Compression of Structured High-Throughput Sequencing Data

Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to quickly adapt to the requirements of new sequencing or analysis methods (because they do not support schema evolution), or fail to provide state of the art compression of the datasets. We have devised new approaches to store HTS data that support seamless data schema evolution and compress datasets substantially better than existing approaches. Building on these new approaches, we discuss and demonstrate how a multi-tier data organization can dramatically reduce the storage, computational and network burden of collecting, analyzing, and archiving large sequencing datasets. For instance, we show that spliced RNA-Seq alignments can be stored in less than 4% the size of a BAM file with perfect data fidelity. Compared to the previous compression state of the art, these methods reduce dataset size more than 40% when storing exome, gene expression or DNA methylation datasets. The approaches have been integrated in a comprehensive suite of software tools (http://goby.campagnelab.org) that support common analyses for a range of high-throughput sequencing assays.     

Cultivating participatory policy processes for genetic resources policy: lessons from the Genetic Resources Policy Initiative (GRPI) project

The purpose of the paper is to draw lessons and document experiences from the Genetic Resources Policy Initiative (GRPI) project, a project which has been underway in six countries and two sub-regions during the last 5 years. Its focus has been to experiment an approach to participatory policy processes, coined by the project, called the multi-stakeholder, multi-disciplinary and multi-sector or in short the 3M. This approach, which was demand-driven due to the nature of the policy problems being examined, aims to create a platform to address competing interests inherent in genetic resources issues from multiple perspectives. It is meant to enable different stakeholders to balance issues they diverge and/or converge upon in genetic resources management, thereby harmonizing trade-offs, objectives and strategies. Experiences from the project in applying the 3M in Egypt, Nepal, Vietnam Peru and Zambia highlight several lessons in participatory policy processes. The experiences show that the success or otherwise of participatory policy making processes is dependent on various factors that have to do with stakeholder capacities, process orientation, shared understanding versus vested interests and institutional functions. They highlight that the most effective approach to stakeholder engagement in policy processes is to construct them around an actively engaged ‘process leader’ that possesses, or has the potential to champion the process by mobilising the required cognitive knowledge and institutional engagement. They further suggest that since genetic resources policy issues are cross-cutting, they will demand a more holistic approach with a clear identification of impact pathways through which policy changes can be expected to influence the outcome variables. Since policy making processes are perpetual, the question of sustaining project ideas and recommendations beyond the life of a project has to be part of the planning exercise in any participatory genetic resources policy research and formulation.

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to previous analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. We conducted performance evaluations of the software and found it to either outperform or have similar performance to analysis programs developed for specialized analyses of HTS data. We found that most biologists who took a one-hour GobyWeb training session were readily able to analyze RNA-Seq data with state of the art analysis tools. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins.     

The Use of Directed Evolution to Create a Stable and Immunogenic Recombinant BCG Expressing a Modified HIV-1 Gag Antigen

Numerous features make Mycobacterium bovis BCG an attractive vaccine vector for HIV. It has a good safety profile, it elicits long-lasting cellular immune responses and in addition manufacturing costs are affordable. Despite these advantages it is often difficult to express viral antigens in BCG, which results in genetic instability and low immunogenicity. The aim of this study was to generate stable recombinant BCG (rBCG) that express high levels of HIV antigens, by modification of the HIV genes. A directed evolution process was applied to recombinant mycobacteria that expressed HIV-1 Gag fused to the green fluorescent protein (GFP). Higher growth rates and increased GFP expression were selected for. Through this process a modified Gag antigen was selected. Recombinant BCG that expressed the modified Gag (BCG[pWB106] and BCG[pWB206]) were more stable, produced higher levels of antigen and grew faster than those that expressed the unmodified Gag (BCG[pWB105]). The recombinant BCG that expressed the modified HIV-1 Gag induced 2 to 3 fold higher levels of Gag-specific CD4 T cells than those expressing the unmodified Gag (BCG[pWB105]). Mice primed with 10⁷ CFU BCG[pWB206] and then boosted with MVA-Gag developed Gag-specific CD8 T cells with a frequency of 1343±17 SFU/10⁶ splenocytes, 16 fold greater than the response induced with MVA-Gag alone. Levels of Gag-specific CD4 T cells were approximately 5 fold higher in mice primed with BCG[pWB206] and boosted with MVA-Gag than in those receiving the MVA-Gag boost alone. In addition mice vaccinated with BCG[pWB206] were protected from a surrogate vaccinia virus challenge.     

Genetic diversity of Biomphalaria pfeifferi,the intermediate host of Schistosoma mansoni in Shamva district,Zimbabwe: role on intestinal schistosomiasis transmission

Molecular Biology Reports - The fresh water snail Biomphalaria pfeifferi is the intermediate host for Schistosoma mansoni, which causes human intestinal schistosomiasis in Zimbabwe. Despite the...