R-Gada: a fast and flexible pipeline for copy number analysis in association studies

<p>Abstract</p> <p>Background</p> <p>Genome-wide association studies (GWAS) using Copy Number Variation (CNV) are becoming a central focus of genetic research. CNVs have successfully provided target genome regions for some disease conditions where simple genetic variation (i.e., SNPs) has previously failed to provide a clear association.</p> <p>Results</p> <p>Here we present a new R package, that integrates: (i) data import from most common formats of Affymetrix, Illumina and aCGH arrays; (ii) a fast and accurate segmentation algorithm to call CNVs based on Genome Alteration Detection Analysis (GADA); and (iii) functions for displaying and exporting the Copy Number calls, identification of recurrent CNVs, multivariate analysis of population structure, and tools for performing association studies. Using a large dataset containing 270 HapMap individuals (Affymetrix Human SNP Array 6.0 Sample Dataset) we demonstrate a flexible pipeline implemented with the package. It requires less than one minute per sample (3 million probe arrays) on a single core computer, and provides a flexible parallelization for very large datasets. Case-control data were generated from the HapMap dataset to demonstrate a GWAS analysis.</p> <p>Conclusions</p> <p>The package provides the tools for creating a complete integrated pipeline from data normalization to statistical association. It can effciently handle a massive volume of data consisting of millions of genetic markers and hundreds or thousands of samples with very accurate results.</p

Experience of sexual coercion and risky sexual behavior among Ugandan university students

<p>Abstract</p> <p>Background</p> <p>Growing worldwide evidence shows that the experience of sexual coercion is fairly prevalent among young people and is associated with risky sexual behavior thereafter. The causal mechanisms behind this are unclear but may be dependent on specific contextual determinants. Little is known about factors that could buffer the negative effects of coercion. The aim of this study was to assess the association between the experience of sexual coercion and risky sexual behavior among university students of both sexes in Uganda.</p> <p>Methods</p> <p>In 2005, 980 (80%) out of a total of 1,220 students enrolled in Mbarara University of Science and Technology in Uganda participated in a self-administered questionnaire covering socio-demographic and religious factors, social capital, mental health, alcohol use, and sexual behavior. A validated scale of six items was used to assess the experience of sexual coercion. Logistic regression analyses were applied to control for confounders. Potential buffering factors were analyzed by testing for effect modification.</p> <p>Results</p> <p>Fifty-nine percent of those who responded had previously had sexual intercourse. Among the male students 29.0%, and among the female students 33.1% reported having had some experience of sexual coercion. After controlling for age, gender, and educational level of household of origin, role of religion and trust in others sexual coercion was found to be statistically significantly associated with previously had sex (OR 1.6, 95% CI; 1.1-2.3), early sexual debut (OR 2.4, 95% CI; 1.5-3.7), as well as with having had a great number of sexual partners (OR 1.9, 95% CI; 1.2-3.0), but not with inconsistent condom use.</p> <p>Scoring low on an assessment of mental health problems, reporting high trust in others, or stating that religion played a major role in one's family of origin seemed to buffer the negative effect that the experience of sexual coercion had on the likelihood of having many sexual partners.</p> <p>Conclusion</p> <p>The findings of this study suggest that the experience of sexual coercion is common among youth/young adults in Uganda and is subsequently associated with risky sexual behavior in both sexes. The existence of individual and contextual factors that buffer the effects mentioned was also demonstrated. In the Ugandan context, this has implications for policy formulation and the implementation of preventive strategies for combating HIV/AIDS.</p

Soft tissue non-Hodgkin lymphoma of shoulder in a HIV patient: a report of a case and review of the literature

The risk of developing lymphoma is greatly increased in HIV infection. Musculoskeletal manifestations of the human immunodeficiency virus (HIV) are common and are sometimes the initial presentation of the disease. Muscle, bone, and joints are involved by septic arthritis, myopathies and neoplasms. HIV-related neoplastic processes that affect the musculoskeletal system include Kaposi's sarcoma and non-Hodgkin's lymphoma, the latter being mainly localized at lower extremities, spine and skull

Plasma proteome changes in cardiovascular disease patients: novel isoforms of apolipoprotein A1

<p>Abstract</p> <p>Background</p> <p>The aim of this proteomic study was to look for changes taking place in plasma proteomes of patients with acute myocardial infarction (AMI), unstable angina pectoris (UAP), and stable angina pectoris (SAP).</p> <p>Methods</p> <p>Depleted plasma proteins were separated by 2D SDS-PAGE (pI 4-7), and proteomes were compared using Progenesis SameSpots statistical software. Proteins were identified by nanoLC-MS/MS. Proteins were quantified using commercial kits. Apolipoprotein A1 was studied using 1D and 2D SDS-PAGE, together with western blotting.</p> <p>Results</p> <p>Reciprocal comparison revealed 46 unique, significantly different spots; proteins in 34 spots were successfully identified and corresponded to 38 different proteins. Discrete comparisons of patient groups showed 45, 41, and 8 significantly different spots when AMI, UAP, and SAP were compared with the control group. On the basis of our proteomic data, plasma levels of two of them, alpha-1 microglobulin and vitamin D-binding protein, were determined. The data, however, failed to prove the proteins to be suitable markers or risk factors in the studied groups. The plasma level and isoform representation of apolipoprotein A1 were also estimated. Using 1D and 2D SDS-PAGE, together with western blotting, we observed extra high-molecular weight apolipoprotein A1 fractions presented only in the patient groups, indicating that the novel high-molecular weight isoforms of apolipoprotein A1 may be potential new markers or possible risk factors of cardiovascular disease.</p> <p>Conclusion</p> <p>The reported data show plasma proteome changes in patients with AMI, UAP, and SAP. We propose some apolipoprotein A1 fractions as a possible new disease-associated marker of cardiovascular disorders.</p

On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing

One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing errors and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with low coverage data. However, % of inversions located between segmental duplications are expected to go undetected by the most common sequencing strategies. In general, longer DNA libraries improve the detectability of inversions far better than increments of the coverage depth or the read length. Finally, we review the performance of three algorithms to detect inversions -SVDetect, GRIAL, and VariationHunter-, identify common pitfalls, and reveal important differences in their breakpoint precisions. These results stress the importance of the sequencing strategy for the detection of structural variants, especially inversions, and offer guidelines for the design of future genome sequencing projects

Soil foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data

<p>Abstract</p> <p>Background</p> <p>Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly defined since it has been only studied systematically in one large-scale study and by using non optimal <it>ad-hoc </it>SNP array data analysis tools, uncovering rather large alterations (> 1 Mb) and affecting a high proportion of cells. Here we propose a novel methodology, Mosaic Alteration Detection-MAD, by providing a software tool that is effective for capturing previously described alterations as wells as new variants that are smaller in size and/or affecting a low percentage of cells.</p> <p>Results</p> <p>The developed method identified all previously known mosaic abnormalities reported in SNP array data obtained from controls, bladder cancer and HapMap individuals. In addition MAD tool was able to detect new mosaic variants not reported before that were smaller in size and with lower percentage of cells affected. The performance of the tool was analysed by studying simulated data for different scenarios. Our method showed high sensitivity and specificity for all assessed scenarios.</p> <p>Conclusions</p> <p>The tool presented here has the ability to identify mosaic abnormalities with high sensitivity and specificity. Our results confirm the lack of sensitivity of former methods by identifying new mosaic variants not reported in previously utilised datasets. Our work suggests that the prevalence of mosaic alterations could be higher than initially thought. The use of appropriate SNP array data analysis methods would help in defining the human genome mosaic map.</p

Space Telescope and Optical Reverberation Mapping Project. VII. Understanding the Ultraviolet Anomaly in NGC 5548 with X-Ray Spectroscopy

During the Space Telescope and Optical Reverberation Mapping Project observations of NGC 5548, the continuum and emission-line variability became decorrelated during the second half of the six-month-long observing campaign. Here we present Swift and Chandra X-ray spectra of NGC 5548 obtained as part of the campaign. The Swift spectra show that excess flux (relative to a power-law continuum) in the soft X-ray band appears before the start of the anomalous emission-line behavior, peaks during the period of the anomaly, and then declines. This is a model-independent result suggesting that the soft excess is related to the anomaly. We divide the Swift data into on- and off-anomaly spectra to characterize the soft excess via spectral fitting. The cause of the spectral differences is likely due to a change in the intrinsic spectrum rather than to variable obscuration or partial covering. The Chandra spectra have lower signal-to-noise ratios, but are consistent with the Swift data. Our preferred model of the soft excess is emission from an optically thick, warm Comptonizing corona, the effective optical depth of which increases during the anomaly. This model simultaneously explains all three observations: the UV emission-line flux decrease, the soft-excess increase, and the emission-line anomaly

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism

Kinetic models of metabolism require detailed knowledge of kinetic parameters. However, due to measurement errors or lack of data this knowledge is often uncertain. The model of glycolysis in the parasitic protozoan Trypanosoma brucei is a particularly well analysed example of a quantitative metabolic model, but so far it has been studied with a fixed set of parameters only. Here we evaluate the effect of parameter uncertainty. In order to define probability distributions for each parameter, information about the experimental sources and confidence intervals for all parameters were collected. We created a wiki-based website dedicated to the detailed documentation of this information: the SilicoTryp wiki (http://silicotryp.ibls.gla.ac.uk/wiki/Glycolysis). Using information collected in the wiki, we then assigned probability distributions to all parameters of the model. This allowed us to sample sets of alternative models, accurately representing our degree of uncertainty. Some properties of the model, such as the repartition of the glycolytic flux between the glycerol and pyruvate producing branches, are robust to these uncertainties. However, our analysis also allowed us to identify fragilities of the model leading to the accumulation of 3-phosphoglycerate and/or pyruvate. The analysis of the control coefficients revealed the importance of taking into account the uncertainties about the parameters, as the ranking of the reactions can be greatly affected. This work will now form the basis for a comprehensive Bayesian analysis and extension of the model considering alternative topologies

A wager on the future: a practicable response to HIV pre-exposure prophylaxis (PrEP) and the stubborn fact of process

In this article we focus on public health’s wager on the social implications of a daily antiretroviral pill to prevent HIV, referred to as PrEP (pre-exposure prophylaxis). The wager is shown to rely on modes of inquiry overly tied to what is known of the present in order to predict the future. Although such inquiry is not unusual when social research is called upon to assist health policy, predictive methodologies are unable to appreciate the dynamic and thus indeterminate nature of process. We ask: what mode of inquiry might practicably appreciate that what happens in the present will have a bearing on the future, without foreclosing on unknown possibles? Drawing on speculative and pragmatic philosophy, we reflect on our own qualitative research on PrEP to suggest that conventional methodological approaches can contribute to the future without seeking to determine what it will become