References of "Charloteaux, Benoît"
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See detailAn efficient algorithm to perform multiple testing in epistasis screening
Van Lishout, François ULg; Mahachie John, Jestinah ULg; Gusareva, Elena ULg et al

in BMC Bioinformatics (2013), 14

Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved ... [more ▼]

Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power. The quest for gene-gene interactions poses severe multiple-testing problems. In this context, the maxT algorithm is one technique to control the false-positive rate. However, the memory needed by this algorithm rises linearly with the amount of hypothesis tests. Gene-gene interaction studies will require a memory proportional to the squared number of SNPs. A genome-wide epistasis search would therefore require terabytes of memory. Hence, cache problems are likely to occur, increasing the computation time. In this work we present a new version of maxT, requiring an amount of memory independent from the number of genetic effects to be investigated. This algorithm was implemented in C++ in our epistasis screening software MBMDR-3.0.3. We evaluate the new implementation in terms of memory efficiency and speed using simulated data. The software is illustrated on real-life data for Crohn's disease. Results: In the case of a binary (affected/unaffected) trait, the parallel workflow of MBMDR-3.0.3 analyzes all gene-gene interactions with a dataset of 100,000 SNPs typed on 1000 individuals within 4 days and 9 hours, using 999 permutations of the trait to assess statistical significance, on a cluster composed of 10 blades, containing each four Quad-Core AMD Opteron Processor 2352 2.1 GHz. In the case of a continuous trait, a similar run takes 9 days. Our program found 14 SNP-SNP interactions with a multiple-testing corrected p-value of less than 0.05 on real-life Crohn's disease data. Conclusions: Our software is the first implementation of the MB-MDR methodology able to solve large-scale SNP-SNP interactions problems within a few days, without using much memory, while adequately controlling the type I error rates. A new implementation to reach genome-wide epistasis screening is under construction. In the context of Crohn's disease, MBMDR-3.0.3 could identify epistasis involving regions that are well known in the field and could be explained from a biological point of view. This demonstrates the power of our software to find relevant phenotype-genotype higher-order associations. [less ▲]

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Peer Reviewed
See detailCaractère bifonctionnel d'une prényltransférase de pucerons
Cusson, Michel; Vandermoten, Sophie ULg; Charloteaux, Benoit et al

Conference (2008, November)

Detailed reference viewed: 3 (1 ULg)
Peer Reviewed
See detailPeculiar hydrophobic properties of the 67-78 fragment of α-synuclein are responsible for membrane destabilization and neurotoxicity
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Dupiereux-Fettweis, Ingrid ULg et al

Poster (2007, March 14)

α-synuclein is a 140 residue protein linked to Parkinson’s disease. Intraneural inclusions called Lewy bodies and Lewy neurites are mainly composed of α-synuclein aggregated in amyloid fibrils. Few years ... [more ▼]

α-synuclein is a 140 residue protein linked to Parkinson’s disease. Intraneural inclusions called Lewy bodies and Lewy neurites are mainly composed of α-synuclein aggregated in amyloid fibrils. Few years ago, tilted peptides have been detected in two other amyloidogenic proteins : the amyloid β peptide involved in Alzheimer’s disease, and the PrP protein linked to Creuztfeldt-Jakob’s disease. Tilted peptides are short protein fragments that adopt an oblique orientation when inserted into biological membranes. Tilted peptides are able to destabilize membranes. In this study, we predicted by sequence analysis and molecular modelling that the 67-78 fragment of α-synuclein is a tilted peptide. Like most of them, the α-syn 67-78 peptide is able to induce lipid mixing and leakage of unilamellar liposomes. A mutant designed by molecular modelling to decrease the destabilizing properties of the peptide was shown to be significantly less fusogenic. The neuronal toxicity was studied using human neuroblastoma cells and we demonstrated that the α-syn 67-78 peptide induces neurotoxicity. In conclusion, we have identified a tilted peptide in α-synuclein which could be involved in the toxicity induced during amyloidogenesis of α-synuclein. [less ▲]

Detailed reference viewed: 6 (0 ULg)
See detailPeculiar hydrophobic properties of the 67-78 fragment of α-synuclein are responsible for membrane destabilization and neurotoxicity
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Dupiereux-Fettweis, Ingrid ULg et al

Poster (2006, December 18)

α-synuclein is a 140 residue protein linked to Parkinson’s disease. Intraneural inclusions called Lewy bodies and Lewy neurites are mainly composed of α-synuclein aggregated in amyloid fibrils. Few years ... [more ▼]

α-synuclein is a 140 residue protein linked to Parkinson’s disease. Intraneural inclusions called Lewy bodies and Lewy neurites are mainly composed of α-synuclein aggregated in amyloid fibrils. Few years ago, tilted peptides have been detected in two other amyloidogenic proteins : the amyloid β peptide involved in Alzheimer’s disease, and the PrP protein linked to Creuztfeldt-Jakob’s disease. Tilted peptides are short protein fragments that adopt an oblique orientation when inserted into biological membranes. Tilted peptides are able to destabilize membranes. In this study, we predicted by sequence analysis and molecular modelling that the 67-78 fragment of α-synuclein is a tilted peptide. Like most of them, the α-syn 67-78 peptide is able to induce lipid mixing and leakage of unilamellar liposomes. A mutant designed by molecular modelling to decrease the destabilizing properties of the peptide was shown to be significantly less fusogenic. The neuronal toxicity was studied using human neuroblastoma cells and we demonstrated that the α-syn 67-78 peptide induces neurotoxicity. In conclusion, we have identified a tilted peptide in α-synuclein which could be involved in the toxicity induced during amyloidogenesis of α-synuclein. [less ▲]

Detailed reference viewed: 5 (1 ULg)