Bio3R: Summary of the Final Report
Gala JL. "Summary of the final report of the Bio3R-2008 project (Reaction, Resilience and Research in Europe - Preparatory Action in the Field of Security and Research)."
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CBRN Mobile Laboratories
The FP7-SECURITY MIRACLE project: major recommendations.
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Mobile Laboratory Capacity for the Rapid Assessment of CBRN Threats Located within and outside the EU.
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All IREC reports since 2012.
The AdvISER-PYRO, AdvISER-M-PYRO, AdvISER-MH-PYRO, and Saturation R packages have been developed by Jérôme Ambroise (Centre de Technologies Moléculaires Appliquées - IREC/CTMA, UCL) under an open-source GPLv2 license.
Inter alia, it allows unrestricted use for academic purposes. For any use in commercial products or question about licensing, you can contact the Louvain Technology Transfer Office of UCL at email@example.com
Copyright ©2011-2017, Université catholique de Louvain – UCL
ESBL detection via multiplex pyrosequencing
This new application was developed using an improved version of three previously published algorithms including AdvISER-PYRO for analyzing low and complex signals resulting from samples including several mycobacteria, AdvISER-M-PYRO for analyzing overlapping pyro-signals generated from multiplex reactions conducted on mono-allelic genes in bacteria, and AdvISER-MH-PYRO for analyzing overlapping pyro-signals generated from multiplex reactions to genotype bi-allelic human SNP.
While the initial version of AdvISER-M-PYRO analyzed multiplex pyrosequencing signals by selecting a single and unique sequence for each genomic region, this new version enables the analysis of multiplex pyrosequencing signals generated from samples including two distinct sequences (i.e., plasmid and chromosomal) for each genomic region.
- Software: https://ucl-irec-ctma.shinyapps.io/Pyrosequencing-TEM-SHV
- Template data set (in the next page, choose 'Télécharger' > 'Télécharger l'original'...)
Interpreting a pyrosequencing signal appears highly challenging when signal intensities are low (unitary peak heights smaller than 5) or when complex signals are produced by more than one target amplicon in the sample. AdvISERPYRO is an efficient algorithm that can reliably be used to identify amplicons in pyrosequencing signals generated by Single Amplicon Samples (SAS) and Multiple Amplicon Samples (MAS). AdvISERPYRO is based on a sparse regression model and deciphers each amplicon-specific signal that contributes to the resulting global signal.
AdvISER-M-PYRO is an efficient algorithm that can reliably be used to translate the global multiplex pyrosequencing signal in sequences corresponding to each genomic region.
The new SENATOR method was developed to select the nucleotide dispensation order to be used all along the multiplex pyrosequencing experiment.
AdvISER-MH-PYRO is an extension of the AdvISER-M-PYRO algorithm that integrates a new feature allowing bi-allelic SNP genotyping. AdvISER-MH-PYRO can be applied in a broad range of clinical and/or research applications relying on Multilocus Genetic Risk Score computation, hence requiring multi-SNP pyrosequencing for each patient. AdvISER-MH-PYRO package also includes 2 dictionaries for quadruplex and quintuplex assays to genotype a set of prostate cancer-related SNPs (n=9).
The main function of the saturation R package is the cms2a function. This function can be used to correct the microarray saturated spots obtained at high PMT voltage by using the corresponding spots acquired at lower PMT voltage. The cms2a algorithm is based on a two-way ANOVA model and on a maximum likelihood estimation of the scanner optical bias.