QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles

Background: Next generation sequencing enables studying heterogeneous populations of viral infections. When the sequencing is done at high coverage depth ("deep sequencing"), low frequency variants can be detected. Here we present QQ-SNV (http://sourceforge.net/projects/qqsnv), a logistic regression classifier model developed for the Illumina sequencing platforms that uses the quantiles of the quality scores, to distinguish true single nucleotide variants from sequencing errors based on the estimated SNV probability. To train the model, we created a dataset of an in silico mixture of five HIV-1 plasmids. Testing of our method in comparison to the existing methods LoFreq, ShoRAH, and V-Phaser 2 was performed on two HIV and four HCV plasmid mixture datasets and one influenza H1N1 clinical dataset. Results: For default application of QQ-SNV, variants were called using a SNV probability cutoff of 0.5 (QQ-SNVD). To improve the sensitivity we used a SNV probability cutoff of 0.0001 (QQ-SNVHS). To also increase specificity, SNVs called were overruled when their frequency was below the 80th percentile calculated on the distribution of error frequencies (QQ-SNVHS-P80). When comparing QQ-SNV versus the other methods on the plasmid mixture test sets, QQ-SNVD performed similarly to the existing approaches. QQ-SNVHS was more sensitive on all test sets but with more false positives. QQ-SNVHS-P80 was found to be the most accurate method over all test sets by balancing sensitivity and specificity. When applied to a paired-end HCV sequencing study, with lowest spiked-in true frequency of 0.5 %, QQ-SNVHS-P80 revealed a sensitivity of 100 % (vs. 40-60 % for the existing methods) and a specificity of 100 % (vs. 98.0-99.7 % for the existing methods). In addition, QQ-SNV required the least overall computation time to process the test sets. Finally, when testing on a clinical sample, four putative true variants with frequency below 0.5 % were consistently detected by QQ-SNVHS-P80 from different generations of Illumina sequencers. Conclusions: We developed and successfully evaluated a novel method, called QQ-SNV, for highly efficient single nucleotide variant calling on Illumina deep sequencing virology data

The Changing Role of Amicus-Curiae in The Relations Between Non-Goverment Organization and The World Trade Organization

This paper attempts to analyse the changing role of amicus-curiae in the WTO dispute settlement system where the Appellate Body was developing and implementing a judicial policy. Although it was a radical step for Appellate Body to engage amici curiae, it has given an indication that this body has opened the possibility for deepening and strengthening the relations between the non-government organization and WTO in order to provide the possibility for a non-government organization to engage in WTO actively

A comparative analysis of HIV drug resistance interpretation based on short reverse transcriptase sequences versus full sequences

<p>Abstract</p> <p>Background</p> <p>As second-line antiretroviral treatment (ART) becomes more accessible in resource-limited settings (RLS), the need for more affordable monitoring tools such as point-of-care viral load assays and simplified genotypic HIV drug resistance (HIVDR) tests increases substantially. The prohibitive expenses of genotypic HIVDR assays could partly be addressed by focusing on a smaller region of the HIV reverse transcriptase gene (RT) that encompasses the majority of HIVDR mutations for people on ART in RLS. In this study, an <it>in silico </it>analysis of 125,329 RT sequences was performed to investigate the effect of submitting short RT sequences (codon 41 to 238) to the commonly used virco^®TYPE and Stanford genotype interpretation tools.</p> <p>Results</p> <p>Pair-wise comparisons between full-length and short RT sequences were performed. Additionally, a non-inferiority approach with a concordance limit of 95% and two-sided 95% confidence intervals was used to demonstrate concordance between HIVDR calls based on full-length and short RT sequences.</p> <p>The results of this analysis showed that HIVDR interpretations based on full-length versus short RT sequences, using the Stanford algorithms, had concordance significantly above 95%. When using the virco^®TYPE algorithm, similar concordance was demonstrated (>95%), but some differences were observed for d4T, AZT and TDF, where predictions were affected in more than 5% of the sequences. Most differences in interpretation, however, were due to shifts from fully susceptible to reduced susceptibility (d4T) or from reduced response to minimal response (AZT, TDF) or vice versa, as compared to the predicted full RT sequence. The virco^®TYPE prediction uses many more mutations outside the RT 41-238 amino acid domain, which significantly contribute to the HIVDR prediction for these 3 antiretroviral agents.</p> <p>Conclusions</p> <p>This study illustrates the acceptability of using a shortened RT sequences (codon 41-238) to obtain reliable genotype interpretations by virco^®TYPE and Stanford algorithms. Implementation of this simplified protocol could significantly reduce the cost of both resistance testing and ARV treatment monitoring in RLS.</p

China and Europe taking care of healthcare solutions “CHETCH”

CHETCH is a research project financed by the European Commission with the 7th Framework Programme - PEOPLE MARIE CURIE ACTIONS - IRSES, with 11 Institutions involved and a budget of 688.800 €. The project intends to contribute actively to the cooperation between Europe and China through the investigating of opportunities for mutual integration in the healthcare sector. Cooperation and potential synergies will be examined from a comprehensive perspective, including policies at national and local level, the legal environment, medical practices, healthcare industries and related businesses. In order to develop a comprehensive understanding of the integration opportunities, an interdisciplinary approach is followed. The primary objective of CHETCH is to increase the availability of interdisciplinary studies providing a comprehensive overview (including medical, legal, economic, and humanities perspectives) of Europe-China relations in healthcare. Potentially, Europe and China have complementarities that could help each other face their specific needs in the long run in the healthcare sector. In particular, China would benefit from gaining knowledge and expertise from European countries at different levels. From how to project and run a universal system; how to plan a specific care program for its ageing population; to the use of western medicine to cope with new and improved medical needs of the population. Europe could “export” to China solutions, best practices and thus find business opportunities. At the same time, China could export to Europe practices and approaches of Traditional Chinese Medicine (TCM) that could be cost saving and effective in specific pathologies. In the specific, the team of experts in the medical field will investigate best practices of traditional medical systems using a modern science framework. The team will develop a process of recognition and scientific validation of TCM versus Complementary Alternative Medicine (CAM) at different levels as recommended by the World Health Organization Traditional medicine Strategy 2003-2005. This strategy includes the following indicators: • policy, i.e. integrate TM/CAM with national health care systems, as appropriate, by developing and implementing national TM/CAM policies and programs; • safety, efficacy and quality, i.e. promote the safety, efficacy and quality of TM/ CAM by expanding the knowledgebase on TM/CAM, and by providing guidance on regulatory and quality assurance standards; • access, i.e. increase the availability and affordability of TM/CAM, as appropriate, with an emphasis on access for poor populations; • rational use, i.e. promote therapeutically sound use of appropriate TM/CAM by providers and consumers

International Trade Under the Rule of Law Conference

The central focus of the conference was the dispute settlement system of the World Trade Organization (WTO), with a view toward exploring the need for a superstructure of international law governing trade and economic cooperation between countries

No. 5 - International Trade under the Rule of Law: An American Society of International Law Centennial Regional Meeting

Organized and sponsored by the Dean Rusk Center and designated an American Society of International Law Centennial Regional Meeting, this conference focused on the Dispute Settlement System (DSS) of the World Trade Organization (WTO) with a view toward discussing the need for a superstructure of international law governing trade and economic cooperation between states

The trafficking pathway of a wheat storage protein in transgenic rice endosperm

Background and Aims The trafficking of proteins in the endoplasmic reticulum (ER) of plant cells is a topic of considerable interest since this organelle serves as an entry point for proteins destined for other organelles, as well as for the ER itself. In the current work, transgenic rice was used to study the pattern and pathway of deposition of the wheat high molecular weight (HMW) glutenin sub-unit (GS) 1Dx5 within the rice endosperm using specific antibodies to determine whether it is deposited in the same or different protein bodies from the rice storage proteins, and whether it is located in the same or separate phases within these. Methods The protein distribution and the expression pattern of HMW sub-unit 1Dx5 in transgenic rice endosperm at different stages of development were determined using light and electron microscopy after labelling with antibodies. Key results The use of HMW-GS-specific antibodies showed that sub-unit 1Dx5 was expressed mainly in the sub-aleurone cells of the endosperm and that it was deposited in both types of protein body present in the rice endosperm: derived from the ER and containing prolamins, and derived from the vacuole and containing glutelins. In addition, new types of protein bodies were also formed within the endosperm cells. Conclusions The results suggest that the HMW 1Dx5 protein could be trafficked by either the ER or vacuolar pathway, possibly depending on the stage of development, and that its accumulation in the rice endosperm could compromise the structural integrity of protein bodies and their segregation into two distinct populations in the mature endosperm