.</p> <p>Results</p> <p>Applying this methodology to an extensive data set for the model yeast <it>Saccharomyces cerevisiae</it>, we found that the relationship between genotype-phenotype involves surprisingly few genes in the sense that an overwhelmingly large fraction of the phenotypic variation can be explained by variation in less than 1% of the full gene reference set containing 5791 genes. These phenotype influencing genes were evolving 20% faster than non-influential genes and were unevenly distributed over cellular functions, with strong enrichments in functions such as cellular respiration and transposition. These genes were also enriched with known paralogs, stop codon variations and copy number variations, suggesting that such molecular adjustments have had a disproportionate influence on <it>Saccharomyces </it>yeasts recent adaptation to environmental changes in its ecological niche.</p> <p>Conclusions</p> <p>BLAST and PLS based multivariate approach derived results that adhere to the known yeast phylogeny and gene ontology and thus verify that the methodology extracts a set of fast evolving genes that capture the phylogeny of the yeast strains. The approach is worth pursuing, and future investigations should be made to improve the computations of genotype signals as well as variable selection procedure within the PLS framework.</p

Acute hunger does not always undermine prosociality

This is the final version. Available on open access from Nature Research via the DOI in this recordData Availability: The data that support the findings of this paper are available on the OSF website (https://osf.io/zexd7/?view_only=480593713c904397a033e751a6da7a69).It has been argued that, when they are acutely hungry, people act in self-protective ways by keeping resources to themselves rather than sharing them. In four studies, using experimental, quasi-experimental, and correlational designs (total N = 795), we examine the effects of acute hunger on prosociality in a wide variety of non-interdependent tasks (e.g. dictator game) and interdependent tasks (e.g. public goods games). While our procedures successfully increase subjective hunger and decrease blood glucose, we do not find significant effects of hunger on prosociality. This is true for both decisions incentivized with money and with food. Metaanalysis across all tasks reveals a very small effect of hunger on prosociality in noninterdependent tasks (d = .108), and a non-significant effect in interdependent tasks (d = -0.076). In study five (N = 197), we show that, in stark contrast to our empirical findings, people hold strong lay theories that hunger undermines prosociality.Volkswagen Foundatio

Disgust sensitivity relates to attitudes toward gay men and lesbian women across 31 nations

Previous work has reported a relation between pathogen-avoidance motivations and prejudice toward various social groups, including gay men and lesbian women. It is currently unknown whether this association is present across cultures, or specific to North America. Analyses of survey data from adult heterosexuals (N = 11,200) from 31 countries showed a small relation between pathogen disgust sensitivity (an individual-difference measure of pathogen-avoidance motivations) and measures of antigay attitudes. Analyses also showed that pathogen disgust sensitivity relates not only to antipathy toward gay men and lesbians, but also to negativity toward other groups, in particular those associated with violations of traditional sexual norms (e.g., prostitutes). These results suggest that the association between pathogen-avoidance motivations and antigay attitudes is relatively stable across cultures and is a manifestation of a more general relation between pathogen-avoidance motivations and prejudice towards groups associated with sexual norm violations